Starting phenix.real_space_refine on Fri Mar 6 11:25:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utp_26786/03_2026/7utp_26786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utp_26786/03_2026/7utp_26786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7utp_26786/03_2026/7utp_26786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utp_26786/03_2026/7utp_26786.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7utp_26786/03_2026/7utp_26786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utp_26786/03_2026/7utp_26786.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 19768 2.51 5 N 5299 2.21 5 O 5873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31056 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "L" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 495 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'TRANS': 98} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "G" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "F" Number of atoms: 4234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4234 Classifications: {'peptide': 531} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 491} Chain breaks: 2 Chain: "D" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2234 Classifications: {'peptide': 276} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 259} Chain breaks: 8 Chain: "E" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "I" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4238 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 492} Chain breaks: 2 Chain: "C" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2394 Classifications: {'peptide': 299} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 278} Chain breaks: 9 Chain: "B" Number of atoms: 4207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4207 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 489} Chain breaks: 3 Time building chain proxies: 6.74, per 1000 atoms: 0.22 Number of scatterers: 31056 At special positions: 0 Unit cell: (191.4, 177.1, 137.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 5873 8.00 N 5299 7.00 C 19768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.07 Simple disulfide: pdb=" SG CYS G 490 " - pdb=" SG CYS G 494 " distance=2.05 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 494 " distance=2.04 Simple disulfide: pdb=" SG CYS E 490 " - pdb=" SG CYS E 494 " distance=2.07 Simple disulfide: pdb=" SG CYS I 490 " - pdb=" SG CYS I 494 " distance=2.03 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 494 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 494 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7424 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 57 sheets defined 10.7% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.809A pdb=" N TRP A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.542A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 191 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.531A pdb=" N VAL A 241 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.560A pdb=" N LEU A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 313 removed outlier: 3.583A pdb=" N ARG A 313 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.731A pdb=" N ASP A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.779A pdb=" N PHE A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 562 removed outlier: 3.663A pdb=" N TYR A 561 " --> pdb=" O GLN A 558 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL A 562 " --> pdb=" O PHE A 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 61 removed outlier: 4.185A pdb=" N UNK H 60 " --> pdb=" O UNK H 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 116 through 121 removed outlier: 3.914A pdb=" N TRP G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 132 removed outlier: 3.610A pdb=" N THR G 132 " --> pdb=" O LEU G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 191 removed outlier: 3.528A pdb=" N MET G 190 " --> pdb=" O PRO G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 241 Processing helix chain 'G' and resid 245 through 250 removed outlier: 3.524A pdb=" N SER G 249 " --> pdb=" O THR G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 313 removed outlier: 3.727A pdb=" N ARG G 313 " --> pdb=" O GLN G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 removed outlier: 3.519A pdb=" N ASP G 413 " --> pdb=" O PRO G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 448 Processing helix chain 'G' and resid 554 through 558 removed outlier: 3.566A pdb=" N GLN G 558 " --> pdb=" O VAL G 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 122 through 132 removed outlier: 3.644A pdb=" N THR F 132 " --> pdb=" O LEU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.720A pdb=" N VAL F 241 " --> pdb=" O PRO F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 250 removed outlier: 3.550A pdb=" N SER F 249 " --> pdb=" O THR F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.762A pdb=" N ARG F 313 " --> pdb=" O GLN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'F' and resid 443 through 448 removed outlier: 4.267A pdb=" N ILE F 447 " --> pdb=" O ASN F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 562 removed outlier: 3.546A pdb=" N ASN F 560 " --> pdb=" O ASN F 557 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR F 561 " --> pdb=" O GLN F 558 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL F 562 " --> pdb=" O PHE F 559 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 557 through 562' Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.897A pdb=" N VAL D 250 " --> pdb=" O ILE D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 558 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 95 through 99 removed outlier: 3.805A pdb=" N LEU E 98 " --> pdb=" O ASN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 121 removed outlier: 4.144A pdb=" N TRP E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 132 removed outlier: 3.551A pdb=" N LEU E 128 " --> pdb=" O GLY E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 381 through 385 removed outlier: 4.195A pdb=" N GLY E 385 " --> pdb=" O ARG E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 558 through 562 removed outlier: 3.922A pdb=" N VAL E 562 " --> pdb=" O PHE E 559 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 removed outlier: 4.070A pdb=" N VAL I 92 " --> pdb=" O ASP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 99 removed outlier: 3.637A pdb=" N ASP I 99 " --> pdb=" O MET I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 120 Processing helix chain 'I' and resid 122 through 131 removed outlier: 3.505A pdb=" N LEU I 128 " --> pdb=" O GLY I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 241 removed outlier: 3.634A pdb=" N ASP I 240 " --> pdb=" O ASP I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 245 through 250 Processing helix chain 'I' and resid 409 through 413 Processing helix chain 'I' and resid 443 through 447 Processing helix chain 'I' and resid 557 through 561 removed outlier: 3.605A pdb=" N ASN I 560 " --> pdb=" O ASN I 557 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR I 561 " --> pdb=" O GLN I 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 557 through 561' Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.167A pdb=" N TRP C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 241 removed outlier: 3.621A pdb=" N ASP C 240 " --> pdb=" O ASP C 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 122 through 132 removed outlier: 3.546A pdb=" N VAL B 130 " --> pdb=" O TRP B 126 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.534A pdb=" N MET B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.820A pdb=" N GLY B 385 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 443 through 447 Processing helix chain 'B' and resid 557 through 562 removed outlier: 3.593A pdb=" N VAL B 562 " --> pdb=" O PHE B 559 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 58 through 72 current: chain 'A' and resid 164 through 167 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.717A pdb=" N GLY A 235 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR A 217 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N TYR A 233 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.237A pdb=" N HIS A 277 " --> pdb=" O ARG A 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 317 removed outlier: 3.507A pdb=" N GLY A 315 " --> pdb=" O ALA G 379 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE G 398 " --> pdb=" O TYR G 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.615A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.625A pdb=" N SER A 348 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 415 " --> pdb=" O LEU F 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 396 through 399 Processing sheet with id=AA9, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.506A pdb=" N SER G 348 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 removed outlier: 4.612A pdb=" N UNK L 18 " --> pdb=" O UNK L 74 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N UNK L 74 " --> pdb=" O UNK L 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 33 through 36 Processing sheet with id=AB3, first strand: chain 'H' and resid 19 through 21 Processing sheet with id=AB4, first strand: chain 'H' and resid 81 through 82 Processing sheet with id=AB5, first strand: chain 'G' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 58 through 72 current: chain 'G' and resid 164 through 167 Processing sheet with id=AB6, first strand: chain 'G' and resid 80 through 84 Processing sheet with id=AB7, first strand: chain 'G' and resid 215 through 217 removed outlier: 5.949A pdb=" N ASP G 215 " --> pdb=" O HIS G 234 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR G 217 " --> pdb=" O ILE G 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE G 232 " --> pdb=" O THR G 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 276 through 278 Processing sheet with id=AB9, first strand: chain 'G' and resid 315 through 317 Processing sheet with id=AC1, first strand: chain 'G' and resid 335 through 336 removed outlier: 6.585A pdb=" N GLU G 335 " --> pdb=" O ALA G 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 429 through 430 removed outlier: 3.729A pdb=" N GLY F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 58 through 72 current: chain 'F' and resid 164 through 167 Processing sheet with id=AC4, first strand: chain 'F' and resid 80 through 84 removed outlier: 3.504A pdb=" N HIS F 102 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 216 through 218 Processing sheet with id=AC6, first strand: chain 'F' and resid 276 through 278 removed outlier: 5.781A pdb=" N HIS F 277 " --> pdb=" O ARG F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.875A pdb=" N GLU F 335 " --> pdb=" O ALA F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 44 through 45 current: chain 'E' and resid 102 through 112 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 72 current: chain 'D' and resid 164 through 167 Processing sheet with id=AD1, first strand: chain 'D' and resid 80 through 82 Processing sheet with id=AD2, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AD3, first strand: chain 'E' and resid 50 through 53 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 58 through 72 current: chain 'E' and resid 164 through 167 Processing sheet with id=AD4, first strand: chain 'E' and resid 217 through 218 removed outlier: 3.640A pdb=" N THR E 217 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 232 " --> pdb=" O THR E 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.637A pdb=" N GLU E 335 " --> pdb=" O ALA E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 345 through 346 Processing sheet with id=AD7, first strand: chain 'E' and resid 377 through 380 Processing sheet with id=AD8, first strand: chain 'E' and resid 463 through 464 removed outlier: 4.354A pdb=" N TYR E 464 " --> pdb=" O GLU E 574 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 574 " --> pdb=" O TYR E 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 58 through 72 current: chain 'I' and resid 164 through 167 Processing sheet with id=AE1, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AE2, first strand: chain 'I' and resid 216 through 218 removed outlier: 3.769A pdb=" N THR I 217 " --> pdb=" O ILE I 232 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE I 232 " --> pdb=" O THR I 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'I' and resid 276 through 277 Processing sheet with id=AE4, first strand: chain 'I' and resid 316 through 317 removed outlier: 3.506A pdb=" N PHE B 380 " --> pdb=" O GLU B 396 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 396 " --> pdb=" O PHE B 380 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 335 through 336 removed outlier: 6.762A pdb=" N GLU I 335 " --> pdb=" O ALA I 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 345 through 348 removed outlier: 3.548A pdb=" N SER I 348 " --> pdb=" O GLY I 351 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 377 through 380 Processing sheet with id=AE8, first strand: chain 'I' and resid 429 through 430 removed outlier: 3.529A pdb=" N SER B 348 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 463 through 464 removed outlier: 4.120A pdb=" N TYR I 464 " --> pdb=" O GLU I 574 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU I 574 " --> pdb=" O TYR I 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'I' and resid 470 through 472 removed outlier: 6.717A pdb=" N ASP I 471 " --> pdb=" O CYS I 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 62 through 72 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 62 through 72 current: chain 'C' and resid 164 through 167 No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 80 through 84 Processing sheet with id=AF4, first strand: chain 'C' and resid 216 through 218 removed outlier: 3.714A pdb=" N THR C 217 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 232 " --> pdb=" O THR C 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF6, first strand: chain 'B' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 58 through 72 current: chain 'B' and resid 164 through 167 Processing sheet with id=AF7, first strand: chain 'B' and resid 80 through 84 Processing sheet with id=AF8, first strand: chain 'B' and resid 215 through 218 removed outlier: 6.698A pdb=" N ASP B 215 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 232 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AG1, first strand: chain 'B' and resid 335 through 336 removed outlier: 6.548A pdb=" N GLU B 335 " --> pdb=" O ALA B 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AG3, first strand: chain 'B' and resid 470 through 472 removed outlier: 6.832A pdb=" N ASP B 471 " --> pdb=" O CYS B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 295 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 10111 1.34 - 1.48: 8893 1.48 - 1.63: 12721 1.63 - 1.77: 1 1.77 - 1.91: 203 Bond restraints: 31929 Sorted by residual: bond pdb=" C LEU A 422 " pdb=" N PRO A 423 " ideal model delta sigma weight residual 1.333 1.374 -0.041 1.20e-02 6.94e+03 1.18e+01 bond pdb=" CB CYS E 490 " pdb=" SG CYS E 490 " ideal model delta sigma weight residual 1.808 1.907 -0.099 3.30e-02 9.18e+02 9.01e+00 bond pdb=" CA ASN I 505 " pdb=" CB ASN I 505 " ideal model delta sigma weight residual 1.526 1.570 -0.044 1.53e-02 4.27e+03 8.15e+00 bond pdb=" CB LYS I 501 " pdb=" CG LYS I 501 " ideal model delta sigma weight residual 1.520 1.605 -0.085 3.00e-02 1.11e+03 8.06e+00 bond pdb=" C TYR E 409 " pdb=" N PRO E 410 " ideal model delta sigma weight residual 1.335 1.372 -0.037 1.30e-02 5.92e+03 7.99e+00 ... (remaining 31924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 42209 2.78 - 5.55: 1244 5.55 - 8.33: 189 8.33 - 11.11: 12 11.11 - 13.89: 6 Bond angle restraints: 43660 Sorted by residual: angle pdb=" CA PRO E 187 " pdb=" N PRO E 187 " pdb=" CD PRO E 187 " ideal model delta sigma weight residual 112.00 98.11 13.89 1.40e+00 5.10e-01 9.84e+01 angle pdb=" CA CYS E 494 " pdb=" CB CYS E 494 " pdb=" SG CYS E 494 " ideal model delta sigma weight residual 114.40 127.09 -12.69 2.30e+00 1.89e-01 3.04e+01 angle pdb=" CA CYS A 494 " pdb=" CB CYS A 494 " pdb=" SG CYS A 494 " ideal model delta sigma weight residual 114.40 126.98 -12.58 2.30e+00 1.89e-01 2.99e+01 angle pdb=" CA GLN I 213 " pdb=" CB GLN I 213 " pdb=" CG GLN I 213 " ideal model delta sigma weight residual 114.10 124.49 -10.39 2.00e+00 2.50e-01 2.70e+01 angle pdb=" CB GLN F 213 " pdb=" CG GLN F 213 " pdb=" CD GLN F 213 " ideal model delta sigma weight residual 112.60 121.16 -8.56 1.70e+00 3.46e-01 2.54e+01 ... (remaining 43655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16486 17.96 - 35.92: 1698 35.92 - 53.87: 383 53.87 - 71.83: 66 71.83 - 89.79: 41 Dihedral angle restraints: 18674 sinusoidal: 7165 harmonic: 11509 Sorted by residual: dihedral pdb=" CA ASN F 426 " pdb=" C ASN F 426 " pdb=" N ASP F 427 " pdb=" CA ASP F 427 " ideal model delta harmonic sigma weight residual 180.00 142.59 37.41 0 5.00e+00 4.00e-02 5.60e+01 dihedral pdb=" CB CYS B 490 " pdb=" SG CYS B 490 " pdb=" SG CYS B 494 " pdb=" CB CYS B 494 " ideal model delta sinusoidal sigma weight residual 93.00 41.23 51.77 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CA ASN A 493 " pdb=" C ASN A 493 " pdb=" N CYS A 494 " pdb=" CA CYS A 494 " ideal model delta harmonic sigma weight residual 180.00 -149.80 -30.20 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 18671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4078 0.077 - 0.154: 629 0.154 - 0.231: 52 0.231 - 0.307: 2 0.307 - 0.384: 3 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CB ILE D 204 " pdb=" CA ILE D 204 " pdb=" CG1 ILE D 204 " pdb=" CG2 ILE D 204 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA SER G 226 " pdb=" N SER G 226 " pdb=" C SER G 226 " pdb=" CB SER G 226 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASN F 428 " pdb=" N ASN F 428 " pdb=" C ASN F 428 " pdb=" CB ASN F 428 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 4761 not shown) Planarity restraints: 5732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 186 " -0.127 5.00e-02 4.00e+02 1.80e-01 5.21e+01 pdb=" N PRO E 187 " 0.311 5.00e-02 4.00e+02 pdb=" CA PRO E 187 " -0.103 5.00e-02 4.00e+02 pdb=" CD PRO E 187 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 464 " -0.026 2.00e-02 2.50e+03 4.08e-02 3.33e+01 pdb=" CG TYR E 464 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TYR E 464 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TYR E 464 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR E 464 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 464 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 464 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 464 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 237 " -0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO E 238 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO E 238 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 238 " -0.059 5.00e-02 4.00e+02 ... (remaining 5729 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 564 2.64 - 3.21: 28791 3.21 - 3.77: 46841 3.77 - 4.34: 65177 4.34 - 4.90: 107423 Nonbonded interactions: 248796 Sorted by model distance: nonbonded pdb=" OH TYR A 524 " pdb=" O LEU B 506 " model vdw 2.076 3.040 nonbonded pdb=" OG1 THR D 42 " pdb=" OE1 GLU D 260 " model vdw 2.091 3.040 nonbonded pdb=" O LEU A 506 " pdb=" OH TYR E 524 " model vdw 2.096 3.040 nonbonded pdb=" O THR F 245 " pdb=" OG SER F 249 " model vdw 2.101 3.040 nonbonded pdb=" O VAL D 149 " pdb=" OG SER D 525 " model vdw 2.121 3.040 ... (remaining 248791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 294 or resid 299 through 584)) selection = (chain 'B' and resid 38 through 584) selection = (chain 'E' and (resid 38 through 294 or resid 299 through 584)) selection = (chain 'F' and (resid 38 through 294 or resid 299 through 584)) selection = (chain 'G' and (resid 38 through 294 or resid 299 through 584)) selection = (chain 'I' and (resid 38 through 294 or resid 299 through 584)) } ncs_group { reference = (chain 'H' and resid 10 through 108) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.260 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 31936 Z= 0.291 Angle : 1.106 13.885 43674 Z= 0.591 Chirality : 0.055 0.384 4764 Planarity : 0.009 0.180 5732 Dihedral : 15.953 89.791 11229 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 0.42 % Allowed : 24.76 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.13), residues: 3686 helix: -2.35 (0.41), residues: 92 sheet: -1.04 (0.17), residues: 859 loop : -0.84 (0.11), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG F 481 TYR 0.098 0.003 TYR E 464 PHE 0.068 0.004 PHE E 243 TRP 0.039 0.002 TRP F 109 HIS 0.020 0.002 HIS F 102 Details of bonding type rmsd covalent geometry : bond 0.00694 (31929) covalent geometry : angle 1.10438 (43660) SS BOND : bond 0.02517 ( 7) SS BOND : angle 3.12519 ( 14) hydrogen bonds : bond 0.28350 ( 295) hydrogen bonds : angle 9.56841 ( 567) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1544 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1530 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7930 (t0) cc_final: 0.7662 (t0) REVERT: A 60 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: A 79 TYR cc_start: 0.8362 (m-80) cc_final: 0.7641 (m-80) REVERT: A 145 ILE cc_start: 0.8856 (mt) cc_final: 0.8576 (mm) REVERT: A 241 VAL cc_start: 0.8220 (m) cc_final: 0.8018 (p) REVERT: A 312 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8092 (mtmt) REVERT: A 335 GLU cc_start: 0.7332 (tt0) cc_final: 0.6277 (tm-30) REVERT: A 346 GLU cc_start: 0.6416 (mt-10) cc_final: 0.5927 (mt-10) REVERT: A 350 GLN cc_start: 0.7384 (mt0) cc_final: 0.6913 (mp10) REVERT: A 380 PHE cc_start: 0.7734 (p90) cc_final: 0.7534 (p90) REVERT: A 396 GLU cc_start: 0.7671 (tt0) cc_final: 0.7266 (tt0) REVERT: A 473 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6664 (mm-30) REVERT: A 501 LYS cc_start: 0.7888 (ttpp) cc_final: 0.7629 (ttpt) REVERT: A 524 TYR cc_start: 0.8165 (p90) cc_final: 0.7942 (p90) REVERT: A 528 TRP cc_start: 0.8260 (m100) cc_final: 0.8000 (m100) REVERT: A 569 MET cc_start: 0.6677 (mmm) cc_final: 0.6432 (tpp) REVERT: A 574 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6761 (mm-30) REVERT: G 62 THR cc_start: 0.8548 (m) cc_final: 0.8066 (t) REVERT: G 73 MET cc_start: 0.7748 (ptm) cc_final: 0.7442 (ptm) REVERT: G 109 TRP cc_start: 0.8347 (m100) cc_final: 0.7646 (m100) REVERT: G 143 GLN cc_start: 0.8067 (mt0) cc_final: 0.7832 (mt0) REVERT: G 193 GLU cc_start: 0.7401 (mp0) cc_final: 0.7143 (mp0) REVERT: G 213 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7169 (tm-30) REVERT: G 327 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6488 (mm-30) REVERT: G 335 GLU cc_start: 0.7231 (tt0) cc_final: 0.6623 (tt0) REVERT: G 342 TYR cc_start: 0.7753 (p90) cc_final: 0.6883 (p90) REVERT: G 345 PHE cc_start: 0.8149 (m-80) cc_final: 0.7467 (m-80) REVERT: G 377 ARG cc_start: 0.8256 (ttt90) cc_final: 0.7653 (tpp80) REVERT: G 398 PHE cc_start: 0.8737 (p90) cc_final: 0.8522 (p90) REVERT: G 479 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8220 (mmtm) REVERT: G 491 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7240 (mm-40) REVERT: G 518 MET cc_start: 0.7710 (ptp) cc_final: 0.7505 (ptp) REVERT: G 530 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7475 (ttpp) REVERT: G 560 ASN cc_start: 0.8248 (m-40) cc_final: 0.7880 (m-40) REVERT: F 65 SER cc_start: 0.8540 (t) cc_final: 0.8158 (p) REVERT: F 73 MET cc_start: 0.7809 (ttp) cc_final: 0.7179 (tmm) REVERT: F 80 ARG cc_start: 0.4416 (tpt90) cc_final: 0.4145 (tpt90) REVERT: F 81 ARG cc_start: 0.5497 (ptp-170) cc_final: 0.3547 (ptp90) REVERT: F 106 VAL cc_start: 0.8873 (t) cc_final: 0.8552 (m) REVERT: F 120 TRP cc_start: 0.8383 (m100) cc_final: 0.7643 (m100) REVERT: F 127 GLN cc_start: 0.8597 (tt0) cc_final: 0.7986 (tp40) REVERT: F 135 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7027 (mp0) REVERT: F 151 LYS cc_start: 0.8310 (mmmm) cc_final: 0.7551 (mmmm) REVERT: F 191 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7973 (mtt90) REVERT: F 225 THR cc_start: 0.7255 (m) cc_final: 0.6876 (p) REVERT: F 230 THR cc_start: 0.8251 (m) cc_final: 0.7935 (p) REVERT: F 335 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6682 (tp30) REVERT: F 386 GLN cc_start: 0.7229 (tt0) cc_final: 0.6809 (tt0) REVERT: F 409 TYR cc_start: 0.8389 (t80) cc_final: 0.8140 (t80) REVERT: F 413 ASP cc_start: 0.7515 (m-30) cc_final: 0.7111 (m-30) REVERT: F 430 LEU cc_start: 0.8801 (tp) cc_final: 0.8542 (tp) REVERT: F 451 TYR cc_start: 0.8548 (t80) cc_final: 0.8276 (t80) REVERT: F 470 TRP cc_start: 0.7642 (p90) cc_final: 0.7380 (p90) REVERT: F 520 ARG cc_start: 0.7583 (mtt90) cc_final: 0.7273 (mtt90) REVERT: F 532 LYS cc_start: 0.8444 (ttmm) cc_final: 0.8025 (ttmm) REVERT: F 545 TRP cc_start: 0.8584 (t-100) cc_final: 0.8347 (t-100) REVERT: F 550 GLN cc_start: 0.8186 (mm110) cc_final: 0.7675 (mm-40) REVERT: F 551 MET cc_start: 0.7480 (ttt) cc_final: 0.6714 (ttt) REVERT: F 562 VAL cc_start: 0.8672 (p) cc_final: 0.8448 (m) REVERT: F 575 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7299 (mmtt) REVERT: D 73 MET cc_start: 0.8165 (ptt) cc_final: 0.7580 (ptp) REVERT: D 256 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7538 (mtm-85) REVERT: E 60 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6905 (tm-30) REVERT: E 61 ILE cc_start: 0.8165 (mt) cc_final: 0.7898 (mt) REVERT: E 62 THR cc_start: 0.8573 (m) cc_final: 0.8024 (m) REVERT: E 86 ASN cc_start: 0.7162 (p0) cc_final: 0.6846 (p0) REVERT: E 131 ASN cc_start: 0.8206 (m-40) cc_final: 0.7685 (t0) REVERT: E 163 LYS cc_start: 0.7785 (mppt) cc_final: 0.7466 (mppt) REVERT: E 210 TYR cc_start: 0.8624 (p90) cc_final: 0.8304 (p90) REVERT: E 266 PHE cc_start: 0.8179 (t80) cc_final: 0.7937 (t80) REVERT: E 342 TYR cc_start: 0.7312 (p90) cc_final: 0.6745 (p90) REVERT: E 386 GLN cc_start: 0.8340 (tt0) cc_final: 0.8048 (tt0) REVERT: E 387 LYS cc_start: 0.8704 (tptm) cc_final: 0.8120 (tptm) REVERT: E 400 TYR cc_start: 0.8107 (t80) cc_final: 0.7299 (t80) REVERT: E 408 ARG cc_start: 0.5797 (tpm170) cc_final: 0.5553 (tpt170) REVERT: E 469 ILE cc_start: 0.8380 (mp) cc_final: 0.8134 (mp) REVERT: E 471 ASP cc_start: 0.5685 (t0) cc_final: 0.5480 (t0) REVERT: E 479 LYS cc_start: 0.8253 (mptt) cc_final: 0.7866 (mptt) REVERT: E 483 HIS cc_start: 0.7822 (m170) cc_final: 0.6823 (m-70) REVERT: E 532 LYS cc_start: 0.8296 (ttpt) cc_final: 0.7813 (ttpt) REVERT: E 551 MET cc_start: 0.7455 (ttt) cc_final: 0.7005 (ttt) REVERT: I 76 SER cc_start: 0.7994 (t) cc_final: 0.7652 (t) REVERT: I 95 ASN cc_start: 0.8192 (m-40) cc_final: 0.7978 (m-40) REVERT: I 96 MET cc_start: 0.4590 (ptt) cc_final: 0.4351 (ptt) REVERT: I 101 ILE cc_start: 0.8554 (mt) cc_final: 0.8297 (mt) REVERT: I 109 TRP cc_start: 0.8685 (m100) cc_final: 0.8476 (m100) REVERT: I 145 ILE cc_start: 0.8840 (mm) cc_final: 0.8434 (mm) REVERT: I 147 ASN cc_start: 0.7952 (t0) cc_final: 0.7631 (t0) REVERT: I 193 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7088 (mp0) REVERT: I 230 THR cc_start: 0.8484 (m) cc_final: 0.8093 (p) REVERT: I 265 THR cc_start: 0.7519 (p) cc_final: 0.7265 (p) REVERT: I 293 SER cc_start: 0.8605 (m) cc_final: 0.7880 (p) REVERT: I 310 GLN cc_start: 0.8322 (mt0) cc_final: 0.8071 (mt0) REVERT: I 318 GLN cc_start: 0.8299 (mt0) cc_final: 0.8088 (mm-40) REVERT: I 348 SER cc_start: 0.8423 (m) cc_final: 0.8073 (p) REVERT: I 378 TYR cc_start: 0.7965 (m-80) cc_final: 0.7652 (m-80) REVERT: I 382 ARG cc_start: 0.8032 (mtt90) cc_final: 0.7827 (mtt90) REVERT: I 491 GLN cc_start: 0.7345 (mm-40) cc_final: 0.6925 (mm-40) REVERT: I 538 LYS cc_start: 0.8088 (tppt) cc_final: 0.7777 (mmtt) REVERT: C 67 ARG cc_start: 0.6817 (mmt-90) cc_final: 0.6603 (mmt-90) REVERT: C 68 LEU cc_start: 0.8022 (tp) cc_final: 0.7360 (mp) REVERT: C 73 MET cc_start: 0.8112 (ptt) cc_final: 0.7666 (ptt) REVERT: C 115 ASN cc_start: 0.7335 (t0) cc_final: 0.6560 (t0) REVERT: C 509 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6988 (tm-30) REVERT: C 528 TRP cc_start: 0.8423 (m100) cc_final: 0.8017 (m100) REVERT: B 95 ASN cc_start: 0.8322 (t0) cc_final: 0.7568 (t0) REVERT: B 152 THR cc_start: 0.7854 (m) cc_final: 0.7580 (m) REVERT: B 198 TYR cc_start: 0.7172 (m-10) cc_final: 0.6857 (m-10) REVERT: B 256 ARG cc_start: 0.7897 (mtp180) cc_final: 0.7686 (mtp85) REVERT: B 266 PHE cc_start: 0.8186 (t80) cc_final: 0.7948 (t80) REVERT: B 331 MET cc_start: 0.7806 (ttm) cc_final: 0.7537 (ttm) REVERT: B 353 PHE cc_start: 0.8047 (p90) cc_final: 0.7819 (p90) REVERT: B 382 ARG cc_start: 0.7933 (mtt90) cc_final: 0.7607 (mtt90) REVERT: B 400 TYR cc_start: 0.7660 (t80) cc_final: 0.7356 (t80) REVERT: B 415 ILE cc_start: 0.8181 (mt) cc_final: 0.7915 (mt) REVERT: B 416 GLN cc_start: 0.8011 (tt0) cc_final: 0.7594 (mp10) REVERT: B 417 ASN cc_start: 0.8020 (t0) cc_final: 0.7724 (t0) REVERT: B 463 VAL cc_start: 0.8115 (p) cc_final: 0.7800 (m) REVERT: B 473 GLU cc_start: 0.7088 (tt0) cc_final: 0.6732 (tt0) REVERT: B 491 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6803 (mm-40) REVERT: B 510 TYR cc_start: 0.8861 (t80) cc_final: 0.8316 (t80) REVERT: B 536 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7812 (tmtt) REVERT: B 558 GLN cc_start: 0.8201 (tt0) cc_final: 0.7882 (tt0) REVERT: B 569 MET cc_start: 0.6969 (mmm) cc_final: 0.6720 (mmm) REVERT: B 575 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7347 (mmtt) outliers start: 14 outliers final: 5 residues processed: 1534 average time/residue: 0.2089 time to fit residues: 502.1874 Evaluate side-chains 1506 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1499 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 570 LYS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 115 ASN A 234 HIS A 242 GLN A 277 HIS A 302 ASN A 426 ASN A 491 GLN A 546 ASN A 549 GLN ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G 468 GLN G 491 GLN G 505 ASN F 93 ASN F 143 GLN F 167 ASN F 234 HIS ** F 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 497 GLN F 565 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 517 ASN E 48 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 ASN E 543 HIS I 280 GLN ** I 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 383 GLN ** I 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.105629 restraints weight = 52808.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.109907 restraints weight = 24449.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.112659 restraints weight = 13699.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114494 restraints weight = 8671.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115716 restraints weight = 6024.759| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.121 31936 Z= 0.312 Angle : 0.687 8.287 43674 Z= 0.357 Chirality : 0.048 0.233 4764 Planarity : 0.006 0.102 5732 Dihedral : 6.557 83.241 4257 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.80 % Allowed : 20.27 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 3686 helix: -1.79 (0.37), residues: 124 sheet: -0.86 (0.17), residues: 890 loop : -0.62 (0.12), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 332 TYR 0.028 0.002 TYR A 561 PHE 0.031 0.002 PHE A 197 TRP 0.030 0.002 TRP E 279 HIS 0.012 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00655 (31929) covalent geometry : angle 0.68678 (43660) SS BOND : bond 0.00769 ( 7) SS BOND : angle 1.28646 ( 14) hydrogen bonds : bond 0.04856 ( 295) hydrogen bonds : angle 6.47142 ( 567) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1727 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1569 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7720 (t0) REVERT: A 104 GLN cc_start: 0.8236 (pt0) cc_final: 0.7782 (pt0) REVERT: A 147 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7855 (t0) REVERT: A 177 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8305 (tp) REVERT: A 214 TRP cc_start: 0.8457 (p90) cc_final: 0.7463 (p90) REVERT: A 215 ASP cc_start: 0.7315 (m-30) cc_final: 0.7063 (m-30) REVERT: A 237 ASP cc_start: 0.7863 (t0) cc_final: 0.7372 (t0) REVERT: A 260 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7139 (tt0) REVERT: A 279 TRP cc_start: 0.8850 (p-90) cc_final: 0.8195 (p-90) REVERT: A 302 ASN cc_start: 0.8074 (m-40) cc_final: 0.7591 (m110) REVERT: A 312 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8128 (mtmt) REVERT: A 335 GLU cc_start: 0.7353 (tt0) cc_final: 0.6153 (tm-30) REVERT: A 346 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6354 (mt-10) REVERT: A 350 GLN cc_start: 0.7571 (mt0) cc_final: 0.7094 (mp10) REVERT: A 380 PHE cc_start: 0.7648 (p90) cc_final: 0.7397 (p90) REVERT: A 396 GLU cc_start: 0.7458 (tt0) cc_final: 0.7131 (tt0) REVERT: A 411 GLU cc_start: 0.7910 (mp0) cc_final: 0.7563 (mp0) REVERT: A 413 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6612 (m-30) REVERT: A 414 TRP cc_start: 0.8084 (p90) cc_final: 0.7681 (p90) REVERT: A 425 THR cc_start: 0.8269 (p) cc_final: 0.8062 (p) REVERT: A 473 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6820 (mm-30) REVERT: A 501 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8409 (ttpt) REVERT: A 523 THR cc_start: 0.8230 (t) cc_final: 0.8026 (p) REVERT: G 50 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: G 109 TRP cc_start: 0.8424 (m100) cc_final: 0.7980 (m100) REVERT: G 120 TRP cc_start: 0.8609 (m100) cc_final: 0.8039 (m100) REVERT: G 135 GLU cc_start: 0.7304 (tp30) cc_final: 0.7038 (tp30) REVERT: G 137 HIS cc_start: 0.8572 (m170) cc_final: 0.8312 (m170) REVERT: G 144 GLU cc_start: 0.7447 (pm20) cc_final: 0.6962 (pm20) REVERT: G 174 MET cc_start: 0.7786 (mtp) cc_final: 0.7278 (mtp) REVERT: G 191 ARG cc_start: 0.8412 (mtt-85) cc_final: 0.8056 (mtt-85) REVERT: G 193 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: G 213 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7360 (tm-30) REVERT: G 237 ASP cc_start: 0.7736 (t0) cc_final: 0.7408 (t0) REVERT: G 263 THR cc_start: 0.8424 (m) cc_final: 0.7787 (p) REVERT: G 266 PHE cc_start: 0.8361 (t80) cc_final: 0.7972 (t80) REVERT: G 268 PHE cc_start: 0.8064 (m-10) cc_final: 0.7829 (m-10) REVERT: G 283 ARG cc_start: 0.8539 (mtp180) cc_final: 0.8153 (mtp180) REVERT: G 327 GLU cc_start: 0.7594 (mm-30) cc_final: 0.6951 (mm-30) REVERT: G 335 GLU cc_start: 0.7232 (tt0) cc_final: 0.6819 (tt0) REVERT: G 342 TYR cc_start: 0.7801 (p90) cc_final: 0.7114 (p90) REVERT: G 345 PHE cc_start: 0.8152 (m-80) cc_final: 0.7544 (m-80) REVERT: G 398 PHE cc_start: 0.8768 (p90) cc_final: 0.8392 (p90) REVERT: G 425 THR cc_start: 0.8164 (p) cc_final: 0.7932 (p) REVERT: G 479 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8407 (mmtm) REVERT: G 505 ASN cc_start: 0.7626 (t0) cc_final: 0.7179 (t0) REVERT: G 518 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7462 (ptp) REVERT: G 528 TRP cc_start: 0.8186 (m100) cc_final: 0.7678 (m100) REVERT: G 530 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7503 (ttpp) REVERT: F 80 ARG cc_start: 0.4375 (tpt90) cc_final: 0.2334 (tpt170) REVERT: F 81 ARG cc_start: 0.5526 (ptp-170) cc_final: 0.3969 (ptt-90) REVERT: F 120 TRP cc_start: 0.8486 (m100) cc_final: 0.7795 (m100) REVERT: F 131 ASN cc_start: 0.8603 (m-40) cc_final: 0.8203 (m-40) REVERT: F 135 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: F 144 GLU cc_start: 0.7254 (pm20) cc_final: 0.6978 (pm20) REVERT: F 151 LYS cc_start: 0.8298 (mmmm) cc_final: 0.7701 (mmmm) REVERT: F 167 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7872 (m-40) REVERT: F 193 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7378 (mt-10) REVERT: F 197 PHE cc_start: 0.8265 (m-10) cc_final: 0.7342 (m-80) REVERT: F 200 TRP cc_start: 0.8495 (p90) cc_final: 0.8284 (p90) REVERT: F 201 LYS cc_start: 0.8101 (mmpt) cc_final: 0.7699 (mmpt) REVERT: F 215 ASP cc_start: 0.7399 (m-30) cc_final: 0.7156 (m-30) REVERT: F 225 THR cc_start: 0.7374 (m) cc_final: 0.7065 (p) REVERT: F 266 PHE cc_start: 0.8405 (t80) cc_final: 0.7857 (t80) REVERT: F 279 TRP cc_start: 0.8395 (p-90) cc_final: 0.8182 (p-90) REVERT: F 302 ASN cc_start: 0.8083 (m-40) cc_final: 0.7254 (p0) REVERT: F 308 VAL cc_start: 0.8777 (p) cc_final: 0.8560 (m) REVERT: F 312 LYS cc_start: 0.8518 (mptt) cc_final: 0.7760 (mptt) REVERT: F 335 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: F 403 HIS cc_start: 0.8084 (m-70) cc_final: 0.7436 (m-70) REVERT: F 409 TYR cc_start: 0.8439 (t80) cc_final: 0.7982 (t80) REVERT: F 426 ASN cc_start: 0.6316 (OUTLIER) cc_final: 0.3573 (t0) REVERT: F 470 TRP cc_start: 0.8162 (p90) cc_final: 0.7862 (p90) REVERT: F 532 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8009 (ttmm) REVERT: F 533 LEU cc_start: 0.8381 (tp) cc_final: 0.7750 (tp) REVERT: F 550 GLN cc_start: 0.8401 (mm110) cc_final: 0.7786 (mm110) REVERT: F 551 MET cc_start: 0.7240 (ttt) cc_final: 0.6704 (ttt) REVERT: F 562 VAL cc_start: 0.8621 (p) cc_final: 0.8412 (m) REVERT: F 575 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7069 (mmmt) REVERT: D 48 GLN cc_start: 0.8149 (mt0) cc_final: 0.7942 (mt0) REVERT: D 49 THR cc_start: 0.7963 (m) cc_final: 0.7494 (p) REVERT: D 50 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6615 (tm-30) REVERT: D 174 MET cc_start: 0.7670 (mtp) cc_final: 0.7154 (mtp) REVERT: D 200 TRP cc_start: 0.8737 (p90) cc_final: 0.8219 (p90) REVERT: D 510 TYR cc_start: 0.8437 (t80) cc_final: 0.8117 (t80) REVERT: D 569 MET cc_start: 0.6685 (mmt) cc_final: 0.6279 (mmt) REVERT: E 51 PHE cc_start: 0.8462 (m-80) cc_final: 0.8221 (m-80) REVERT: E 106 VAL cc_start: 0.8018 (t) cc_final: 0.7620 (p) REVERT: E 133 MET cc_start: 0.7438 (mmt) cc_final: 0.7229 (mmt) REVERT: E 142 GLU cc_start: 0.7856 (pt0) cc_final: 0.6925 (pt0) REVERT: E 163 LYS cc_start: 0.7833 (mppt) cc_final: 0.7298 (mppt) REVERT: E 213 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7664 (tm-30) REVERT: E 237 ASP cc_start: 0.7668 (t0) cc_final: 0.7350 (t0) REVERT: E 240 ASP cc_start: 0.7312 (m-30) cc_final: 0.7096 (m-30) REVERT: E 245 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7902 (p) REVERT: E 247 GLU cc_start: 0.7806 (mp0) cc_final: 0.7262 (mp0) REVERT: E 266 PHE cc_start: 0.8278 (t80) cc_final: 0.8024 (t80) REVERT: E 280 GLN cc_start: 0.6017 (pt0) cc_final: 0.5646 (pt0) REVERT: E 342 TYR cc_start: 0.7249 (p90) cc_final: 0.6981 (p90) REVERT: E 387 LYS cc_start: 0.8691 (tptm) cc_final: 0.8246 (tptm) REVERT: E 400 TYR cc_start: 0.8064 (t80) cc_final: 0.7293 (t80) REVERT: E 464 TYR cc_start: 0.7987 (t80) cc_final: 0.7534 (t80) REVERT: E 472 LYS cc_start: 0.3253 (OUTLIER) cc_final: 0.0956 (tmmt) REVERT: E 479 LYS cc_start: 0.8336 (mptt) cc_final: 0.7993 (mptt) REVERT: E 501 LYS cc_start: 0.8065 (tttt) cc_final: 0.7283 (tttt) REVERT: E 508 ASN cc_start: 0.8033 (p0) cc_final: 0.6285 (p0) REVERT: E 509 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7244 (mm-30) REVERT: E 520 ARG cc_start: 0.7620 (mtp85) cc_final: 0.7080 (mtp85) REVERT: E 532 LYS cc_start: 0.8328 (ttpt) cc_final: 0.7724 (ttpt) REVERT: E 538 LYS cc_start: 0.8049 (ttmm) cc_final: 0.7639 (ttmm) REVERT: E 582 LYS cc_start: 0.6926 (pmtt) cc_final: 0.6555 (pmtt) REVERT: I 95 ASN cc_start: 0.8356 (m-40) cc_final: 0.8060 (m-40) REVERT: I 96 MET cc_start: 0.4416 (OUTLIER) cc_final: 0.3997 (ptt) REVERT: I 101 ILE cc_start: 0.8485 (mt) cc_final: 0.8229 (mt) REVERT: I 109 TRP cc_start: 0.8786 (m100) cc_final: 0.7883 (m100) REVERT: I 122 ASN cc_start: 0.8135 (p0) cc_final: 0.7689 (p0) REVERT: I 147 ASN cc_start: 0.8143 (t0) cc_final: 0.7580 (t0) REVERT: I 237 ASP cc_start: 0.7393 (t0) cc_final: 0.6969 (t0) REVERT: I 269 ASP cc_start: 0.6892 (p0) cc_final: 0.6338 (p0) REVERT: I 310 GLN cc_start: 0.8364 (mt0) cc_final: 0.8069 (mt0) REVERT: I 314 ARG cc_start: 0.8043 (ptp-170) cc_final: 0.7825 (ptp90) REVERT: I 318 GLN cc_start: 0.8553 (mt0) cc_final: 0.8161 (mm-40) REVERT: I 446 ASN cc_start: 0.8469 (m110) cc_final: 0.8233 (m-40) REVERT: I 485 ASN cc_start: 0.7221 (p0) cc_final: 0.6407 (p0) REVERT: I 491 GLN cc_start: 0.7399 (mm-40) cc_final: 0.6808 (mm-40) REVERT: I 501 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8030 (ttpt) REVERT: I 528 TRP cc_start: 0.8359 (m100) cc_final: 0.7558 (m100) REVERT: I 552 SER cc_start: 0.7994 (t) cc_final: 0.7770 (p) REVERT: I 565 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7949 (t0) REVERT: I 582 LYS cc_start: 0.8302 (pttm) cc_final: 0.8013 (pttm) REVERT: C 47 ASN cc_start: 0.7907 (t0) cc_final: 0.7557 (t160) REVERT: C 67 ARG cc_start: 0.7330 (mmt-90) cc_final: 0.6895 (mmt-90) REVERT: C 73 MET cc_start: 0.8078 (ptt) cc_final: 0.7702 (ptt) REVERT: C 77 GLU cc_start: 0.6840 (tp30) cc_final: 0.6310 (tp30) REVERT: C 154 SER cc_start: 0.8291 (p) cc_final: 0.8091 (p) REVERT: C 193 GLU cc_start: 0.7027 (tp30) cc_final: 0.6299 (tp30) REVERT: C 509 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: C 528 TRP cc_start: 0.8656 (m100) cc_final: 0.8250 (m100) REVERT: B 46 ASN cc_start: 0.8240 (t0) cc_final: 0.7982 (t0) REVERT: B 53 PHE cc_start: 0.8327 (m-80) cc_final: 0.7854 (p90) REVERT: B 68 LEU cc_start: 0.8687 (tp) cc_final: 0.8418 (tp) REVERT: B 80 ARG cc_start: 0.8130 (mmm-85) cc_final: 0.7849 (mmm-85) REVERT: B 109 TRP cc_start: 0.8874 (m100) cc_final: 0.8235 (m100) REVERT: B 117 TRP cc_start: 0.8117 (m100) cc_final: 0.7608 (m100) REVERT: B 125 ASP cc_start: 0.7377 (m-30) cc_final: 0.6955 (m-30) REVERT: B 151 LYS cc_start: 0.8415 (mttm) cc_final: 0.8172 (mttm) REVERT: B 193 GLU cc_start: 0.7595 (tt0) cc_final: 0.6842 (tt0) REVERT: B 198 TYR cc_start: 0.7561 (m-10) cc_final: 0.7305 (m-10) REVERT: B 216 ARG cc_start: 0.7841 (tpt-90) cc_final: 0.7536 (tpt-90) REVERT: B 256 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7347 (mtp85) REVERT: B 415 ILE cc_start: 0.8361 (mt) cc_final: 0.8113 (mt) REVERT: B 416 GLN cc_start: 0.7876 (tt0) cc_final: 0.7599 (mp10) REVERT: B 417 ASN cc_start: 0.8055 (t0) cc_final: 0.7676 (t0) REVERT: B 491 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7211 (mm-40) REVERT: B 501 LYS cc_start: 0.8704 (tttm) cc_final: 0.8184 (tttm) REVERT: B 511 ASP cc_start: 0.8160 (t0) cc_final: 0.7837 (t0) REVERT: B 528 TRP cc_start: 0.8750 (m100) cc_final: 0.8332 (m100) REVERT: B 535 PHE cc_start: 0.8105 (m-80) cc_final: 0.7864 (m-80) REVERT: B 569 MET cc_start: 0.7062 (mmm) cc_final: 0.6821 (mmm) outliers start: 158 outliers final: 93 residues processed: 1614 average time/residue: 0.2060 time to fit residues: 521.2004 Evaluate side-chains 1668 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1558 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 273 CYS Chi-restraints excluded: chain G residue 277 HIS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 518 MET Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 426 ASN Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 70 HIS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 106 VAL Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 204 ILE Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 494 CYS Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 565 ASN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 549 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 265 optimal weight: 0.0870 chunk 129 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 252 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 307 optimal weight: 6.9990 chunk 38 optimal weight: 0.0670 chunk 267 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 overall best weight: 2.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 277 HIS A 384 HIS G 104 GLN ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 GLN G 497 GLN F 93 ASN ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN F 167 ASN F 403 HIS D 70 HIS E 72 ASN E 127 GLN E 143 GLN E 403 HIS I 48 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 318 GLN I 403 HIS ** I 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN ** C 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS B 137 HIS B 549 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106342 restraints weight = 52547.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110633 restraints weight = 24428.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.113399 restraints weight = 13711.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115234 restraints weight = 8701.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116431 restraints weight = 6080.880| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 31936 Z= 0.187 Angle : 0.612 10.666 43674 Z= 0.310 Chirality : 0.045 0.183 4764 Planarity : 0.005 0.079 5732 Dihedral : 5.710 70.171 4241 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.19 % Allowed : 23.13 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 3686 helix: -1.51 (0.39), residues: 124 sheet: -0.59 (0.17), residues: 836 loop : -0.51 (0.12), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 332 TYR 0.025 0.002 TYR I 464 PHE 0.028 0.002 PHE B 197 TRP 0.025 0.001 TRP E 279 HIS 0.008 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00400 (31929) covalent geometry : angle 0.61130 (43660) SS BOND : bond 0.00580 ( 7) SS BOND : angle 1.23492 ( 14) hydrogen bonds : bond 0.03707 ( 295) hydrogen bonds : angle 6.24442 ( 567) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1581 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7526 (tt0) cc_final: 0.7169 (tp30) REVERT: A 79 TYR cc_start: 0.8349 (m-80) cc_final: 0.7815 (m-80) REVERT: A 104 GLN cc_start: 0.8225 (pt0) cc_final: 0.7577 (pt0) REVERT: A 109 TRP cc_start: 0.8585 (m100) cc_final: 0.8006 (m100) REVERT: A 147 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7814 (t0) REVERT: A 163 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8300 (mtpt) REVERT: A 174 MET cc_start: 0.8385 (mtp) cc_final: 0.7648 (mtp) REVERT: A 177 LEU cc_start: 0.8503 (tt) cc_final: 0.8283 (tp) REVERT: A 192 SER cc_start: 0.7985 (t) cc_final: 0.7717 (t) REVERT: A 215 ASP cc_start: 0.7287 (m-30) cc_final: 0.7039 (m-30) REVERT: A 237 ASP cc_start: 0.7780 (t0) cc_final: 0.7260 (t0) REVERT: A 244 TYR cc_start: 0.7748 (m-80) cc_final: 0.7415 (m-80) REVERT: A 247 GLU cc_start: 0.7683 (mp0) cc_final: 0.7289 (mp0) REVERT: A 256 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7799 (mmt90) REVERT: A 260 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: A 266 PHE cc_start: 0.7957 (t80) cc_final: 0.7748 (t80) REVERT: A 269 ASP cc_start: 0.7268 (p0) cc_final: 0.6996 (p0) REVERT: A 302 ASN cc_start: 0.8260 (m-40) cc_final: 0.7634 (m110) REVERT: A 312 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8114 (mtmt) REVERT: A 331 MET cc_start: 0.7618 (ttm) cc_final: 0.7381 (ttm) REVERT: A 335 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6106 (tm-30) REVERT: A 346 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6365 (mt-10) REVERT: A 350 GLN cc_start: 0.7409 (mt0) cc_final: 0.6978 (mp10) REVERT: A 380 PHE cc_start: 0.7550 (p90) cc_final: 0.7238 (p90) REVERT: A 396 GLU cc_start: 0.7518 (tt0) cc_final: 0.7300 (tt0) REVERT: A 411 GLU cc_start: 0.7815 (mp0) cc_final: 0.7388 (mp0) REVERT: A 413 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6578 (m-30) REVERT: A 414 TRP cc_start: 0.7975 (p90) cc_final: 0.7596 (p90) REVERT: A 425 THR cc_start: 0.8226 (p) cc_final: 0.8021 (p) REVERT: A 426 ASN cc_start: 0.8544 (t0) cc_final: 0.7954 (t0) REVERT: A 473 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6808 (mm-30) REVERT: A 501 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8173 (ttpp) REVERT: A 502 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8617 (m) REVERT: A 528 TRP cc_start: 0.8352 (m100) cc_final: 0.7999 (m100) REVERT: A 530 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7851 (ttpp) REVERT: A 536 LYS cc_start: 0.8389 (tttm) cc_final: 0.8045 (tttm) REVERT: G 50 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6608 (mp0) REVERT: G 60 GLU cc_start: 0.7501 (tp30) cc_final: 0.7082 (tp30) REVERT: G 62 THR cc_start: 0.8424 (m) cc_final: 0.7926 (t) REVERT: G 73 MET cc_start: 0.7758 (ptm) cc_final: 0.7230 (ptm) REVERT: G 109 TRP cc_start: 0.8489 (m100) cc_final: 0.8134 (m100) REVERT: G 120 TRP cc_start: 0.8546 (m100) cc_final: 0.8035 (m100) REVERT: G 135 GLU cc_start: 0.7270 (tp30) cc_final: 0.6926 (tp30) REVERT: G 144 GLU cc_start: 0.7385 (pm20) cc_final: 0.6938 (pm20) REVERT: G 174 MET cc_start: 0.7898 (mtp) cc_final: 0.7357 (mtp) REVERT: G 193 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6604 (mp0) REVERT: G 213 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7233 (tm-30) REVERT: G 245 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7787 (t) REVERT: G 263 THR cc_start: 0.8470 (m) cc_final: 0.7900 (p) REVERT: G 266 PHE cc_start: 0.8321 (t80) cc_final: 0.7951 (t80) REVERT: G 268 PHE cc_start: 0.8077 (m-10) cc_final: 0.7829 (m-10) REVERT: G 283 ARG cc_start: 0.8443 (mtp180) cc_final: 0.8049 (mtp180) REVERT: G 327 GLU cc_start: 0.7497 (mm-30) cc_final: 0.6948 (mm-30) REVERT: G 335 GLU cc_start: 0.7266 (tt0) cc_final: 0.6870 (tt0) REVERT: G 342 TYR cc_start: 0.7767 (p90) cc_final: 0.7196 (p90) REVERT: G 345 PHE cc_start: 0.8005 (m-80) cc_final: 0.7479 (m-80) REVERT: G 382 ARG cc_start: 0.5570 (mtm180) cc_final: 0.5058 (mtm180) REVERT: G 398 PHE cc_start: 0.8720 (p90) cc_final: 0.8191 (p90) REVERT: G 425 THR cc_start: 0.8103 (p) cc_final: 0.7869 (p) REVERT: G 479 LYS cc_start: 0.8672 (mmtm) cc_final: 0.8426 (mmtm) REVERT: G 501 LYS cc_start: 0.8445 (ttpp) cc_final: 0.7978 (ttpp) REVERT: G 505 ASN cc_start: 0.7640 (t0) cc_final: 0.7021 (t0) REVERT: G 510 TYR cc_start: 0.8023 (t80) cc_final: 0.7739 (t80) REVERT: G 518 MET cc_start: 0.7723 (ptp) cc_final: 0.7435 (ptp) REVERT: G 520 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7760 (mtm-85) REVERT: G 528 TRP cc_start: 0.8173 (m100) cc_final: 0.7687 (m100) REVERT: G 530 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7207 (ttpp) REVERT: F 67 ARG cc_start: 0.8348 (mmt180) cc_final: 0.8108 (mmt180) REVERT: F 72 ASN cc_start: 0.8325 (t0) cc_final: 0.8081 (t0) REVERT: F 73 MET cc_start: 0.7793 (ttt) cc_final: 0.7318 (tmm) REVERT: F 80 ARG cc_start: 0.4074 (tpt90) cc_final: 0.1615 (mmt180) REVERT: F 81 ARG cc_start: 0.5542 (ptp-170) cc_final: 0.5280 (ptp-170) REVERT: F 120 TRP cc_start: 0.8435 (m100) cc_final: 0.7794 (m100) REVERT: F 135 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: F 144 GLU cc_start: 0.7295 (pm20) cc_final: 0.7002 (pm20) REVERT: F 151 LYS cc_start: 0.8332 (mmmm) cc_final: 0.7871 (mmmm) REVERT: F 191 ARG cc_start: 0.8364 (mtt90) cc_final: 0.8066 (mtp85) REVERT: F 193 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: F 195 LEU cc_start: 0.7714 (mt) cc_final: 0.7450 (mt) REVERT: F 197 PHE cc_start: 0.8339 (m-10) cc_final: 0.7536 (m-80) REVERT: F 201 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7661 (mmpt) REVERT: F 213 GLN cc_start: 0.7746 (tm-30) cc_final: 0.6966 (tm-30) REVERT: F 225 THR cc_start: 0.7439 (m) cc_final: 0.7119 (p) REVERT: F 237 ASP cc_start: 0.8295 (t0) cc_final: 0.8034 (t0) REVERT: F 266 PHE cc_start: 0.8361 (t80) cc_final: 0.7782 (t80) REVERT: F 279 TRP cc_start: 0.8305 (p-90) cc_final: 0.8082 (p-90) REVERT: F 302 ASN cc_start: 0.7912 (m-40) cc_final: 0.7071 (p0) REVERT: F 317 THR cc_start: 0.8248 (p) cc_final: 0.7947 (t) REVERT: F 335 GLU cc_start: 0.7245 (tt0) cc_final: 0.6828 (tt0) REVERT: F 403 HIS cc_start: 0.7766 (m90) cc_final: 0.7407 (m-70) REVERT: F 409 TYR cc_start: 0.8397 (t80) cc_final: 0.8013 (t80) REVERT: F 439 LYS cc_start: 0.8103 (mmtp) cc_final: 0.7373 (mmtp) REVERT: F 451 TYR cc_start: 0.8545 (t80) cc_final: 0.8293 (t80) REVERT: F 459 ASN cc_start: 0.8062 (m-40) cc_final: 0.7799 (m110) REVERT: F 481 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.8003 (mmm-85) REVERT: F 497 GLN cc_start: 0.8453 (mt0) cc_final: 0.8238 (mt0) REVERT: F 518 MET cc_start: 0.7935 (ptp) cc_final: 0.7423 (ptp) REVERT: F 532 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8036 (ttmm) REVERT: F 533 LEU cc_start: 0.8436 (tp) cc_final: 0.7817 (tp) REVERT: F 538 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7568 (ttpt) REVERT: F 550 GLN cc_start: 0.8267 (mm110) cc_final: 0.8042 (mm110) REVERT: F 551 MET cc_start: 0.7125 (ttt) cc_final: 0.6693 (ttt) REVERT: F 562 VAL cc_start: 0.8615 (p) cc_final: 0.8395 (m) REVERT: F 575 LYS cc_start: 0.7439 (mmtt) cc_final: 0.6982 (mmmt) REVERT: D 49 THR cc_start: 0.7990 (m) cc_final: 0.7501 (p) REVERT: D 50 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6652 (tm-30) REVERT: D 73 MET cc_start: 0.8235 (ptt) cc_final: 0.7735 (ptm) REVERT: D 174 MET cc_start: 0.7675 (mtp) cc_final: 0.7158 (mtp) REVERT: D 200 TRP cc_start: 0.8759 (p90) cc_final: 0.8308 (p90) REVERT: D 510 TYR cc_start: 0.8379 (t80) cc_final: 0.8092 (t80) REVERT: E 95 ASN cc_start: 0.8222 (t0) cc_final: 0.7904 (t0) REVERT: E 131 ASN cc_start: 0.8366 (m-40) cc_final: 0.7973 (t0) REVERT: E 142 GLU cc_start: 0.7751 (pt0) cc_final: 0.6944 (pt0) REVERT: E 163 LYS cc_start: 0.7904 (mppt) cc_final: 0.7443 (mppt) REVERT: E 237 ASP cc_start: 0.7547 (t0) cc_final: 0.7261 (t0) REVERT: E 240 ASP cc_start: 0.7254 (m-30) cc_final: 0.7018 (m-30) REVERT: E 243 PHE cc_start: 0.8483 (t80) cc_final: 0.8219 (t80) REVERT: E 245 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7626 (p) REVERT: E 247 GLU cc_start: 0.7641 (mp0) cc_final: 0.7136 (mp0) REVERT: E 256 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7605 (mtp85) REVERT: E 266 PHE cc_start: 0.8253 (t80) cc_final: 0.8038 (t80) REVERT: E 280 GLN cc_start: 0.5814 (pt0) cc_final: 0.5460 (pt0) REVERT: E 335 GLU cc_start: 0.6625 (tm-30) cc_final: 0.6245 (tm-30) REVERT: E 342 TYR cc_start: 0.7139 (p90) cc_final: 0.6863 (p90) REVERT: E 387 LYS cc_start: 0.8675 (tptm) cc_final: 0.8188 (tptm) REVERT: E 400 TYR cc_start: 0.8051 (t80) cc_final: 0.7307 (t80) REVERT: E 451 TYR cc_start: 0.3569 (OUTLIER) cc_final: 0.3000 (t80) REVERT: E 464 TYR cc_start: 0.8020 (t80) cc_final: 0.7541 (t80) REVERT: E 472 LYS cc_start: 0.3323 (OUTLIER) cc_final: 0.1071 (tmmt) REVERT: E 479 LYS cc_start: 0.8361 (mptt) cc_final: 0.7998 (mptt) REVERT: E 501 LYS cc_start: 0.8170 (tttt) cc_final: 0.7399 (tttt) REVERT: E 508 ASN cc_start: 0.8125 (p0) cc_final: 0.6345 (p0) REVERT: E 509 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7233 (mm-30) REVERT: E 520 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7219 (mtp85) REVERT: E 530 LYS cc_start: 0.8010 (tmtt) cc_final: 0.7506 (tttt) REVERT: E 532 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7726 (ttpt) REVERT: E 538 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7426 (mtpp) REVERT: E 581 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7960 (ttp-170) REVERT: E 582 LYS cc_start: 0.6769 (pmtt) cc_final: 0.6347 (pmtt) REVERT: I 81 ARG cc_start: 0.5781 (ptp90) cc_final: 0.4192 (ptp90) REVERT: I 95 ASN cc_start: 0.8302 (m-40) cc_final: 0.7964 (m-40) REVERT: I 105 ILE cc_start: 0.8634 (mm) cc_final: 0.8373 (mm) REVERT: I 109 TRP cc_start: 0.8752 (m100) cc_final: 0.7847 (m100) REVERT: I 120 TRP cc_start: 0.8926 (m100) cc_final: 0.8502 (m100) REVERT: I 122 ASN cc_start: 0.8112 (p0) cc_final: 0.7672 (p0) REVERT: I 147 ASN cc_start: 0.8168 (t0) cc_final: 0.7568 (t0) REVERT: I 150 LEU cc_start: 0.8476 (mt) cc_final: 0.8110 (mp) REVERT: I 193 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7116 (mp0) REVERT: I 237 ASP cc_start: 0.7438 (t0) cc_final: 0.6886 (t0) REVERT: I 269 ASP cc_start: 0.6807 (p0) cc_final: 0.6522 (p0) REVERT: I 446 ASN cc_start: 0.8539 (m110) cc_final: 0.8319 (m-40) REVERT: I 479 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8229 (mmtt) REVERT: I 485 ASN cc_start: 0.7214 (p0) cc_final: 0.6333 (p0) REVERT: I 501 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8182 (ttpt) REVERT: I 528 TRP cc_start: 0.8340 (m100) cc_final: 0.7494 (m100) REVERT: I 565 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7923 (t0) REVERT: I 582 LYS cc_start: 0.8291 (pttm) cc_final: 0.8011 (pttm) REVERT: C 46 ASN cc_start: 0.8406 (t0) cc_final: 0.8150 (t0) REVERT: C 47 ASN cc_start: 0.7831 (t0) cc_final: 0.7579 (t160) REVERT: C 67 ARG cc_start: 0.7110 (mmt-90) cc_final: 0.6884 (mmt-90) REVERT: C 68 LEU cc_start: 0.8155 (tp) cc_final: 0.7610 (tp) REVERT: C 73 MET cc_start: 0.7951 (ptt) cc_final: 0.7613 (ptt) REVERT: C 77 GLU cc_start: 0.6885 (tp30) cc_final: 0.6274 (tp30) REVERT: C 193 GLU cc_start: 0.7036 (tp30) cc_final: 0.6375 (tp30) REVERT: C 501 LYS cc_start: 0.8630 (tttp) cc_final: 0.8117 (tttm) REVERT: C 509 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: C 528 TRP cc_start: 0.8634 (m100) cc_final: 0.7900 (m100) REVERT: B 46 ASN cc_start: 0.8249 (t0) cc_final: 0.7894 (t0) REVERT: B 53 PHE cc_start: 0.8340 (m-80) cc_final: 0.7736 (p90) REVERT: B 68 LEU cc_start: 0.8628 (tp) cc_final: 0.8409 (tp) REVERT: B 80 ARG cc_start: 0.8148 (mmm-85) cc_final: 0.7772 (mmm-85) REVERT: B 117 TRP cc_start: 0.8057 (m100) cc_final: 0.7418 (m100) REVERT: B 122 ASN cc_start: 0.7627 (p0) cc_final: 0.7294 (p0) REVERT: B 152 THR cc_start: 0.8541 (m) cc_final: 0.8013 (p) REVERT: B 182 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7790 (m) REVERT: B 240 ASP cc_start: 0.7134 (m-30) cc_final: 0.6877 (m-30) REVERT: B 256 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7524 (mtp180) REVERT: B 415 ILE cc_start: 0.8369 (mt) cc_final: 0.8100 (mt) REVERT: B 416 GLN cc_start: 0.7874 (tt0) cc_final: 0.7627 (mp-120) REVERT: B 491 GLN cc_start: 0.7543 (mm-40) cc_final: 0.7134 (mm-40) REVERT: B 511 ASP cc_start: 0.8110 (t0) cc_final: 0.7749 (t0) REVERT: B 528 TRP cc_start: 0.8786 (m100) cc_final: 0.8320 (m100) REVERT: B 535 PHE cc_start: 0.8082 (m-80) cc_final: 0.7807 (m-80) REVERT: B 569 MET cc_start: 0.7082 (mmm) cc_final: 0.6736 (mmm) outliers start: 138 outliers final: 89 residues processed: 1616 average time/residue: 0.2068 time to fit residues: 524.6664 Evaluate side-chains 1651 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1544 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 277 HIS Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 93 ASN Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 521 ILE Chi-restraints excluded: chain F residue 538 LYS Chi-restraints excluded: chain F residue 570 LYS Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 318 GLN Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 494 CYS Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 565 ASN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 92 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 307 optimal weight: 5.9990 chunk 337 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 240 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 HIS G 181 ASN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 GLN G 458 ASN G 468 GLN F 93 ASN F 95 ASN ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 HIS E 403 HIS ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN I 426 ASN C 46 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 280 GLN B 318 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.125373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107141 restraints weight = 52348.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.111430 restraints weight = 24345.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.114183 restraints weight = 13663.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116009 restraints weight = 8684.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117239 restraints weight = 6066.880| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 31936 Z= 0.176 Angle : 0.596 11.453 43674 Z= 0.301 Chirality : 0.044 0.185 4764 Planarity : 0.005 0.066 5732 Dihedral : 5.372 69.757 4238 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.73 % Allowed : 25.19 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 3686 helix: -1.36 (0.40), residues: 124 sheet: -0.54 (0.17), residues: 855 loop : -0.44 (0.12), residues: 2707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 216 TYR 0.025 0.002 TYR A 210 PHE 0.028 0.002 PHE G 527 TRP 0.024 0.001 TRP E 279 HIS 0.006 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00379 (31929) covalent geometry : angle 0.59517 (43660) SS BOND : bond 0.00515 ( 7) SS BOND : angle 1.29638 ( 14) hydrogen bonds : bond 0.03367 ( 295) hydrogen bonds : angle 6.07737 ( 567) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1716 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1560 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7455 (tt0) cc_final: 0.7125 (tp30) REVERT: A 79 TYR cc_start: 0.8345 (m-80) cc_final: 0.7781 (m-80) REVERT: A 104 GLN cc_start: 0.8180 (pt0) cc_final: 0.7460 (pt0) REVERT: A 109 TRP cc_start: 0.8588 (m100) cc_final: 0.8122 (m100) REVERT: A 147 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7949 (t0) REVERT: A 169 LEU cc_start: 0.7805 (mp) cc_final: 0.7528 (mp) REVERT: A 192 SER cc_start: 0.8033 (t) cc_final: 0.7792 (t) REVERT: A 200 TRP cc_start: 0.8411 (p90) cc_final: 0.8100 (p90) REVERT: A 215 ASP cc_start: 0.7304 (m-30) cc_final: 0.7062 (m-30) REVERT: A 237 ASP cc_start: 0.7710 (t0) cc_final: 0.7220 (t0) REVERT: A 247 GLU cc_start: 0.7668 (mp0) cc_final: 0.7312 (mp0) REVERT: A 256 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7785 (mmt90) REVERT: A 260 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: A 269 ASP cc_start: 0.7256 (p0) cc_final: 0.7024 (p0) REVERT: A 302 ASN cc_start: 0.8275 (m-40) cc_final: 0.7750 (m110) REVERT: A 312 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8123 (mtmt) REVERT: A 335 GLU cc_start: 0.7247 (tt0) cc_final: 0.6065 (tm-30) REVERT: A 346 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6369 (mt-10) REVERT: A 350 GLN cc_start: 0.7451 (mt0) cc_final: 0.6989 (mp10) REVERT: A 380 PHE cc_start: 0.7550 (p90) cc_final: 0.7228 (p90) REVERT: A 382 ARG cc_start: 0.8205 (mmt90) cc_final: 0.7679 (mtt90) REVERT: A 411 GLU cc_start: 0.7764 (mp0) cc_final: 0.7455 (mp0) REVERT: A 413 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6587 (m-30) REVERT: A 414 TRP cc_start: 0.7970 (p90) cc_final: 0.7578 (p90) REVERT: A 425 THR cc_start: 0.8128 (p) cc_final: 0.7896 (p) REVERT: A 426 ASN cc_start: 0.8489 (t0) cc_final: 0.7922 (t0) REVERT: A 446 ASN cc_start: 0.8118 (m110) cc_final: 0.7883 (m110) REVERT: A 468 GLN cc_start: 0.7838 (tt0) cc_final: 0.7562 (tt0) REVERT: A 473 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6894 (mm-30) REVERT: A 501 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8105 (ttpp) REVERT: A 502 VAL cc_start: 0.8889 (OUTLIER) cc_final: 0.8594 (m) REVERT: A 530 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7946 (ttpp) REVERT: A 536 LYS cc_start: 0.8373 (tttm) cc_final: 0.7964 (tttm) REVERT: G 60 GLU cc_start: 0.7493 (tp30) cc_final: 0.7056 (tp30) REVERT: G 62 THR cc_start: 0.8395 (m) cc_final: 0.7866 (t) REVERT: G 67 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7851 (mtt90) REVERT: G 73 MET cc_start: 0.7750 (ptm) cc_final: 0.7373 (ptm) REVERT: G 104 GLN cc_start: 0.7998 (pt0) cc_final: 0.7511 (pt0) REVERT: G 109 TRP cc_start: 0.8430 (m100) cc_final: 0.8102 (m100) REVERT: G 120 TRP cc_start: 0.8537 (m100) cc_final: 0.8126 (m100) REVERT: G 135 GLU cc_start: 0.7265 (tp30) cc_final: 0.6880 (tp30) REVERT: G 137 HIS cc_start: 0.8480 (m90) cc_final: 0.8232 (m170) REVERT: G 144 GLU cc_start: 0.7266 (pm20) cc_final: 0.7012 (pm20) REVERT: G 174 MET cc_start: 0.7856 (mtp) cc_final: 0.7210 (mtp) REVERT: G 185 PHE cc_start: 0.8177 (t80) cc_final: 0.7846 (t80) REVERT: G 193 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: G 213 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7343 (tm-30) REVERT: G 245 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7762 (t) REVERT: G 263 THR cc_start: 0.8468 (m) cc_final: 0.7938 (p) REVERT: G 266 PHE cc_start: 0.8312 (t80) cc_final: 0.7934 (t80) REVERT: G 268 PHE cc_start: 0.8092 (m-10) cc_final: 0.7832 (m-10) REVERT: G 287 LEU cc_start: 0.8448 (tp) cc_final: 0.8222 (tp) REVERT: G 312 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8130 (mtpp) REVERT: G 327 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7080 (mm-30) REVERT: G 335 GLU cc_start: 0.7304 (tt0) cc_final: 0.6910 (tt0) REVERT: G 342 TYR cc_start: 0.7685 (p90) cc_final: 0.7200 (p90) REVERT: G 345 PHE cc_start: 0.7959 (m-80) cc_final: 0.7415 (m-80) REVERT: G 382 ARG cc_start: 0.5408 (mtm180) cc_final: 0.4757 (mtm180) REVERT: G 398 PHE cc_start: 0.8673 (p90) cc_final: 0.8263 (p90) REVERT: G 425 THR cc_start: 0.8114 (p) cc_final: 0.7907 (p) REVERT: G 426 ASN cc_start: 0.8632 (t0) cc_final: 0.7367 (t0) REVERT: G 479 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8378 (mmtm) REVERT: G 501 LYS cc_start: 0.8476 (ttpp) cc_final: 0.7918 (ttpp) REVERT: G 505 ASN cc_start: 0.7713 (t0) cc_final: 0.7093 (t0) REVERT: G 518 MET cc_start: 0.7700 (ptp) cc_final: 0.7420 (ptp) REVERT: G 528 TRP cc_start: 0.8163 (m100) cc_final: 0.7649 (m100) REVERT: G 530 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7346 (ttpp) REVERT: G 535 PHE cc_start: 0.8264 (m-80) cc_final: 0.7612 (m-80) REVERT: F 67 ARG cc_start: 0.8320 (mmt180) cc_final: 0.8062 (mmt90) REVERT: F 72 ASN cc_start: 0.8430 (t0) cc_final: 0.8159 (t0) REVERT: F 73 MET cc_start: 0.7570 (ttt) cc_final: 0.7250 (ttp) REVERT: F 80 ARG cc_start: 0.4196 (tpt90) cc_final: 0.1746 (mmt180) REVERT: F 81 ARG cc_start: 0.5420 (ptp-170) cc_final: 0.5068 (ptp-170) REVERT: F 120 TRP cc_start: 0.8427 (m100) cc_final: 0.7889 (m100) REVERT: F 125 ASP cc_start: 0.7655 (m-30) cc_final: 0.7426 (m-30) REVERT: F 135 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: F 137 HIS cc_start: 0.8434 (m90) cc_final: 0.8199 (m170) REVERT: F 144 GLU cc_start: 0.7380 (pm20) cc_final: 0.7058 (pm20) REVERT: F 151 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7787 (mmmm) REVERT: F 191 ARG cc_start: 0.8347 (mtt90) cc_final: 0.7935 (mtp85) REVERT: F 193 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: F 195 LEU cc_start: 0.7655 (mt) cc_final: 0.7385 (mt) REVERT: F 197 PHE cc_start: 0.8304 (m-10) cc_final: 0.7512 (m-80) REVERT: F 201 LYS cc_start: 0.8041 (mmpt) cc_final: 0.7631 (mmpt) REVERT: F 213 GLN cc_start: 0.7667 (tm-30) cc_final: 0.6975 (tm-30) REVERT: F 237 ASP cc_start: 0.8224 (t0) cc_final: 0.7959 (t0) REVERT: F 242 GLN cc_start: 0.7570 (pt0) cc_final: 0.7218 (pp30) REVERT: F 266 PHE cc_start: 0.8341 (t80) cc_final: 0.7754 (t80) REVERT: F 302 ASN cc_start: 0.7934 (m-40) cc_final: 0.7727 (m-40) REVERT: F 317 THR cc_start: 0.8187 (p) cc_final: 0.7843 (t) REVERT: F 335 GLU cc_start: 0.7351 (tt0) cc_final: 0.6907 (tt0) REVERT: F 336 VAL cc_start: 0.8816 (t) cc_final: 0.8469 (p) REVERT: F 409 TYR cc_start: 0.8379 (t80) cc_final: 0.8052 (t80) REVERT: F 419 ASN cc_start: 0.8429 (m110) cc_final: 0.8088 (m110) REVERT: F 451 TYR cc_start: 0.8395 (t80) cc_final: 0.7850 (t80) REVERT: F 459 ASN cc_start: 0.8112 (m-40) cc_final: 0.7851 (m110) REVERT: F 475 ASP cc_start: 0.7959 (t0) cc_final: 0.7471 (t0) REVERT: F 501 LYS cc_start: 0.8530 (ttpp) cc_final: 0.7852 (pttp) REVERT: F 518 MET cc_start: 0.7902 (ptp) cc_final: 0.7318 (ptp) REVERT: F 532 LYS cc_start: 0.8505 (ttmm) cc_final: 0.8029 (ttmm) REVERT: F 533 LEU cc_start: 0.8408 (tp) cc_final: 0.7697 (tp) REVERT: F 538 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7499 (ttpt) REVERT: F 550 GLN cc_start: 0.8231 (mm110) cc_final: 0.7840 (mm-40) REVERT: F 551 MET cc_start: 0.7114 (ttt) cc_final: 0.6786 (ttt) REVERT: F 562 VAL cc_start: 0.8628 (p) cc_final: 0.8381 (m) REVERT: D 46 ASN cc_start: 0.7780 (t0) cc_final: 0.7305 (t0) REVERT: D 48 GLN cc_start: 0.8196 (mt0) cc_final: 0.7476 (mt0) REVERT: D 50 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6606 (tm-30) REVERT: D 73 MET cc_start: 0.8209 (ptt) cc_final: 0.7699 (ptm) REVERT: D 107 THR cc_start: 0.8399 (m) cc_final: 0.7812 (p) REVERT: D 174 MET cc_start: 0.7661 (mtp) cc_final: 0.7117 (mtp) REVERT: D 200 TRP cc_start: 0.8796 (p90) cc_final: 0.8265 (p90) REVERT: D 256 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7497 (mtm-85) REVERT: E 95 ASN cc_start: 0.8212 (t0) cc_final: 0.7888 (t0) REVERT: E 142 GLU cc_start: 0.7726 (pt0) cc_final: 0.6732 (pt0) REVERT: E 143 GLN cc_start: 0.8272 (mt0) cc_final: 0.8025 (mt0) REVERT: E 163 LYS cc_start: 0.7934 (mppt) cc_final: 0.7466 (mppt) REVERT: E 209 ARG cc_start: 0.5469 (OUTLIER) cc_final: 0.4641 (ptt180) REVERT: E 210 TYR cc_start: 0.8572 (p90) cc_final: 0.8284 (p90) REVERT: E 237 ASP cc_start: 0.7492 (t0) cc_final: 0.7129 (t0) REVERT: E 240 ASP cc_start: 0.7210 (m-30) cc_final: 0.6978 (m-30) REVERT: E 243 PHE cc_start: 0.8490 (t80) cc_final: 0.8165 (t80) REVERT: E 256 ARG cc_start: 0.7967 (mtp180) cc_final: 0.7470 (mtp85) REVERT: E 266 PHE cc_start: 0.8259 (t80) cc_final: 0.8026 (t80) REVERT: E 280 GLN cc_start: 0.5747 (pt0) cc_final: 0.5290 (pt0) REVERT: E 335 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6150 (tm-30) REVERT: E 342 TYR cc_start: 0.7148 (p90) cc_final: 0.6872 (p90) REVERT: E 387 LYS cc_start: 0.8682 (tptm) cc_final: 0.8176 (tptm) REVERT: E 396 GLU cc_start: 0.7362 (tt0) cc_final: 0.7032 (tt0) REVERT: E 400 TYR cc_start: 0.8060 (t80) cc_final: 0.7286 (t80) REVERT: E 451 TYR cc_start: 0.3518 (OUTLIER) cc_final: 0.2963 (t80) REVERT: E 464 TYR cc_start: 0.8073 (t80) cc_final: 0.7535 (t80) REVERT: E 472 LYS cc_start: 0.3439 (OUTLIER) cc_final: 0.1465 (tmmt) REVERT: E 479 LYS cc_start: 0.8314 (mptt) cc_final: 0.7937 (mptt) REVERT: E 483 HIS cc_start: 0.7759 (m170) cc_final: 0.7112 (m-70) REVERT: E 501 LYS cc_start: 0.8167 (tttt) cc_final: 0.7597 (tttt) REVERT: E 508 ASN cc_start: 0.8036 (p0) cc_final: 0.6204 (p0) REVERT: E 509 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7238 (mm-30) REVERT: E 520 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7329 (mtp85) REVERT: E 530 LYS cc_start: 0.8040 (tmtt) cc_final: 0.7507 (tttt) REVERT: E 532 LYS cc_start: 0.8298 (ttpt) cc_final: 0.7553 (ttpt) REVERT: E 581 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7910 (ttp-170) REVERT: E 582 LYS cc_start: 0.6715 (pmtt) cc_final: 0.6297 (pmtt) REVERT: I 67 ARG cc_start: 0.7806 (mmt90) cc_final: 0.7169 (mmt90) REVERT: I 81 ARG cc_start: 0.5788 (ptp90) cc_final: 0.4137 (ptp90) REVERT: I 95 ASN cc_start: 0.8278 (m-40) cc_final: 0.7958 (m-40) REVERT: I 105 ILE cc_start: 0.8610 (mm) cc_final: 0.8364 (mm) REVERT: I 109 TRP cc_start: 0.8716 (m100) cc_final: 0.7826 (m100) REVERT: I 120 TRP cc_start: 0.8901 (m100) cc_final: 0.8591 (m100) REVERT: I 122 ASN cc_start: 0.8070 (p0) cc_final: 0.7659 (p0) REVERT: I 147 ASN cc_start: 0.8178 (t0) cc_final: 0.7757 (t0) REVERT: I 150 LEU cc_start: 0.8467 (mt) cc_final: 0.8096 (mp) REVERT: I 178 ASP cc_start: 0.6647 (t0) cc_final: 0.6417 (t0) REVERT: I 193 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7121 (mp0) REVERT: I 236 THR cc_start: 0.7931 (p) cc_final: 0.7690 (p) REVERT: I 237 ASP cc_start: 0.7425 (t0) cc_final: 0.6882 (t0) REVERT: I 269 ASP cc_start: 0.6882 (p0) cc_final: 0.6577 (p0) REVERT: I 314 ARG cc_start: 0.8087 (ptp-170) cc_final: 0.7859 (ptp90) REVERT: I 318 GLN cc_start: 0.8556 (mt0) cc_final: 0.8213 (mm110) REVERT: I 406 THR cc_start: 0.7708 (p) cc_final: 0.7478 (t) REVERT: I 446 ASN cc_start: 0.8511 (m110) cc_final: 0.8211 (m110) REVERT: I 479 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8230 (mmtt) REVERT: I 485 ASN cc_start: 0.7170 (p0) cc_final: 0.6397 (p0) REVERT: I 501 LYS cc_start: 0.8830 (ttpt) cc_final: 0.7969 (ttpt) REVERT: I 528 TRP cc_start: 0.8340 (m100) cc_final: 0.7551 (m100) REVERT: I 582 LYS cc_start: 0.8343 (pttm) cc_final: 0.8059 (pttm) REVERT: C 47 ASN cc_start: 0.7847 (t0) cc_final: 0.7599 (t160) REVERT: C 67 ARG cc_start: 0.7094 (mmt-90) cc_final: 0.6851 (mmt-90) REVERT: C 68 LEU cc_start: 0.8155 (tp) cc_final: 0.7585 (tp) REVERT: C 77 GLU cc_start: 0.6862 (tp30) cc_final: 0.6261 (tp30) REVERT: C 193 GLU cc_start: 0.7059 (tp30) cc_final: 0.6391 (tp30) REVERT: C 501 LYS cc_start: 0.8632 (tttp) cc_final: 0.8110 (tttm) REVERT: C 509 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: C 528 TRP cc_start: 0.8574 (m100) cc_final: 0.7786 (m100) REVERT: C 564 SER cc_start: 0.7738 (t) cc_final: 0.7304 (t) REVERT: B 53 PHE cc_start: 0.8357 (m-80) cc_final: 0.7810 (p90) REVERT: B 122 ASN cc_start: 0.7614 (p0) cc_final: 0.7404 (p0) REVERT: B 182 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.7892 (m) REVERT: B 201 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8524 (mmmt) REVERT: B 240 ASP cc_start: 0.7104 (m-30) cc_final: 0.6871 (m-30) REVERT: B 256 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7574 (mtp180) REVERT: B 268 PHE cc_start: 0.8427 (m-80) cc_final: 0.8167 (m-10) REVERT: B 415 ILE cc_start: 0.8427 (mt) cc_final: 0.8115 (mt) REVERT: B 424 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7941 (m) REVERT: B 463 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7801 (m) REVERT: B 535 PHE cc_start: 0.8098 (m-80) cc_final: 0.7885 (m-80) REVERT: B 565 ASN cc_start: 0.8109 (m110) cc_final: 0.7828 (m110) REVERT: B 569 MET cc_start: 0.7017 (mmm) cc_final: 0.6765 (mmm) outliers start: 156 outliers final: 97 residues processed: 1605 average time/residue: 0.2102 time to fit residues: 528.3645 Evaluate side-chains 1670 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1555 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 277 HIS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 458 ASN Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 538 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 494 CYS Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 192 optimal weight: 4.9990 chunk 379 optimal weight: 6.9990 chunk 280 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 212 optimal weight: 0.4980 chunk 61 optimal weight: 30.0000 chunk 387 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 ASN ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 GLN ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 HIS F 350 GLN ** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 ASN E 558 GLN I 48 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 234 HIS I 565 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 483 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.105461 restraints weight = 52685.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109710 restraints weight = 24519.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112467 restraints weight = 13786.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114261 restraints weight = 8753.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115469 restraints weight = 6120.326| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 31936 Z= 0.211 Angle : 0.607 11.506 43674 Z= 0.307 Chirality : 0.044 0.185 4764 Planarity : 0.005 0.057 5732 Dihedral : 5.279 69.660 4237 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.13 % Allowed : 25.49 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 3686 helix: -1.20 (0.46), residues: 100 sheet: -0.53 (0.18), residues: 833 loop : -0.44 (0.12), residues: 2753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 67 TYR 0.025 0.002 TYR A 210 PHE 0.034 0.002 PHE A 266 TRP 0.027 0.002 TRP G 200 HIS 0.006 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00449 (31929) covalent geometry : angle 0.60632 (43660) SS BOND : bond 0.00556 ( 7) SS BOND : angle 1.32133 ( 14) hydrogen bonds : bond 0.03283 ( 295) hydrogen bonds : angle 6.03173 ( 567) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1750 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 1581 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7480 (tt0) cc_final: 0.7062 (tp30) REVERT: A 79 TYR cc_start: 0.8359 (m-80) cc_final: 0.7778 (m-80) REVERT: A 104 GLN cc_start: 0.8120 (pt0) cc_final: 0.7435 (pt0) REVERT: A 109 TRP cc_start: 0.8641 (m100) cc_final: 0.8414 (m100) REVERT: A 147 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7969 (t0) REVERT: A 163 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8172 (mtpt) REVERT: A 192 SER cc_start: 0.8069 (t) cc_final: 0.7842 (t) REVERT: A 214 TRP cc_start: 0.8512 (p90) cc_final: 0.7371 (p90) REVERT: A 216 ARG cc_start: 0.6979 (ttt-90) cc_final: 0.6754 (ttt180) REVERT: A 237 ASP cc_start: 0.7817 (t0) cc_final: 0.7357 (t0) REVERT: A 247 GLU cc_start: 0.7702 (mp0) cc_final: 0.7393 (mp0) REVERT: A 260 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: A 269 ASP cc_start: 0.7245 (p0) cc_final: 0.7012 (p0) REVERT: A 302 ASN cc_start: 0.8277 (m-40) cc_final: 0.7671 (m110) REVERT: A 312 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8122 (mtmt) REVERT: A 335 GLU cc_start: 0.7193 (tt0) cc_final: 0.6064 (tm-30) REVERT: A 346 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6455 (mt-10) REVERT: A 350 GLN cc_start: 0.7427 (mt0) cc_final: 0.7053 (mp10) REVERT: A 380 PHE cc_start: 0.7574 (p90) cc_final: 0.7239 (p90) REVERT: A 382 ARG cc_start: 0.8210 (mmt90) cc_final: 0.7746 (mtt90) REVERT: A 411 GLU cc_start: 0.7767 (mp0) cc_final: 0.7436 (mp0) REVERT: A 413 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6601 (m-30) REVERT: A 414 TRP cc_start: 0.8054 (p90) cc_final: 0.7652 (p90) REVERT: A 446 ASN cc_start: 0.8126 (m110) cc_final: 0.7883 (m110) REVERT: A 473 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6909 (mm-30) REVERT: A 502 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8617 (m) REVERT: A 530 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7966 (ttpp) REVERT: G 50 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: G 60 GLU cc_start: 0.7498 (tp30) cc_final: 0.7058 (tp30) REVERT: G 62 THR cc_start: 0.8409 (m) cc_final: 0.7902 (t) REVERT: G 67 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7785 (mtt90) REVERT: G 104 GLN cc_start: 0.8021 (pt0) cc_final: 0.7551 (pt0) REVERT: G 109 TRP cc_start: 0.8415 (m100) cc_final: 0.8008 (m100) REVERT: G 120 TRP cc_start: 0.8532 (m100) cc_final: 0.8245 (m100) REVERT: G 135 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6913 (tp30) REVERT: G 137 HIS cc_start: 0.8494 (m90) cc_final: 0.8148 (m170) REVERT: G 144 GLU cc_start: 0.7284 (pm20) cc_final: 0.7084 (pm20) REVERT: G 174 MET cc_start: 0.7905 (mtp) cc_final: 0.7515 (mtp) REVERT: G 185 PHE cc_start: 0.8207 (t80) cc_final: 0.7832 (t80) REVERT: G 191 ARG cc_start: 0.8345 (mtt-85) cc_final: 0.7912 (mtt-85) REVERT: G 193 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: G 213 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7416 (tm-30) REVERT: G 237 ASP cc_start: 0.7465 (t0) cc_final: 0.6965 (t0) REVERT: G 245 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7852 (t) REVERT: G 260 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: G 263 THR cc_start: 0.8585 (m) cc_final: 0.8065 (p) REVERT: G 266 PHE cc_start: 0.8319 (t80) cc_final: 0.7931 (t80) REVERT: G 268 PHE cc_start: 0.8121 (m-10) cc_final: 0.7822 (m-10) REVERT: G 312 LYS cc_start: 0.8418 (mtpp) cc_final: 0.8164 (mtpp) REVERT: G 313 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7022 (mtm-85) REVERT: G 327 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7093 (mm-30) REVERT: G 335 GLU cc_start: 0.7327 (tt0) cc_final: 0.6928 (tt0) REVERT: G 342 TYR cc_start: 0.7679 (p90) cc_final: 0.7234 (p90) REVERT: G 345 PHE cc_start: 0.7930 (m-80) cc_final: 0.7448 (m-80) REVERT: G 386 GLN cc_start: 0.7741 (mt0) cc_final: 0.7482 (mm-40) REVERT: G 398 PHE cc_start: 0.8741 (p90) cc_final: 0.8314 (p90) REVERT: G 475 ASP cc_start: 0.7514 (t0) cc_final: 0.6868 (t0) REVERT: G 479 LYS cc_start: 0.8624 (mmtm) cc_final: 0.8364 (mmtm) REVERT: G 505 ASN cc_start: 0.7719 (t0) cc_final: 0.7067 (t0) REVERT: G 518 MET cc_start: 0.7708 (ptp) cc_final: 0.7424 (ptp) REVERT: G 520 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7968 (mtm-85) REVERT: G 530 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7467 (ttpp) REVERT: G 560 ASN cc_start: 0.8176 (m-40) cc_final: 0.7857 (m-40) REVERT: F 72 ASN cc_start: 0.8450 (t0) cc_final: 0.8211 (t0) REVERT: F 73 MET cc_start: 0.7732 (ttt) cc_final: 0.7213 (ttp) REVERT: F 80 ARG cc_start: 0.4262 (tpt90) cc_final: 0.1832 (mmt180) REVERT: F 81 ARG cc_start: 0.5445 (ptp-170) cc_final: 0.5035 (ptp-170) REVERT: F 120 TRP cc_start: 0.8418 (m100) cc_final: 0.7915 (m100) REVERT: F 125 ASP cc_start: 0.7648 (m-30) cc_final: 0.7309 (m-30) REVERT: F 135 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: F 137 HIS cc_start: 0.8438 (m90) cc_final: 0.8202 (m170) REVERT: F 144 GLU cc_start: 0.7372 (pm20) cc_final: 0.7047 (pm20) REVERT: F 151 LYS cc_start: 0.8291 (mmmm) cc_final: 0.7758 (mmmm) REVERT: F 193 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7558 (mt-10) REVERT: F 195 LEU cc_start: 0.7583 (mt) cc_final: 0.7344 (mt) REVERT: F 197 PHE cc_start: 0.8263 (m-10) cc_final: 0.7500 (m-80) REVERT: F 201 LYS cc_start: 0.8041 (mmpt) cc_final: 0.7621 (mmpt) REVERT: F 213 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7040 (tm-30) REVERT: F 237 ASP cc_start: 0.8244 (t0) cc_final: 0.7977 (t0) REVERT: F 242 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7248 (pp30) REVERT: F 266 PHE cc_start: 0.8309 (t80) cc_final: 0.7807 (t80) REVERT: F 279 TRP cc_start: 0.8333 (p-90) cc_final: 0.8052 (p-90) REVERT: F 312 LYS cc_start: 0.8594 (mptt) cc_final: 0.7923 (mptt) REVERT: F 317 THR cc_start: 0.8251 (p) cc_final: 0.7856 (t) REVERT: F 335 GLU cc_start: 0.7444 (tt0) cc_final: 0.6949 (tt0) REVERT: F 336 VAL cc_start: 0.8760 (t) cc_final: 0.8405 (p) REVERT: F 409 TYR cc_start: 0.8404 (t80) cc_final: 0.8037 (t80) REVERT: F 419 ASN cc_start: 0.8542 (m110) cc_final: 0.8256 (m110) REVERT: F 439 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7673 (mmtp) REVERT: F 459 ASN cc_start: 0.8109 (m-40) cc_final: 0.7837 (m110) REVERT: F 475 ASP cc_start: 0.7986 (t0) cc_final: 0.7404 (t0) REVERT: F 495 PRO cc_start: 0.8766 (Cg_endo) cc_final: 0.8555 (Cg_endo) REVERT: F 501 LYS cc_start: 0.8526 (ttpp) cc_final: 0.7869 (pttp) REVERT: F 518 MET cc_start: 0.7875 (ptp) cc_final: 0.7371 (ptp) REVERT: F 520 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7546 (mtm110) REVERT: F 532 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8011 (ttmm) REVERT: F 533 LEU cc_start: 0.8406 (tp) cc_final: 0.7720 (tp) REVERT: F 538 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7467 (ttpt) REVERT: F 550 GLN cc_start: 0.8164 (mm110) cc_final: 0.7736 (mm-40) REVERT: F 551 MET cc_start: 0.7055 (ttt) cc_final: 0.6691 (ttt) REVERT: F 562 VAL cc_start: 0.8636 (p) cc_final: 0.8391 (m) REVERT: D 46 ASN cc_start: 0.7938 (t0) cc_final: 0.7268 (t0) REVERT: D 48 GLN cc_start: 0.8257 (mt0) cc_final: 0.7527 (mt0) REVERT: D 50 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6618 (tm-30) REVERT: D 70 HIS cc_start: 0.7863 (t-90) cc_final: 0.7465 (t-90) REVERT: D 73 MET cc_start: 0.8194 (ptt) cc_final: 0.7737 (ptm) REVERT: D 107 THR cc_start: 0.8365 (m) cc_final: 0.7725 (p) REVERT: D 174 MET cc_start: 0.7633 (mtp) cc_final: 0.7110 (mtp) REVERT: D 190 MET cc_start: 0.7822 (mmm) cc_final: 0.7566 (mmm) REVERT: D 200 TRP cc_start: 0.8773 (p90) cc_final: 0.8374 (p90) REVERT: D 256 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7566 (mtm-85) REVERT: E 51 PHE cc_start: 0.8475 (m-80) cc_final: 0.8224 (m-80) REVERT: E 95 ASN cc_start: 0.8247 (t0) cc_final: 0.7704 (t0) REVERT: E 142 GLU cc_start: 0.7628 (pt0) cc_final: 0.6615 (pt0) REVERT: E 143 GLN cc_start: 0.8255 (mt0) cc_final: 0.8048 (mt0) REVERT: E 163 LYS cc_start: 0.8003 (mppt) cc_final: 0.7516 (mppt) REVERT: E 209 ARG cc_start: 0.5254 (OUTLIER) cc_final: 0.4406 (ptt180) REVERT: E 210 TYR cc_start: 0.8550 (p90) cc_final: 0.8256 (p90) REVERT: E 213 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8127 (tm-30) REVERT: E 237 ASP cc_start: 0.7502 (t0) cc_final: 0.7207 (t0) REVERT: E 266 PHE cc_start: 0.8273 (t80) cc_final: 0.8022 (t80) REVERT: E 280 GLN cc_start: 0.5747 (pt0) cc_final: 0.5309 (pt0) REVERT: E 335 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6096 (tm-30) REVERT: E 342 TYR cc_start: 0.7139 (p90) cc_final: 0.6813 (p90) REVERT: E 387 LYS cc_start: 0.8711 (tptm) cc_final: 0.8388 (tptm) REVERT: E 396 GLU cc_start: 0.7324 (tt0) cc_final: 0.6976 (tt0) REVERT: E 400 TYR cc_start: 0.8091 (t80) cc_final: 0.7352 (t80) REVERT: E 451 TYR cc_start: 0.3643 (OUTLIER) cc_final: 0.3232 (t80) REVERT: E 464 TYR cc_start: 0.8112 (t80) cc_final: 0.7602 (t80) REVERT: E 472 LYS cc_start: 0.3476 (OUTLIER) cc_final: 0.1384 (tmmt) REVERT: E 479 LYS cc_start: 0.8277 (mptt) cc_final: 0.7902 (mptt) REVERT: E 501 LYS cc_start: 0.8181 (tttt) cc_final: 0.7689 (tttt) REVERT: E 508 ASN cc_start: 0.8126 (p0) cc_final: 0.6397 (p0) REVERT: E 509 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7236 (mm-30) REVERT: E 526 ASP cc_start: 0.6702 (p0) cc_final: 0.6271 (p0) REVERT: E 530 LYS cc_start: 0.8087 (tmtt) cc_final: 0.7592 (tttt) REVERT: E 532 LYS cc_start: 0.8328 (ttpt) cc_final: 0.7596 (ttpt) REVERT: E 538 LYS cc_start: 0.7926 (ttmm) cc_final: 0.7414 (mtpp) REVERT: E 550 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7245 (mm-40) REVERT: E 581 ARG cc_start: 0.8237 (ttp80) cc_final: 0.8035 (ttp80) REVERT: E 582 LYS cc_start: 0.6717 (pmtt) cc_final: 0.6254 (pmtt) REVERT: I 67 ARG cc_start: 0.7812 (mmt90) cc_final: 0.7171 (mmt90) REVERT: I 95 ASN cc_start: 0.8283 (m-40) cc_final: 0.7921 (m-40) REVERT: I 109 TRP cc_start: 0.8688 (m100) cc_final: 0.7628 (m100) REVERT: I 144 GLU cc_start: 0.7774 (pt0) cc_final: 0.7239 (pt0) REVERT: I 147 ASN cc_start: 0.8192 (t0) cc_final: 0.7777 (t0) REVERT: I 150 LEU cc_start: 0.8432 (mt) cc_final: 0.8007 (mp) REVERT: I 178 ASP cc_start: 0.6666 (t0) cc_final: 0.6380 (t0) REVERT: I 183 MET cc_start: 0.7263 (mmm) cc_final: 0.6982 (mmm) REVERT: I 193 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7124 (mp0) REVERT: I 214 TRP cc_start: -0.1185 (OUTLIER) cc_final: -0.3666 (p90) REVERT: I 237 ASP cc_start: 0.7395 (t0) cc_final: 0.6797 (t0) REVERT: I 269 ASP cc_start: 0.6926 (p0) cc_final: 0.6611 (p0) REVERT: I 314 ARG cc_start: 0.8084 (ptp-170) cc_final: 0.7828 (ptp90) REVERT: I 318 GLN cc_start: 0.8590 (mt0) cc_final: 0.8188 (mm110) REVERT: I 386 GLN cc_start: 0.7662 (tt0) cc_final: 0.7212 (tt0) REVERT: I 406 THR cc_start: 0.7774 (p) cc_final: 0.7511 (t) REVERT: I 446 ASN cc_start: 0.8511 (m110) cc_final: 0.8250 (m110) REVERT: I 485 ASN cc_start: 0.7385 (p0) cc_final: 0.6725 (p0) REVERT: I 501 LYS cc_start: 0.8818 (ttpt) cc_final: 0.7321 (ttpp) REVERT: I 528 TRP cc_start: 0.8416 (m100) cc_final: 0.7564 (m100) REVERT: I 577 GLN cc_start: 0.8138 (mt0) cc_final: 0.7925 (mt0) REVERT: I 582 LYS cc_start: 0.8367 (pttm) cc_final: 0.8070 (pttm) REVERT: C 47 ASN cc_start: 0.7838 (t0) cc_final: 0.7590 (t160) REVERT: C 68 LEU cc_start: 0.8171 (tp) cc_final: 0.7540 (tp) REVERT: C 193 GLU cc_start: 0.7098 (tp30) cc_final: 0.6734 (tp30) REVERT: C 501 LYS cc_start: 0.8642 (tttp) cc_final: 0.8090 (tttm) REVERT: C 509 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6882 (tm-30) REVERT: C 528 TRP cc_start: 0.8573 (m100) cc_final: 0.7717 (m100) REVERT: C 564 SER cc_start: 0.7843 (t) cc_final: 0.7413 (t) REVERT: B 53 PHE cc_start: 0.8385 (m-80) cc_final: 0.7815 (p90) REVERT: B 68 LEU cc_start: 0.8569 (tp) cc_final: 0.8327 (tp) REVERT: B 109 TRP cc_start: 0.8769 (m100) cc_final: 0.7837 (m100) REVERT: B 117 TRP cc_start: 0.8014 (m100) cc_final: 0.7436 (m100) REVERT: B 122 ASN cc_start: 0.7544 (p0) cc_final: 0.7333 (p0) REVERT: B 167 ASN cc_start: 0.7850 (m-40) cc_final: 0.7508 (m-40) REVERT: B 201 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8622 (mmmt) REVERT: B 332 ARG cc_start: 0.8064 (mmt90) cc_final: 0.7711 (mtt180) REVERT: B 397 ARG cc_start: 0.8555 (ptp-170) cc_final: 0.8108 (mtm180) REVERT: B 424 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7918 (m) REVERT: B 463 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7783 (m) REVERT: B 491 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7074 (mm-40) REVERT: B 506 LEU cc_start: 0.8569 (mt) cc_final: 0.8272 (mp) REVERT: B 528 TRP cc_start: 0.8730 (m100) cc_final: 0.8264 (m100) REVERT: B 535 PHE cc_start: 0.8096 (m-80) cc_final: 0.7857 (m-80) REVERT: B 565 ASN cc_start: 0.8093 (m110) cc_final: 0.7817 (m110) REVERT: B 569 MET cc_start: 0.7000 (mmm) cc_final: 0.6717 (mmm) REVERT: B 575 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7493 (mmtt) outliers start: 169 outliers final: 116 residues processed: 1628 average time/residue: 0.2208 time to fit residues: 562.7548 Evaluate side-chains 1700 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1562 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 277 HIS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 458 ASN Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 520 ARG Chi-restraints excluded: chain F residue 538 LYS Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 482 LEU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain I residue 571 ILE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 549 GLN Chi-restraints excluded: chain B residue 553 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 48 optimal weight: 4.9990 chunk 307 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 372 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 ASN ** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107145 restraints weight = 52231.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111388 restraints weight = 24228.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.114136 restraints weight = 13608.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115939 restraints weight = 8636.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117164 restraints weight = 6021.249| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31936 Z= 0.174 Angle : 0.600 12.015 43674 Z= 0.301 Chirality : 0.044 0.215 4764 Planarity : 0.005 0.059 5732 Dihedral : 5.149 70.156 4237 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.92 % Allowed : 26.59 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 3686 helix: -1.17 (0.46), residues: 100 sheet: -0.48 (0.18), residues: 834 loop : -0.41 (0.12), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 67 TYR 0.032 0.002 TYR G 211 PHE 0.033 0.002 PHE A 266 TRP 0.034 0.002 TRP G 200 HIS 0.005 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00376 (31929) covalent geometry : angle 0.59987 (43660) SS BOND : bond 0.00521 ( 7) SS BOND : angle 1.14284 ( 14) hydrogen bonds : bond 0.03109 ( 295) hydrogen bonds : angle 5.96424 ( 567) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1720 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1558 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7352 (tt0) cc_final: 0.6947 (tp30) REVERT: A 79 TYR cc_start: 0.8339 (m-80) cc_final: 0.7744 (m-80) REVERT: A 104 GLN cc_start: 0.8148 (pt0) cc_final: 0.7419 (pt0) REVERT: A 109 TRP cc_start: 0.8616 (m100) cc_final: 0.8299 (m100) REVERT: A 147 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7877 (t0) REVERT: A 163 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8191 (mtpt) REVERT: A 183 MET cc_start: 0.7764 (mmm) cc_final: 0.7520 (mmm) REVERT: A 192 SER cc_start: 0.8007 (t) cc_final: 0.7775 (t) REVERT: A 214 TRP cc_start: 0.8499 (p90) cc_final: 0.7298 (p90) REVERT: A 216 ARG cc_start: 0.6952 (ttt-90) cc_final: 0.6717 (ttt-90) REVERT: A 247 GLU cc_start: 0.7676 (mp0) cc_final: 0.7376 (mp0) REVERT: A 260 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7270 (tt0) REVERT: A 269 ASP cc_start: 0.7289 (p0) cc_final: 0.7073 (p0) REVERT: A 302 ASN cc_start: 0.8265 (m-40) cc_final: 0.7645 (m110) REVERT: A 312 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8130 (mtmt) REVERT: A 335 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6117 (tm-30) REVERT: A 346 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6471 (mt-10) REVERT: A 350 GLN cc_start: 0.7463 (mt0) cc_final: 0.7117 (mp10) REVERT: A 380 PHE cc_start: 0.7568 (p90) cc_final: 0.7233 (p90) REVERT: A 411 GLU cc_start: 0.7760 (mp0) cc_final: 0.7439 (mp0) REVERT: A 413 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6589 (m-30) REVERT: A 414 TRP cc_start: 0.7995 (p90) cc_final: 0.7703 (p90) REVERT: A 426 ASN cc_start: 0.8261 (t0) cc_final: 0.7659 (t0) REVERT: A 446 ASN cc_start: 0.8196 (m110) cc_final: 0.7858 (m110) REVERT: A 468 GLN cc_start: 0.7865 (tt0) cc_final: 0.7575 (tt0) REVERT: A 473 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6890 (mm-30) REVERT: A 502 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8600 (m) REVERT: A 536 LYS cc_start: 0.8360 (tttm) cc_final: 0.8145 (tttm) REVERT: G 48 GLN cc_start: 0.2660 (mm-40) cc_final: 0.2056 (mm-40) REVERT: G 50 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6667 (mp0) REVERT: G 60 GLU cc_start: 0.7490 (tp30) cc_final: 0.7060 (tp30) REVERT: G 62 THR cc_start: 0.8405 (m) cc_final: 0.7860 (t) REVERT: G 67 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7815 (mtt90) REVERT: G 68 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8042 (tt) REVERT: G 104 GLN cc_start: 0.8050 (pt0) cc_final: 0.7563 (pt0) REVERT: G 109 TRP cc_start: 0.8400 (m100) cc_final: 0.8050 (m100) REVERT: G 135 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: G 136 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8140 (tp) REVERT: G 137 HIS cc_start: 0.8479 (m90) cc_final: 0.8035 (m170) REVERT: G 143 GLN cc_start: 0.8383 (mt0) cc_final: 0.7810 (mt0) REVERT: G 174 MET cc_start: 0.7930 (mtp) cc_final: 0.7335 (mtp) REVERT: G 193 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: G 213 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7454 (tm-30) REVERT: G 237 ASP cc_start: 0.7580 (t0) cc_final: 0.7112 (t0) REVERT: G 245 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7862 (t) REVERT: G 263 THR cc_start: 0.8584 (m) cc_final: 0.8080 (p) REVERT: G 266 PHE cc_start: 0.8286 (t80) cc_final: 0.7931 (t80) REVERT: G 268 PHE cc_start: 0.8128 (m-80) cc_final: 0.7836 (m-10) REVERT: G 312 LYS cc_start: 0.8425 (mtpp) cc_final: 0.8156 (mtpp) REVERT: G 327 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7033 (mm-30) REVERT: G 335 GLU cc_start: 0.7364 (tt0) cc_final: 0.6961 (tt0) REVERT: G 345 PHE cc_start: 0.7916 (m-80) cc_final: 0.7447 (m-80) REVERT: G 382 ARG cc_start: 0.5432 (mtm180) cc_final: 0.4652 (mtm110) REVERT: G 386 GLN cc_start: 0.7785 (mt0) cc_final: 0.7547 (mm-40) REVERT: G 398 PHE cc_start: 0.8694 (p90) cc_final: 0.8327 (p90) REVERT: G 434 ASP cc_start: 0.7608 (m-30) cc_final: 0.7327 (t0) REVERT: G 457 LEU cc_start: 0.8183 (mt) cc_final: 0.7895 (mp) REVERT: G 475 ASP cc_start: 0.7514 (t0) cc_final: 0.6854 (t0) REVERT: G 479 LYS cc_start: 0.8615 (mmtm) cc_final: 0.8367 (mmtm) REVERT: G 501 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8029 (ttpp) REVERT: G 505 ASN cc_start: 0.7719 (t0) cc_final: 0.7039 (t0) REVERT: G 518 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7391 (ptp) REVERT: G 528 TRP cc_start: 0.8137 (m100) cc_final: 0.7542 (m100) REVERT: G 530 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7600 (ttpp) REVERT: G 560 ASN cc_start: 0.8166 (m-40) cc_final: 0.7859 (m-40) REVERT: G 581 ARG cc_start: 0.7906 (ptt90) cc_final: 0.7490 (ptt90) REVERT: F 72 ASN cc_start: 0.8451 (t0) cc_final: 0.8199 (t0) REVERT: F 73 MET cc_start: 0.7769 (ttt) cc_final: 0.7205 (ttp) REVERT: F 80 ARG cc_start: 0.4444 (tpt90) cc_final: 0.1919 (mmt180) REVERT: F 81 ARG cc_start: 0.5464 (ptp-170) cc_final: 0.5053 (ptp-170) REVERT: F 109 TRP cc_start: 0.8415 (m100) cc_final: 0.7515 (m100) REVERT: F 120 TRP cc_start: 0.8391 (m100) cc_final: 0.7901 (m100) REVERT: F 125 ASP cc_start: 0.7617 (m-30) cc_final: 0.7253 (m-30) REVERT: F 135 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: F 144 GLU cc_start: 0.7367 (pm20) cc_final: 0.7050 (pm20) REVERT: F 151 LYS cc_start: 0.8261 (mmmm) cc_final: 0.7486 (mmmm) REVERT: F 167 ASN cc_start: 0.8263 (m110) cc_final: 0.7911 (m-40) REVERT: F 193 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7629 (mt-10) REVERT: F 197 PHE cc_start: 0.8256 (m-10) cc_final: 0.7530 (m-80) REVERT: F 201 LYS cc_start: 0.8029 (mmpt) cc_final: 0.7606 (mmpt) REVERT: F 213 GLN cc_start: 0.7709 (tm-30) cc_final: 0.7043 (tm-30) REVERT: F 237 ASP cc_start: 0.8221 (t0) cc_final: 0.7944 (t0) REVERT: F 242 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7247 (pp30) REVERT: F 266 PHE cc_start: 0.8277 (t80) cc_final: 0.7824 (t80) REVERT: F 279 TRP cc_start: 0.8304 (p-90) cc_final: 0.7983 (p-90) REVERT: F 335 GLU cc_start: 0.7460 (tt0) cc_final: 0.6935 (tt0) REVERT: F 336 VAL cc_start: 0.8764 (t) cc_final: 0.8401 (p) REVERT: F 409 TYR cc_start: 0.8381 (t80) cc_final: 0.8075 (t80) REVERT: F 419 ASN cc_start: 0.8544 (m110) cc_final: 0.8213 (m110) REVERT: F 439 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7750 (mmtp) REVERT: F 459 ASN cc_start: 0.8120 (m-40) cc_final: 0.7838 (m110) REVERT: F 475 ASP cc_start: 0.8036 (t0) cc_final: 0.7683 (t0) REVERT: F 481 ARG cc_start: 0.8329 (mmm-85) cc_final: 0.8040 (mmm-85) REVERT: F 495 PRO cc_start: 0.8744 (Cg_exo) cc_final: 0.8473 (Cg_endo) REVERT: F 497 GLN cc_start: 0.8382 (mt0) cc_final: 0.7915 (mt0) REVERT: F 501 LYS cc_start: 0.8526 (ttpp) cc_final: 0.7694 (ttpp) REVERT: F 518 MET cc_start: 0.7823 (ptp) cc_final: 0.7346 (ptp) REVERT: F 520 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7557 (mtm110) REVERT: F 532 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8034 (ttmm) REVERT: F 533 LEU cc_start: 0.8410 (tp) cc_final: 0.7708 (tp) REVERT: F 550 GLN cc_start: 0.8189 (mm110) cc_final: 0.7792 (mm-40) REVERT: F 562 VAL cc_start: 0.8632 (p) cc_final: 0.8398 (m) REVERT: D 46 ASN cc_start: 0.8011 (t0) cc_final: 0.7301 (t0) REVERT: D 48 GLN cc_start: 0.8263 (mt0) cc_final: 0.7653 (mt0) REVERT: D 50 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6592 (tm-30) REVERT: D 73 MET cc_start: 0.8225 (ptt) cc_final: 0.7823 (ptm) REVERT: D 107 THR cc_start: 0.8369 (m) cc_final: 0.7727 (p) REVERT: D 174 MET cc_start: 0.7615 (mtp) cc_final: 0.7153 (mtp) REVERT: D 190 MET cc_start: 0.7806 (mmm) cc_final: 0.7555 (mmm) REVERT: D 200 TRP cc_start: 0.8752 (p90) cc_final: 0.8384 (p90) REVERT: D 256 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7621 (mtm-85) REVERT: E 95 ASN cc_start: 0.8229 (t0) cc_final: 0.7680 (t0) REVERT: E 142 GLU cc_start: 0.7586 (pt0) cc_final: 0.6551 (pt0) REVERT: E 143 GLN cc_start: 0.8274 (mt0) cc_final: 0.8053 (mt0) REVERT: E 163 LYS cc_start: 0.8024 (mppt) cc_final: 0.7557 (mppt) REVERT: E 209 ARG cc_start: 0.5230 (OUTLIER) cc_final: 0.4394 (ptt180) REVERT: E 210 TYR cc_start: 0.8551 (p90) cc_final: 0.8248 (p90) REVERT: E 213 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7749 (tm-30) REVERT: E 237 ASP cc_start: 0.7467 (t0) cc_final: 0.7190 (t0) REVERT: E 256 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7563 (mtp85) REVERT: E 266 PHE cc_start: 0.8257 (t80) cc_final: 0.8000 (t80) REVERT: E 280 GLN cc_start: 0.5660 (pt0) cc_final: 0.5198 (pt0) REVERT: E 335 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6131 (tm-30) REVERT: E 342 TYR cc_start: 0.7152 (p90) cc_final: 0.6895 (p90) REVERT: E 377 ARG cc_start: 0.5426 (mtt180) cc_final: 0.5101 (mtt180) REVERT: E 382 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7625 (mtt90) REVERT: E 387 LYS cc_start: 0.8719 (tptm) cc_final: 0.8444 (tptm) REVERT: E 396 GLU cc_start: 0.7309 (tt0) cc_final: 0.6962 (tt0) REVERT: E 400 TYR cc_start: 0.8058 (t80) cc_final: 0.7288 (t80) REVERT: E 430 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7620 (tt) REVERT: E 451 TYR cc_start: 0.3696 (OUTLIER) cc_final: 0.3225 (t80) REVERT: E 464 TYR cc_start: 0.8131 (t80) cc_final: 0.7568 (t80) REVERT: E 472 LYS cc_start: 0.3438 (OUTLIER) cc_final: 0.1409 (tmmt) REVERT: E 479 LYS cc_start: 0.8313 (mptt) cc_final: 0.7972 (mptt) REVERT: E 501 LYS cc_start: 0.8119 (tttt) cc_final: 0.7702 (tttt) REVERT: E 508 ASN cc_start: 0.8140 (p0) cc_final: 0.6365 (p0) REVERT: E 509 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7234 (mm-30) REVERT: E 520 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7422 (mtp85) REVERT: E 526 ASP cc_start: 0.6641 (p0) cc_final: 0.6192 (p0) REVERT: E 530 LYS cc_start: 0.8084 (tmtt) cc_final: 0.7558 (tttt) REVERT: E 532 LYS cc_start: 0.8332 (ttpt) cc_final: 0.7575 (ttpt) REVERT: E 582 LYS cc_start: 0.6685 (pmtt) cc_final: 0.6198 (pmtt) REVERT: I 67 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7202 (mmt90) REVERT: I 95 ASN cc_start: 0.8298 (m-40) cc_final: 0.7945 (m-40) REVERT: I 109 TRP cc_start: 0.8678 (m100) cc_final: 0.7769 (m100) REVERT: I 144 GLU cc_start: 0.7820 (pt0) cc_final: 0.7372 (pt0) REVERT: I 147 ASN cc_start: 0.8173 (t0) cc_final: 0.7736 (t0) REVERT: I 178 ASP cc_start: 0.6632 (t0) cc_final: 0.6363 (t0) REVERT: I 193 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7086 (mp0) REVERT: I 214 TRP cc_start: -0.1540 (OUTLIER) cc_final: -0.3913 (p90) REVERT: I 237 ASP cc_start: 0.7439 (t0) cc_final: 0.6827 (t0) REVERT: I 269 ASP cc_start: 0.6895 (p0) cc_final: 0.6589 (p0) REVERT: I 318 GLN cc_start: 0.8577 (mt0) cc_final: 0.8218 (mm110) REVERT: I 386 GLN cc_start: 0.7663 (tt0) cc_final: 0.7221 (tt0) REVERT: I 446 ASN cc_start: 0.8487 (m110) cc_final: 0.8227 (m110) REVERT: I 485 ASN cc_start: 0.7359 (p0) cc_final: 0.6651 (p0) REVERT: I 501 LYS cc_start: 0.8734 (ttpt) cc_final: 0.7774 (ttpt) REVERT: I 528 TRP cc_start: 0.8399 (m100) cc_final: 0.7531 (m100) REVERT: I 532 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8257 (ttpp) REVERT: I 577 GLN cc_start: 0.8156 (mt0) cc_final: 0.7886 (mt0) REVERT: I 582 LYS cc_start: 0.8383 (pttm) cc_final: 0.8090 (pttm) REVERT: C 67 ARG cc_start: 0.7121 (mmt-90) cc_final: 0.6702 (mmt-90) REVERT: C 193 GLU cc_start: 0.7117 (tp30) cc_final: 0.6750 (tp30) REVERT: C 501 LYS cc_start: 0.8650 (tttp) cc_final: 0.8104 (tttm) REVERT: C 509 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: C 564 SER cc_start: 0.7711 (t) cc_final: 0.7372 (t) REVERT: C 569 MET cc_start: 0.5495 (mmm) cc_final: 0.5280 (mmm) REVERT: B 53 PHE cc_start: 0.8389 (m-80) cc_final: 0.7813 (p90) REVERT: B 117 TRP cc_start: 0.8047 (m100) cc_final: 0.7457 (m100) REVERT: B 151 LYS cc_start: 0.8702 (mttm) cc_final: 0.8336 (mttm) REVERT: B 167 ASN cc_start: 0.7785 (m-40) cc_final: 0.7444 (m-40) REVERT: B 255 LEU cc_start: 0.8482 (mt) cc_final: 0.8091 (mm) REVERT: B 256 ARG cc_start: 0.8005 (mtp180) cc_final: 0.7742 (mtp180) REVERT: B 268 PHE cc_start: 0.8482 (m-80) cc_final: 0.8144 (m-10) REVERT: B 332 ARG cc_start: 0.8021 (mmt90) cc_final: 0.7656 (mtt180) REVERT: B 424 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7915 (m) REVERT: B 463 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7804 (m) REVERT: B 491 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7043 (mm-40) REVERT: B 501 LYS cc_start: 0.8767 (tttm) cc_final: 0.8397 (tttm) REVERT: B 506 LEU cc_start: 0.8529 (mt) cc_final: 0.8263 (mp) REVERT: B 535 PHE cc_start: 0.8102 (m-80) cc_final: 0.7861 (m-80) REVERT: B 565 ASN cc_start: 0.8093 (m110) cc_final: 0.7799 (m110) REVERT: B 569 MET cc_start: 0.7000 (mmm) cc_final: 0.6721 (mmm) outliers start: 162 outliers final: 113 residues processed: 1604 average time/residue: 0.2131 time to fit residues: 536.9090 Evaluate side-chains 1678 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1541 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 416 GLN Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 277 HIS Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 518 MET Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 321 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 458 ASN Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 482 LEU Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 520 ARG Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 520 ARG Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 549 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 169 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 354 optimal weight: 5.9990 chunk 59 optimal weight: 30.0000 chunk 363 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 324 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 ASN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 HIS F 234 HIS F 321 ASN F 403 HIS E 127 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111115 restraints weight = 52332.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115426 restraints weight = 24265.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118159 restraints weight = 13603.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119929 restraints weight = 8650.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121069 restraints weight = 6081.428| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31936 Z= 0.127 Angle : 0.591 14.104 43674 Z= 0.294 Chirality : 0.043 0.202 4764 Planarity : 0.005 0.054 5732 Dihedral : 4.947 69.434 4237 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.73 % Allowed : 27.77 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 3686 helix: -1.22 (0.47), residues: 100 sheet: -0.31 (0.18), residues: 838 loop : -0.37 (0.12), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 67 TYR 0.036 0.001 TYR A 561 PHE 0.035 0.002 PHE G 527 TRP 0.033 0.002 TRP G 200 HIS 0.005 0.001 HIS F 222 Details of bonding type rmsd covalent geometry : bond 0.00286 (31929) covalent geometry : angle 0.59080 (43660) SS BOND : bond 0.00543 ( 7) SS BOND : angle 0.94073 ( 14) hydrogen bonds : bond 0.02939 ( 295) hydrogen bonds : angle 5.88913 ( 567) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1715 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1559 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7300 (tt0) cc_final: 0.6881 (tp30) REVERT: A 67 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8026 (mmt180) REVERT: A 79 TYR cc_start: 0.8312 (m-80) cc_final: 0.7751 (m-80) REVERT: A 104 GLN cc_start: 0.8079 (pt0) cc_final: 0.7379 (pt0) REVERT: A 109 TRP cc_start: 0.8627 (m100) cc_final: 0.8066 (m100) REVERT: A 147 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7924 (t0) REVERT: A 163 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8263 (mtpt) REVERT: A 192 SER cc_start: 0.7940 (t) cc_final: 0.7681 (t) REVERT: A 200 TRP cc_start: 0.8462 (p90) cc_final: 0.8230 (p90) REVERT: A 216 ARG cc_start: 0.6915 (ttt-90) cc_final: 0.6623 (ttt180) REVERT: A 247 GLU cc_start: 0.7612 (mp0) cc_final: 0.7354 (mp0) REVERT: A 260 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7215 (tt0) REVERT: A 269 ASP cc_start: 0.7284 (p0) cc_final: 0.7033 (p0) REVERT: A 279 TRP cc_start: 0.8822 (p-90) cc_final: 0.8299 (p-90) REVERT: A 302 ASN cc_start: 0.8232 (m-40) cc_final: 0.7542 (m110) REVERT: A 312 LYS cc_start: 0.8448 (mtmt) cc_final: 0.8161 (mtmt) REVERT: A 335 GLU cc_start: 0.7159 (tt0) cc_final: 0.6125 (tm-30) REVERT: A 346 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6477 (mt-10) REVERT: A 350 GLN cc_start: 0.7457 (mt0) cc_final: 0.7153 (mp10) REVERT: A 382 ARG cc_start: 0.8130 (mmt90) cc_final: 0.7710 (mtt90) REVERT: A 411 GLU cc_start: 0.7724 (mp0) cc_final: 0.7373 (mp0) REVERT: A 414 TRP cc_start: 0.7960 (p90) cc_final: 0.7667 (p90) REVERT: A 446 ASN cc_start: 0.8185 (m110) cc_final: 0.7819 (m110) REVERT: A 473 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6862 (mm-30) REVERT: A 501 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8051 (ttpp) REVERT: A 502 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8658 (m) REVERT: A 530 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7863 (ttpp) REVERT: G 50 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: G 60 GLU cc_start: 0.7500 (tp30) cc_final: 0.7029 (tp30) REVERT: G 62 THR cc_start: 0.8313 (m) cc_final: 0.7740 (t) REVERT: G 68 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8031 (tt) REVERT: G 83 VAL cc_start: 0.8684 (t) cc_final: 0.8338 (m) REVERT: G 104 GLN cc_start: 0.8040 (pt0) cc_final: 0.7604 (pt0) REVERT: G 109 TRP cc_start: 0.8392 (m100) cc_final: 0.7971 (m100) REVERT: G 135 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6787 (tp30) REVERT: G 137 HIS cc_start: 0.8417 (m90) cc_final: 0.8098 (m170) REVERT: G 143 GLN cc_start: 0.8433 (mt0) cc_final: 0.7982 (mt0) REVERT: G 144 GLU cc_start: 0.7267 (pm20) cc_final: 0.6870 (pm20) REVERT: G 174 MET cc_start: 0.7808 (mtp) cc_final: 0.7284 (mtp) REVERT: G 185 PHE cc_start: 0.8138 (t80) cc_final: 0.7811 (t80) REVERT: G 193 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: G 213 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7454 (tm-30) REVERT: G 237 ASP cc_start: 0.7554 (t0) cc_final: 0.7151 (t0) REVERT: G 242 GLN cc_start: 0.7860 (mt0) cc_final: 0.7611 (mt0) REVERT: G 245 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.7845 (t) REVERT: G 263 THR cc_start: 0.8546 (m) cc_final: 0.8025 (p) REVERT: G 266 PHE cc_start: 0.8245 (t80) cc_final: 0.7905 (t80) REVERT: G 268 PHE cc_start: 0.8118 (m-80) cc_final: 0.7791 (m-10) REVERT: G 312 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8161 (mtpp) REVERT: G 327 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7006 (mm-30) REVERT: G 335 GLU cc_start: 0.7446 (tt0) cc_final: 0.6896 (tt0) REVERT: G 342 TYR cc_start: 0.7576 (p90) cc_final: 0.7220 (p90) REVERT: G 345 PHE cc_start: 0.7913 (m-80) cc_final: 0.7470 (m-80) REVERT: G 382 ARG cc_start: 0.5388 (mtm180) cc_final: 0.4927 (mtm180) REVERT: G 398 PHE cc_start: 0.8642 (p90) cc_final: 0.8294 (p90) REVERT: G 434 ASP cc_start: 0.7611 (m-30) cc_final: 0.7369 (t0) REVERT: G 464 TYR cc_start: 0.7996 (t80) cc_final: 0.7782 (t80) REVERT: G 479 LYS cc_start: 0.8622 (mmtm) cc_final: 0.8326 (mmtm) REVERT: G 501 LYS cc_start: 0.8493 (ttpp) cc_final: 0.7967 (ttpp) REVERT: G 505 ASN cc_start: 0.7705 (t0) cc_final: 0.6763 (t0) REVERT: G 518 MET cc_start: 0.7672 (ptp) cc_final: 0.7395 (ptp) REVERT: G 520 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7872 (mtm110) REVERT: G 521 ILE cc_start: 0.8763 (mt) cc_final: 0.8455 (mt) REVERT: G 528 TRP cc_start: 0.8159 (m100) cc_final: 0.7582 (m100) REVERT: G 530 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7260 (ttpp) REVERT: G 560 ASN cc_start: 0.8121 (m-40) cc_final: 0.7812 (m-40) REVERT: G 582 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8255 (pttm) REVERT: F 72 ASN cc_start: 0.8453 (t0) cc_final: 0.8196 (t0) REVERT: F 73 MET cc_start: 0.7735 (ttt) cc_final: 0.7208 (ttp) REVERT: F 80 ARG cc_start: 0.4298 (tpt90) cc_final: 0.1917 (mmt180) REVERT: F 81 ARG cc_start: 0.5476 (ptp-170) cc_final: 0.5043 (ptp-170) REVERT: F 95 ASN cc_start: 0.7376 (m-40) cc_final: 0.6996 (m110) REVERT: F 109 TRP cc_start: 0.8365 (m100) cc_final: 0.7739 (m100) REVERT: F 120 TRP cc_start: 0.8386 (m100) cc_final: 0.7888 (m100) REVERT: F 125 ASP cc_start: 0.7579 (m-30) cc_final: 0.7194 (m-30) REVERT: F 135 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: F 144 GLU cc_start: 0.7365 (pm20) cc_final: 0.7046 (pm20) REVERT: F 151 LYS cc_start: 0.8253 (mmmm) cc_final: 0.7556 (mmmm) REVERT: F 167 ASN cc_start: 0.8262 (m110) cc_final: 0.7921 (m-40) REVERT: F 193 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7520 (mt-10) REVERT: F 197 PHE cc_start: 0.8240 (m-10) cc_final: 0.7533 (m-80) REVERT: F 201 LYS cc_start: 0.8026 (mmpt) cc_final: 0.7617 (mmpt) REVERT: F 213 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7135 (tm-30) REVERT: F 237 ASP cc_start: 0.8218 (t0) cc_final: 0.7947 (t0) REVERT: F 242 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7347 (pp30) REVERT: F 245 THR cc_start: 0.8224 (t) cc_final: 0.7818 (p) REVERT: F 266 PHE cc_start: 0.8252 (t80) cc_final: 0.7787 (t80) REVERT: F 279 TRP cc_start: 0.8347 (p-90) cc_final: 0.8025 (p-90) REVERT: F 312 LYS cc_start: 0.8623 (mptt) cc_final: 0.8076 (mptt) REVERT: F 336 VAL cc_start: 0.8755 (t) cc_final: 0.8401 (p) REVERT: F 353 PHE cc_start: 0.7311 (p90) cc_final: 0.6947 (p90) REVERT: F 409 TYR cc_start: 0.8310 (t80) cc_final: 0.8046 (t80) REVERT: F 419 ASN cc_start: 0.8522 (m110) cc_final: 0.8185 (m110) REVERT: F 439 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7688 (mmtp) REVERT: F 459 ASN cc_start: 0.8093 (m-40) cc_final: 0.7813 (m110) REVERT: F 470 TRP cc_start: 0.8091 (p90) cc_final: 0.7871 (p90) REVERT: F 473 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7189 (tm-30) REVERT: F 474 PHE cc_start: 0.8066 (m-10) cc_final: 0.7476 (m-10) REVERT: F 475 ASP cc_start: 0.8000 (t0) cc_final: 0.7333 (t0) REVERT: F 495 PRO cc_start: 0.8741 (Cg_exo) cc_final: 0.8500 (Cg_endo) REVERT: F 501 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8037 (ttpp) REVERT: F 518 MET cc_start: 0.7826 (ptp) cc_final: 0.7372 (ptp) REVERT: F 520 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7463 (mtm110) REVERT: F 532 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8050 (ttmm) REVERT: F 550 GLN cc_start: 0.8118 (mm110) cc_final: 0.7632 (mm-40) REVERT: F 562 VAL cc_start: 0.8630 (p) cc_final: 0.8404 (m) REVERT: D 46 ASN cc_start: 0.7929 (t0) cc_final: 0.7386 (t0) REVERT: D 48 GLN cc_start: 0.8191 (mt0) cc_final: 0.7948 (mt0) REVERT: D 50 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6544 (tm-30) REVERT: D 73 MET cc_start: 0.8277 (ptt) cc_final: 0.7858 (ptm) REVERT: D 107 THR cc_start: 0.8366 (m) cc_final: 0.7683 (p) REVERT: D 174 MET cc_start: 0.7668 (mtp) cc_final: 0.7105 (mtp) REVERT: D 190 MET cc_start: 0.7780 (mmm) cc_final: 0.7536 (mmm) REVERT: D 208 TRP cc_start: 0.8166 (t60) cc_final: 0.7684 (t60) REVERT: D 209 ARG cc_start: 0.4618 (OUTLIER) cc_final: 0.4103 (pmt170) REVERT: D 256 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7585 (mtm-85) REVERT: E 95 ASN cc_start: 0.8177 (t0) cc_final: 0.7606 (t0) REVERT: E 142 GLU cc_start: 0.7574 (pt0) cc_final: 0.6539 (pt0) REVERT: E 163 LYS cc_start: 0.8004 (mppt) cc_final: 0.7559 (mppt) REVERT: E 209 ARG cc_start: 0.5116 (OUTLIER) cc_final: 0.4311 (ptt180) REVERT: E 210 TYR cc_start: 0.8507 (p90) cc_final: 0.8203 (p90) REVERT: E 213 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7715 (tm-30) REVERT: E 237 ASP cc_start: 0.7490 (t0) cc_final: 0.7174 (t0) REVERT: E 256 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7515 (mtp85) REVERT: E 266 PHE cc_start: 0.8229 (t80) cc_final: 0.7960 (t80) REVERT: E 280 GLN cc_start: 0.5426 (pt0) cc_final: 0.4920 (pt0) REVERT: E 335 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6149 (tm-30) REVERT: E 342 TYR cc_start: 0.7083 (p90) cc_final: 0.6770 (p90) REVERT: E 377 ARG cc_start: 0.5328 (mtt180) cc_final: 0.4943 (mtt180) REVERT: E 382 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7591 (mtt90) REVERT: E 387 LYS cc_start: 0.8705 (tptm) cc_final: 0.8423 (tptm) REVERT: E 396 GLU cc_start: 0.7260 (tt0) cc_final: 0.6911 (tt0) REVERT: E 400 TYR cc_start: 0.8084 (t80) cc_final: 0.7360 (t80) REVERT: E 430 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7591 (tt) REVERT: E 451 TYR cc_start: 0.3632 (OUTLIER) cc_final: 0.3273 (t80) REVERT: E 464 TYR cc_start: 0.8091 (t80) cc_final: 0.7600 (t80) REVERT: E 472 LYS cc_start: 0.3558 (OUTLIER) cc_final: 0.1609 (tmmt) REVERT: E 479 LYS cc_start: 0.8327 (mptt) cc_final: 0.7962 (mptt) REVERT: E 501 LYS cc_start: 0.8127 (tttt) cc_final: 0.7700 (tttt) REVERT: E 508 ASN cc_start: 0.8054 (p0) cc_final: 0.6216 (p0) REVERT: E 509 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7207 (mm-30) REVERT: E 520 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7436 (mtp85) REVERT: E 526 ASP cc_start: 0.6597 (p0) cc_final: 0.6160 (p0) REVERT: E 530 LYS cc_start: 0.8037 (tmtt) cc_final: 0.7498 (tttt) REVERT: E 532 LYS cc_start: 0.8312 (ttpt) cc_final: 0.7552 (ttpt) REVERT: E 538 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7359 (mtpp) REVERT: E 581 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7927 (ttp80) REVERT: I 82 VAL cc_start: 0.8310 (t) cc_final: 0.7985 (p) REVERT: I 95 ASN cc_start: 0.8272 (m-40) cc_final: 0.7879 (m-40) REVERT: I 109 TRP cc_start: 0.8661 (m100) cc_final: 0.7769 (m100) REVERT: I 144 GLU cc_start: 0.7777 (pt0) cc_final: 0.7393 (pt0) REVERT: I 178 ASP cc_start: 0.6673 (t0) cc_final: 0.6347 (t0) REVERT: I 193 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7023 (mp0) REVERT: I 214 TRP cc_start: -0.1686 (OUTLIER) cc_final: -0.3971 (p90) REVERT: I 237 ASP cc_start: 0.7408 (t0) cc_final: 0.6787 (t0) REVERT: I 269 ASP cc_start: 0.6893 (p0) cc_final: 0.6532 (p0) REVERT: I 279 TRP cc_start: 0.8885 (p-90) cc_final: 0.7828 (p-90) REVERT: I 318 GLN cc_start: 0.8566 (mt0) cc_final: 0.8157 (mm110) REVERT: I 386 GLN cc_start: 0.7645 (tt0) cc_final: 0.7260 (tt0) REVERT: I 446 ASN cc_start: 0.8461 (m110) cc_final: 0.8203 (m110) REVERT: I 485 ASN cc_start: 0.7318 (p0) cc_final: 0.6776 (p0) REVERT: I 501 LYS cc_start: 0.8677 (ttpt) cc_final: 0.7900 (ttpt) REVERT: I 532 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8201 (ttpp) REVERT: I 577 GLN cc_start: 0.8134 (mt0) cc_final: 0.7872 (mt0) REVERT: I 582 LYS cc_start: 0.8286 (pttm) cc_final: 0.7974 (pttm) REVERT: C 193 GLU cc_start: 0.7106 (tp30) cc_final: 0.6674 (tp30) REVERT: C 501 LYS cc_start: 0.8674 (tttp) cc_final: 0.8120 (tttm) REVERT: C 509 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: C 564 SER cc_start: 0.7761 (t) cc_final: 0.7370 (t) REVERT: C 569 MET cc_start: 0.5537 (mmm) cc_final: 0.5257 (mmm) REVERT: B 52 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7951 (ttmm) REVERT: B 53 PHE cc_start: 0.8381 (m-80) cc_final: 0.7792 (p90) REVERT: B 117 TRP cc_start: 0.7997 (m100) cc_final: 0.7385 (m100) REVERT: B 120 TRP cc_start: 0.8350 (m100) cc_final: 0.8135 (m100) REVERT: B 133 MET cc_start: 0.6940 (mmt) cc_final: 0.6738 (mmt) REVERT: B 167 ASN cc_start: 0.7873 (m-40) cc_final: 0.7594 (m-40) REVERT: B 255 LEU cc_start: 0.8510 (mt) cc_final: 0.8143 (mm) REVERT: B 268 PHE cc_start: 0.8473 (m-80) cc_final: 0.8124 (m-10) REVERT: B 424 VAL cc_start: 0.8095 (OUTLIER) cc_final: 0.7865 (m) REVERT: B 430 LEU cc_start: 0.8447 (tp) cc_final: 0.8109 (tp) REVERT: B 463 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7785 (m) REVERT: B 491 GLN cc_start: 0.7474 (mm-40) cc_final: 0.6910 (mm-40) REVERT: B 506 LEU cc_start: 0.8533 (mt) cc_final: 0.8271 (mp) REVERT: B 535 PHE cc_start: 0.8093 (m-80) cc_final: 0.7882 (m-80) REVERT: B 569 MET cc_start: 0.6991 (mmm) cc_final: 0.6695 (mmm) outliers start: 156 outliers final: 105 residues processed: 1605 average time/residue: 0.2156 time to fit residues: 542.7440 Evaluate side-chains 1666 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1536 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 318 GLN Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 321 ASN Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 520 ARG Chi-restraints excluded: chain F residue 582 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 509 GLU Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 520 ARG Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 551 MET Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 94 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 198 optimal weight: 0.0020 chunk 55 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 112 optimal weight: 0.1980 chunk 280 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 overall best weight: 2.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 497 GLN G 560 ASN ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 HIS E 127 GLN I 147 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.110977 restraints weight = 52550.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115309 restraints weight = 24392.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118056 restraints weight = 13636.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119821 restraints weight = 8669.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120963 restraints weight = 6060.546| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31936 Z= 0.149 Angle : 0.616 16.123 43674 Z= 0.304 Chirality : 0.044 0.206 4764 Planarity : 0.005 0.053 5732 Dihedral : 4.926 67.723 4237 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.73 % Allowed : 29.14 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.14), residues: 3686 helix: -1.20 (0.47), residues: 100 sheet: -0.36 (0.18), residues: 861 loop : -0.35 (0.12), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 67 TYR 0.046 0.002 TYR A 561 PHE 0.031 0.002 PHE A 197 TRP 0.046 0.002 TRP C 528 HIS 0.007 0.001 HIS F 222 Details of bonding type rmsd covalent geometry : bond 0.00333 (31929) covalent geometry : angle 0.61628 (43660) SS BOND : bond 0.00479 ( 7) SS BOND : angle 0.99304 ( 14) hydrogen bonds : bond 0.02920 ( 295) hydrogen bonds : angle 5.88229 ( 567) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1684 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1528 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7285 (tt0) cc_final: 0.6884 (tp30) REVERT: A 67 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8013 (mmt180) REVERT: A 104 GLN cc_start: 0.8069 (pt0) cc_final: 0.7349 (pt0) REVERT: A 109 TRP cc_start: 0.8657 (m100) cc_final: 0.8081 (m100) REVERT: A 165 TYR cc_start: 0.8097 (m-80) cc_final: 0.7719 (m-80) REVERT: A 175 VAL cc_start: 0.8542 (t) cc_final: 0.8118 (p) REVERT: A 182 THR cc_start: 0.8443 (m) cc_final: 0.8101 (t) REVERT: A 192 SER cc_start: 0.7891 (t) cc_final: 0.7664 (t) REVERT: A 200 TRP cc_start: 0.8485 (p90) cc_final: 0.8245 (p90) REVERT: A 216 ARG cc_start: 0.6947 (ttt-90) cc_final: 0.6718 (ttt-90) REVERT: A 237 ASP cc_start: 0.7871 (t0) cc_final: 0.7435 (t0) REVERT: A 260 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: A 269 ASP cc_start: 0.7271 (p0) cc_final: 0.7015 (p0) REVERT: A 302 ASN cc_start: 0.8173 (m-40) cc_final: 0.7559 (m110) REVERT: A 312 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8051 (mtmt) REVERT: A 335 GLU cc_start: 0.7153 (tt0) cc_final: 0.6102 (tm-30) REVERT: A 346 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6471 (mt-10) REVERT: A 350 GLN cc_start: 0.7473 (mt0) cc_final: 0.7147 (mp10) REVERT: A 411 GLU cc_start: 0.7723 (mp0) cc_final: 0.7402 (mp0) REVERT: A 413 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: A 414 TRP cc_start: 0.8040 (p90) cc_final: 0.7828 (p90) REVERT: A 446 ASN cc_start: 0.8178 (m110) cc_final: 0.7815 (m110) REVERT: A 448 PHE cc_start: 0.7884 (t80) cc_final: 0.7594 (t80) REVERT: A 468 GLN cc_start: 0.7802 (tt0) cc_final: 0.7511 (tt0) REVERT: A 473 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6856 (mm-30) REVERT: A 501 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8090 (ttpp) REVERT: A 502 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8667 (m) REVERT: G 50 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: G 60 GLU cc_start: 0.7476 (tp30) cc_final: 0.7059 (tp30) REVERT: G 62 THR cc_start: 0.8331 (m) cc_final: 0.7748 (t) REVERT: G 68 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8039 (tt) REVERT: G 73 MET cc_start: 0.7686 (ttp) cc_final: 0.7163 (ptm) REVERT: G 80 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7678 (tpp80) REVERT: G 83 VAL cc_start: 0.8696 (t) cc_final: 0.8327 (m) REVERT: G 104 GLN cc_start: 0.8035 (pt0) cc_final: 0.7629 (pt0) REVERT: G 109 TRP cc_start: 0.8434 (m100) cc_final: 0.8010 (m100) REVERT: G 135 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6822 (tp30) REVERT: G 136 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8149 (tp) REVERT: G 137 HIS cc_start: 0.8443 (m90) cc_final: 0.8057 (m170) REVERT: G 143 GLN cc_start: 0.8359 (mt0) cc_final: 0.7876 (mt0) REVERT: G 144 GLU cc_start: 0.7301 (pm20) cc_final: 0.7038 (pm20) REVERT: G 174 MET cc_start: 0.7891 (mtp) cc_final: 0.7384 (mtp) REVERT: G 193 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: G 213 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7505 (tm-30) REVERT: G 237 ASP cc_start: 0.7549 (t0) cc_final: 0.7102 (t0) REVERT: G 242 GLN cc_start: 0.7853 (mt0) cc_final: 0.7618 (mt0) REVERT: G 245 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7871 (t) REVERT: G 263 THR cc_start: 0.8584 (m) cc_final: 0.8019 (p) REVERT: G 266 PHE cc_start: 0.8263 (t80) cc_final: 0.7936 (t80) REVERT: G 268 PHE cc_start: 0.8114 (m-80) cc_final: 0.7799 (m-10) REVERT: G 312 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8241 (mtpp) REVERT: G 327 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7030 (mm-30) REVERT: G 333 PRO cc_start: 0.8951 (Cg_exo) cc_final: 0.8709 (Cg_endo) REVERT: G 335 GLU cc_start: 0.7445 (tt0) cc_final: 0.6911 (tt0) REVERT: G 342 TYR cc_start: 0.7553 (p90) cc_final: 0.7333 (p90) REVERT: G 345 PHE cc_start: 0.7886 (m-80) cc_final: 0.7418 (m-80) REVERT: G 382 ARG cc_start: 0.5419 (mtm180) cc_final: 0.4613 (mtm110) REVERT: G 398 PHE cc_start: 0.8649 (p90) cc_final: 0.8272 (p90) REVERT: G 434 ASP cc_start: 0.7608 (m-30) cc_final: 0.7369 (t0) REVERT: G 457 LEU cc_start: 0.8227 (mt) cc_final: 0.7941 (mp) REVERT: G 464 TYR cc_start: 0.7980 (t80) cc_final: 0.7672 (t80) REVERT: G 475 ASP cc_start: 0.7462 (t0) cc_final: 0.6781 (t0) REVERT: G 479 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8324 (mmtm) REVERT: G 501 LYS cc_start: 0.8513 (ttpp) cc_final: 0.8035 (ttpp) REVERT: G 505 ASN cc_start: 0.7725 (t0) cc_final: 0.7016 (t0) REVERT: G 518 MET cc_start: 0.7655 (ptp) cc_final: 0.7386 (ptp) REVERT: G 520 ARG cc_start: 0.8135 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: G 528 TRP cc_start: 0.8157 (m100) cc_final: 0.7626 (m100) REVERT: G 530 LYS cc_start: 0.8085 (ttpp) cc_final: 0.7386 (ttpp) REVERT: G 556 ASP cc_start: 0.7538 (m-30) cc_final: 0.7296 (t0) REVERT: F 72 ASN cc_start: 0.8461 (t0) cc_final: 0.8120 (t0) REVERT: F 73 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7146 (ttp) REVERT: F 80 ARG cc_start: 0.4361 (tpt90) cc_final: 0.4135 (tpt90) REVERT: F 81 ARG cc_start: 0.5516 (ptp-170) cc_final: 0.4608 (ptp-170) REVERT: F 95 ASN cc_start: 0.7164 (m-40) cc_final: 0.6945 (m-40) REVERT: F 109 TRP cc_start: 0.8394 (m100) cc_final: 0.7869 (m100) REVERT: F 120 TRP cc_start: 0.8395 (m100) cc_final: 0.7918 (m100) REVERT: F 125 ASP cc_start: 0.7602 (m-30) cc_final: 0.7192 (m-30) REVERT: F 135 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: F 144 GLU cc_start: 0.7349 (pm20) cc_final: 0.7038 (pm20) REVERT: F 151 LYS cc_start: 0.8245 (mmmm) cc_final: 0.7518 (mmmm) REVERT: F 167 ASN cc_start: 0.8281 (m110) cc_final: 0.7907 (m-40) REVERT: F 193 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7552 (mt-10) REVERT: F 197 PHE cc_start: 0.8231 (m-10) cc_final: 0.7557 (m-80) REVERT: F 201 LYS cc_start: 0.8038 (mmpt) cc_final: 0.7619 (mmpt) REVERT: F 213 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7135 (tm-30) REVERT: F 237 ASP cc_start: 0.8228 (t0) cc_final: 0.7936 (t0) REVERT: F 245 THR cc_start: 0.8105 (t) cc_final: 0.7672 (p) REVERT: F 266 PHE cc_start: 0.8272 (t80) cc_final: 0.7970 (t80) REVERT: F 279 TRP cc_start: 0.8366 (p-90) cc_final: 0.8031 (p-90) REVERT: F 312 LYS cc_start: 0.8645 (mptt) cc_final: 0.8093 (mptt) REVERT: F 336 VAL cc_start: 0.8768 (t) cc_final: 0.8410 (p) REVERT: F 353 PHE cc_start: 0.7418 (p90) cc_final: 0.7026 (p90) REVERT: F 409 TYR cc_start: 0.8304 (t80) cc_final: 0.8059 (t80) REVERT: F 419 ASN cc_start: 0.8538 (m110) cc_final: 0.8216 (m110) REVERT: F 439 LYS cc_start: 0.8022 (mmtp) cc_final: 0.7670 (mmtp) REVERT: F 459 ASN cc_start: 0.8097 (m-40) cc_final: 0.7796 (m110) REVERT: F 470 TRP cc_start: 0.8125 (p90) cc_final: 0.7846 (p90) REVERT: F 473 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7214 (tm-30) REVERT: F 474 PHE cc_start: 0.8071 (m-10) cc_final: 0.7494 (m-10) REVERT: F 475 ASP cc_start: 0.8042 (t0) cc_final: 0.7319 (t0) REVERT: F 492 ASN cc_start: 0.8706 (p0) cc_final: 0.8506 (p0) REVERT: F 497 GLN cc_start: 0.8373 (mt0) cc_final: 0.7940 (mt0) REVERT: F 501 LYS cc_start: 0.8528 (ttpp) cc_final: 0.7886 (pttp) REVERT: F 518 MET cc_start: 0.7749 (ptp) cc_final: 0.7308 (ptp) REVERT: F 520 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7461 (mtm110) REVERT: F 532 LYS cc_start: 0.8492 (ttmm) cc_final: 0.8002 (ttmm) REVERT: F 550 GLN cc_start: 0.8070 (mm110) cc_final: 0.7517 (mm-40) REVERT: F 562 VAL cc_start: 0.8632 (p) cc_final: 0.8403 (m) REVERT: D 46 ASN cc_start: 0.7984 (t0) cc_final: 0.7411 (t0) REVERT: D 50 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6546 (tm-30) REVERT: D 70 HIS cc_start: 0.7752 (t-90) cc_final: 0.7421 (t-90) REVERT: D 73 MET cc_start: 0.8286 (ptt) cc_final: 0.7884 (ptm) REVERT: D 107 THR cc_start: 0.8370 (m) cc_final: 0.7694 (p) REVERT: D 142 GLU cc_start: 0.7738 (pt0) cc_final: 0.7120 (pm20) REVERT: D 144 GLU cc_start: 0.7197 (pm20) cc_final: 0.6535 (pm20) REVERT: D 174 MET cc_start: 0.7608 (mtp) cc_final: 0.6959 (mtp) REVERT: D 190 MET cc_start: 0.7793 (mmm) cc_final: 0.7548 (mmm) REVERT: D 200 TRP cc_start: 0.8762 (p90) cc_final: 0.8347 (p90) REVERT: D 208 TRP cc_start: 0.8133 (t60) cc_final: 0.7709 (t60) REVERT: D 209 ARG cc_start: 0.4690 (OUTLIER) cc_final: 0.4160 (pmt170) REVERT: D 256 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7669 (mtm-85) REVERT: D 532 LYS cc_start: 0.8312 (tttt) cc_final: 0.8051 (tttt) REVERT: D 569 MET cc_start: 0.6808 (mmp) cc_final: 0.6600 (mmp) REVERT: E 95 ASN cc_start: 0.8146 (t0) cc_final: 0.7575 (t0) REVERT: E 142 GLU cc_start: 0.7593 (pt0) cc_final: 0.6543 (pt0) REVERT: E 163 LYS cc_start: 0.8018 (mppt) cc_final: 0.7558 (mppt) REVERT: E 209 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.4310 (ptt180) REVERT: E 210 TYR cc_start: 0.8508 (p90) cc_final: 0.8207 (p90) REVERT: E 213 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7699 (tm-30) REVERT: E 237 ASP cc_start: 0.7490 (t0) cc_final: 0.7182 (t0) REVERT: E 256 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7469 (mtp85) REVERT: E 266 PHE cc_start: 0.8233 (t80) cc_final: 0.7943 (t80) REVERT: E 335 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6224 (tm-30) REVERT: E 342 TYR cc_start: 0.7102 (p90) cc_final: 0.6781 (p90) REVERT: E 377 ARG cc_start: 0.5354 (mtt180) cc_final: 0.4977 (mtt180) REVERT: E 382 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7590 (mtt90) REVERT: E 387 LYS cc_start: 0.8720 (tptm) cc_final: 0.8429 (tptm) REVERT: E 396 GLU cc_start: 0.7261 (tt0) cc_final: 0.6917 (tt0) REVERT: E 400 TYR cc_start: 0.8068 (t80) cc_final: 0.7354 (t80) REVERT: E 430 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7625 (tt) REVERT: E 451 TYR cc_start: 0.3752 (OUTLIER) cc_final: 0.3346 (t80) REVERT: E 464 TYR cc_start: 0.8101 (t80) cc_final: 0.7612 (t80) REVERT: E 472 LYS cc_start: 0.3592 (OUTLIER) cc_final: 0.1617 (tmmt) REVERT: E 479 LYS cc_start: 0.8328 (mptt) cc_final: 0.7968 (mptt) REVERT: E 501 LYS cc_start: 0.8119 (tttt) cc_final: 0.7739 (tttt) REVERT: E 508 ASN cc_start: 0.8033 (p0) cc_final: 0.6188 (p0) REVERT: E 509 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7312 (mm-30) REVERT: E 520 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7441 (mtp85) REVERT: E 526 ASP cc_start: 0.6584 (p0) cc_final: 0.6136 (p0) REVERT: E 532 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7531 (ttpt) REVERT: E 538 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7494 (mtpp) REVERT: E 560 ASN cc_start: 0.8316 (m-40) cc_final: 0.7964 (m110) REVERT: I 82 VAL cc_start: 0.8293 (t) cc_final: 0.7965 (p) REVERT: I 95 ASN cc_start: 0.8269 (m-40) cc_final: 0.7851 (m-40) REVERT: I 109 TRP cc_start: 0.8636 (m100) cc_final: 0.7724 (m100) REVERT: I 178 ASP cc_start: 0.6641 (t0) cc_final: 0.6346 (t0) REVERT: I 193 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7035 (mp0) REVERT: I 214 TRP cc_start: -0.1533 (OUTLIER) cc_final: -0.3870 (p90) REVERT: I 237 ASP cc_start: 0.7435 (t0) cc_final: 0.6779 (t0) REVERT: I 269 ASP cc_start: 0.6911 (p0) cc_final: 0.6569 (p0) REVERT: I 318 GLN cc_start: 0.8551 (mt0) cc_final: 0.8148 (mm110) REVERT: I 386 GLN cc_start: 0.7669 (tt0) cc_final: 0.7247 (tt0) REVERT: I 446 ASN cc_start: 0.8460 (m110) cc_final: 0.8145 (m110) REVERT: I 485 ASN cc_start: 0.7280 (p0) cc_final: 0.6844 (p0) REVERT: I 501 LYS cc_start: 0.8649 (ttpt) cc_final: 0.7846 (ttpt) REVERT: I 532 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8206 (ttpp) REVERT: I 577 GLN cc_start: 0.8158 (mt0) cc_final: 0.7885 (mt0) REVERT: I 582 LYS cc_start: 0.8341 (pttm) cc_final: 0.8055 (pttm) REVERT: C 193 GLU cc_start: 0.7130 (tp30) cc_final: 0.6671 (tp30) REVERT: C 378 TYR cc_start: 0.2676 (OUTLIER) cc_final: 0.0755 (m-80) REVERT: C 501 LYS cc_start: 0.8652 (tttp) cc_final: 0.8099 (tttm) REVERT: C 509 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6835 (tm-30) REVERT: C 564 SER cc_start: 0.7816 (t) cc_final: 0.7405 (t) REVERT: C 569 MET cc_start: 0.5620 (mmm) cc_final: 0.5302 (mmm) REVERT: B 52 LYS cc_start: 0.8329 (ttmm) cc_final: 0.7988 (ttmm) REVERT: B 53 PHE cc_start: 0.8375 (m-80) cc_final: 0.7777 (p90) REVERT: B 117 TRP cc_start: 0.7979 (m100) cc_final: 0.7386 (m100) REVERT: B 120 TRP cc_start: 0.8373 (m100) cc_final: 0.8168 (m100) REVERT: B 133 MET cc_start: 0.6903 (mmt) cc_final: 0.6654 (mmt) REVERT: B 143 GLN cc_start: 0.7947 (pt0) cc_final: 0.7721 (pt0) REVERT: B 151 LYS cc_start: 0.8709 (mttm) cc_final: 0.8332 (mttm) REVERT: B 167 ASN cc_start: 0.7812 (m-40) cc_final: 0.7568 (m-40) REVERT: B 201 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8538 (mtmt) REVERT: B 256 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7359 (mtp85) REVERT: B 268 PHE cc_start: 0.8457 (m-80) cc_final: 0.8088 (m-10) REVERT: B 424 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7875 (m) REVERT: B 430 LEU cc_start: 0.8449 (tp) cc_final: 0.8111 (tp) REVERT: B 449 ASN cc_start: 0.8233 (t0) cc_final: 0.7997 (t0) REVERT: B 463 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7794 (m) REVERT: B 491 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7022 (mm-40) REVERT: B 501 LYS cc_start: 0.8884 (tttm) cc_final: 0.8634 (pttp) REVERT: B 535 PHE cc_start: 0.8079 (m-80) cc_final: 0.7863 (m-80) REVERT: B 569 MET cc_start: 0.7005 (mmm) cc_final: 0.6707 (mmm) outliers start: 156 outliers final: 111 residues processed: 1574 average time/residue: 0.2160 time to fit residues: 534.4030 Evaluate side-chains 1650 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1513 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 404 GLN Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 321 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 520 ARG Chi-restraints excluded: chain F residue 582 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 520 ARG Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 551 MET Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 336 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 366 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 233 optimal weight: 0.2980 chunk 248 optimal weight: 0.0040 overall best weight: 1.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 HIS ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 ASN ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN I 147 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS B 458 ASN B 493 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111729 restraints weight = 52415.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116033 restraints weight = 24330.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118787 restraints weight = 13633.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.120595 restraints weight = 8651.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121788 restraints weight = 6036.559| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31936 Z= 0.125 Angle : 0.622 16.809 43674 Z= 0.304 Chirality : 0.044 0.217 4764 Planarity : 0.005 0.053 5732 Dihedral : 4.829 66.962 4237 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.31 % Allowed : 30.17 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.14), residues: 3686 helix: -1.19 (0.47), residues: 100 sheet: -0.31 (0.18), residues: 861 loop : -0.33 (0.12), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 67 TYR 0.049 0.001 TYR A 561 PHE 0.030 0.002 PHE C 243 TRP 0.065 0.002 TRP C 528 HIS 0.004 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00286 (31929) covalent geometry : angle 0.62156 (43660) SS BOND : bond 0.00460 ( 7) SS BOND : angle 0.95718 ( 14) hydrogen bonds : bond 0.02847 ( 295) hydrogen bonds : angle 5.85298 ( 567) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1520 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7278 (tt0) cc_final: 0.6871 (tp30) REVERT: A 79 TYR cc_start: 0.8253 (m-80) cc_final: 0.7763 (m-80) REVERT: A 104 GLN cc_start: 0.8075 (pt0) cc_final: 0.7351 (pt0) REVERT: A 109 TRP cc_start: 0.8593 (m100) cc_final: 0.8355 (m100) REVERT: A 165 TYR cc_start: 0.8093 (m-80) cc_final: 0.7441 (m-80) REVERT: A 182 THR cc_start: 0.8405 (m) cc_final: 0.8090 (t) REVERT: A 192 SER cc_start: 0.7835 (t) cc_final: 0.7599 (t) REVERT: A 216 ARG cc_start: 0.6970 (ttt-90) cc_final: 0.6720 (ttt-90) REVERT: A 237 ASP cc_start: 0.7785 (t0) cc_final: 0.7328 (t0) REVERT: A 260 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: A 302 ASN cc_start: 0.8225 (m-40) cc_final: 0.7613 (m110) REVERT: A 312 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8067 (mtmt) REVERT: A 335 GLU cc_start: 0.7156 (tt0) cc_final: 0.6119 (tm-30) REVERT: A 346 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6595 (mt-10) REVERT: A 350 GLN cc_start: 0.7456 (mt0) cc_final: 0.7127 (mp10) REVERT: A 411 GLU cc_start: 0.7693 (mp0) cc_final: 0.7352 (mp0) REVERT: A 414 TRP cc_start: 0.8076 (p90) cc_final: 0.7781 (p90) REVERT: A 443 ASN cc_start: 0.8264 (p0) cc_final: 0.7898 (p0) REVERT: A 473 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6838 (mm-30) REVERT: A 502 VAL cc_start: 0.8921 (OUTLIER) cc_final: 0.8660 (m) REVERT: A 530 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7890 (ttpp) REVERT: A 554 ASN cc_start: 0.7682 (p0) cc_final: 0.7458 (p0) REVERT: G 50 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: G 51 PHE cc_start: 0.7758 (m-10) cc_final: 0.7513 (m-10) REVERT: G 53 PHE cc_start: 0.5445 (p90) cc_final: 0.4851 (p90) REVERT: G 60 GLU cc_start: 0.7431 (tp30) cc_final: 0.7030 (tp30) REVERT: G 62 THR cc_start: 0.8265 (m) cc_final: 0.7661 (t) REVERT: G 68 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8024 (tt) REVERT: G 73 MET cc_start: 0.7629 (ttp) cc_final: 0.7250 (ptm) REVERT: G 83 VAL cc_start: 0.8694 (t) cc_final: 0.8357 (m) REVERT: G 109 TRP cc_start: 0.8417 (m100) cc_final: 0.7988 (m100) REVERT: G 135 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6786 (tp30) REVERT: G 136 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8150 (tp) REVERT: G 137 HIS cc_start: 0.8439 (m90) cc_final: 0.8068 (m170) REVERT: G 144 GLU cc_start: 0.7279 (pm20) cc_final: 0.7014 (pm20) REVERT: G 151 LYS cc_start: 0.7974 (mttm) cc_final: 0.7718 (mmtm) REVERT: G 174 MET cc_start: 0.7887 (mtp) cc_final: 0.7330 (mtp) REVERT: G 185 PHE cc_start: 0.8151 (t80) cc_final: 0.7891 (t80) REVERT: G 193 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6559 (mp0) REVERT: G 213 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7494 (tm-30) REVERT: G 242 GLN cc_start: 0.7841 (mt0) cc_final: 0.7626 (mt0) REVERT: G 245 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7784 (t) REVERT: G 263 THR cc_start: 0.8548 (m) cc_final: 0.8008 (p) REVERT: G 266 PHE cc_start: 0.8242 (t80) cc_final: 0.7925 (t80) REVERT: G 268 PHE cc_start: 0.8124 (m-80) cc_final: 0.7804 (m-10) REVERT: G 283 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7679 (ptm160) REVERT: G 312 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8212 (mtpp) REVERT: G 327 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6939 (mm-30) REVERT: G 333 PRO cc_start: 0.8865 (Cg_exo) cc_final: 0.8621 (Cg_endo) REVERT: G 335 GLU cc_start: 0.7437 (tt0) cc_final: 0.6928 (tt0) REVERT: G 345 PHE cc_start: 0.7907 (m-80) cc_final: 0.7494 (m-80) REVERT: G 382 ARG cc_start: 0.5378 (mtm180) cc_final: 0.4774 (mtm180) REVERT: G 386 GLN cc_start: 0.7700 (mt0) cc_final: 0.7432 (mm-40) REVERT: G 398 PHE cc_start: 0.8640 (p90) cc_final: 0.8234 (p90) REVERT: G 416 GLN cc_start: 0.8050 (pt0) cc_final: 0.7786 (pt0) REVERT: G 434 ASP cc_start: 0.7605 (m-30) cc_final: 0.7388 (t0) REVERT: G 457 LEU cc_start: 0.8242 (mt) cc_final: 0.7973 (mp) REVERT: G 464 TYR cc_start: 0.7956 (t80) cc_final: 0.7589 (t80) REVERT: G 475 ASP cc_start: 0.7436 (t0) cc_final: 0.6756 (t0) REVERT: G 479 LYS cc_start: 0.8606 (mmtm) cc_final: 0.8300 (mmtm) REVERT: G 501 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8052 (ttpp) REVERT: G 505 ASN cc_start: 0.7722 (t0) cc_final: 0.7009 (t0) REVERT: G 509 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7551 (mm-30) REVERT: G 518 MET cc_start: 0.7647 (ptp) cc_final: 0.7367 (ptp) REVERT: G 528 TRP cc_start: 0.8191 (m100) cc_final: 0.7555 (m100) REVERT: G 530 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7342 (ttpp) REVERT: G 556 ASP cc_start: 0.7545 (m-30) cc_final: 0.7306 (t0) REVERT: F 72 ASN cc_start: 0.8474 (t0) cc_final: 0.8135 (t0) REVERT: F 73 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7098 (ttp) REVERT: F 80 ARG cc_start: 0.4200 (tpt90) cc_final: 0.1721 (mmt180) REVERT: F 81 ARG cc_start: 0.5446 (ptp-170) cc_final: 0.5011 (ptp-170) REVERT: F 109 TRP cc_start: 0.8391 (m100) cc_final: 0.7918 (m100) REVERT: F 120 TRP cc_start: 0.8415 (m100) cc_final: 0.7917 (m100) REVERT: F 125 ASP cc_start: 0.7581 (m-30) cc_final: 0.7181 (m-30) REVERT: F 135 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: F 144 GLU cc_start: 0.7351 (pm20) cc_final: 0.7032 (pm20) REVERT: F 151 LYS cc_start: 0.8233 (mmmm) cc_final: 0.7518 (mmmm) REVERT: F 167 ASN cc_start: 0.8312 (m110) cc_final: 0.7924 (m-40) REVERT: F 193 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7532 (mt-10) REVERT: F 197 PHE cc_start: 0.8271 (m-10) cc_final: 0.7524 (m-80) REVERT: F 201 LYS cc_start: 0.8043 (mmpt) cc_final: 0.7636 (mmpt) REVERT: F 213 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7152 (tm-30) REVERT: F 237 ASP cc_start: 0.8211 (t0) cc_final: 0.7922 (t0) REVERT: F 245 THR cc_start: 0.8031 (t) cc_final: 0.7681 (p) REVERT: F 266 PHE cc_start: 0.8263 (t80) cc_final: 0.7802 (t80) REVERT: F 279 TRP cc_start: 0.8378 (p-90) cc_final: 0.8018 (p-90) REVERT: F 335 GLU cc_start: 0.7478 (tt0) cc_final: 0.7007 (tt0) REVERT: F 336 VAL cc_start: 0.8777 (t) cc_final: 0.8410 (p) REVERT: F 353 PHE cc_start: 0.7301 (p90) cc_final: 0.6996 (p90) REVERT: F 419 ASN cc_start: 0.8531 (m110) cc_final: 0.8204 (m110) REVERT: F 439 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7611 (mmtp) REVERT: F 470 TRP cc_start: 0.8144 (p90) cc_final: 0.7842 (p90) REVERT: F 473 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7220 (tm-30) REVERT: F 474 PHE cc_start: 0.8055 (m-10) cc_final: 0.7446 (m-10) REVERT: F 475 ASP cc_start: 0.8016 (t0) cc_final: 0.7298 (t0) REVERT: F 497 GLN cc_start: 0.8365 (mt0) cc_final: 0.8014 (mt0) REVERT: F 501 LYS cc_start: 0.8549 (ttpp) cc_final: 0.7974 (pttp) REVERT: F 518 MET cc_start: 0.7738 (ptp) cc_final: 0.7281 (ptp) REVERT: F 520 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7395 (mtm110) REVERT: F 532 LYS cc_start: 0.8470 (ttmm) cc_final: 0.7992 (ttmm) REVERT: F 550 GLN cc_start: 0.8080 (mm110) cc_final: 0.7689 (mm110) REVERT: F 562 VAL cc_start: 0.8624 (p) cc_final: 0.8403 (m) REVERT: D 46 ASN cc_start: 0.7977 (t0) cc_final: 0.7459 (t0) REVERT: D 50 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6548 (tm-30) REVERT: D 70 HIS cc_start: 0.7711 (t-90) cc_final: 0.7437 (t-90) REVERT: D 73 MET cc_start: 0.8305 (ptt) cc_final: 0.7956 (ptm) REVERT: D 142 GLU cc_start: 0.7630 (pt0) cc_final: 0.7389 (pt0) REVERT: D 144 GLU cc_start: 0.7221 (pm20) cc_final: 0.6571 (pm20) REVERT: D 174 MET cc_start: 0.7636 (mtp) cc_final: 0.7112 (mtp) REVERT: D 190 MET cc_start: 0.7785 (mmm) cc_final: 0.7515 (mmm) REVERT: D 209 ARG cc_start: 0.4669 (OUTLIER) cc_final: 0.3621 (pmt170) REVERT: D 256 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7711 (mtm-85) REVERT: E 95 ASN cc_start: 0.8101 (t0) cc_final: 0.7731 (t0) REVERT: E 142 GLU cc_start: 0.7583 (pt0) cc_final: 0.6548 (pt0) REVERT: E 163 LYS cc_start: 0.7973 (mppt) cc_final: 0.7555 (mppt) REVERT: E 209 ARG cc_start: 0.5097 (OUTLIER) cc_final: 0.4297 (ptt180) REVERT: E 210 TYR cc_start: 0.8500 (p90) cc_final: 0.8196 (p90) REVERT: E 213 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7678 (tm-30) REVERT: E 256 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7442 (mtp85) REVERT: E 266 PHE cc_start: 0.8199 (t80) cc_final: 0.7901 (t80) REVERT: E 335 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6232 (tm-30) REVERT: E 342 TYR cc_start: 0.7111 (p90) cc_final: 0.6892 (p90) REVERT: E 377 ARG cc_start: 0.5316 (mtt180) cc_final: 0.4935 (mtt180) REVERT: E 382 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7578 (mtt90) REVERT: E 387 LYS cc_start: 0.8727 (tptm) cc_final: 0.8428 (tptm) REVERT: E 400 TYR cc_start: 0.8054 (t80) cc_final: 0.7360 (t80) REVERT: E 404 GLN cc_start: 0.8038 (pt0) cc_final: 0.7452 (pt0) REVERT: E 430 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7614 (tt) REVERT: E 451 TYR cc_start: 0.3580 (OUTLIER) cc_final: 0.3228 (t80) REVERT: E 464 TYR cc_start: 0.8066 (t80) cc_final: 0.7557 (t80) REVERT: E 479 LYS cc_start: 0.8331 (mptt) cc_final: 0.7937 (mptt) REVERT: E 501 LYS cc_start: 0.8099 (tttt) cc_final: 0.7630 (tttt) REVERT: E 520 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7456 (mtp85) REVERT: E 526 ASP cc_start: 0.6538 (p0) cc_final: 0.6128 (p0) REVERT: E 530 LYS cc_start: 0.8053 (tmtt) cc_final: 0.7483 (tttt) REVERT: E 532 LYS cc_start: 0.8296 (ttpt) cc_final: 0.7570 (ttpt) REVERT: E 538 LYS cc_start: 0.7974 (ttmm) cc_final: 0.7546 (mtpp) REVERT: E 560 ASN cc_start: 0.8308 (m-40) cc_final: 0.7963 (m110) REVERT: I 60 GLU cc_start: 0.7268 (tt0) cc_final: 0.6988 (tt0) REVERT: I 82 VAL cc_start: 0.8227 (t) cc_final: 0.7896 (p) REVERT: I 95 ASN cc_start: 0.8262 (m-40) cc_final: 0.7825 (m-40) REVERT: I 109 TRP cc_start: 0.8622 (m100) cc_final: 0.7842 (m100) REVERT: I 144 GLU cc_start: 0.7768 (pt0) cc_final: 0.7467 (pt0) REVERT: I 178 ASP cc_start: 0.6657 (t0) cc_final: 0.6333 (t0) REVERT: I 193 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7007 (mp0) REVERT: I 214 TRP cc_start: -0.1545 (OUTLIER) cc_final: -0.4063 (p90) REVERT: I 237 ASP cc_start: 0.7391 (t0) cc_final: 0.6790 (t0) REVERT: I 269 ASP cc_start: 0.6871 (p0) cc_final: 0.6532 (p0) REVERT: I 279 TRP cc_start: 0.8873 (p-90) cc_final: 0.8587 (p-90) REVERT: I 318 GLN cc_start: 0.8583 (mt0) cc_final: 0.8162 (mm110) REVERT: I 386 GLN cc_start: 0.7670 (tt0) cc_final: 0.7247 (tt0) REVERT: I 446 ASN cc_start: 0.8368 (m110) cc_final: 0.8082 (m110) REVERT: I 485 ASN cc_start: 0.7293 (p0) cc_final: 0.6843 (p0) REVERT: I 501 LYS cc_start: 0.8643 (ttpt) cc_final: 0.7819 (ttpt) REVERT: I 532 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8212 (ttpp) REVERT: I 577 GLN cc_start: 0.8144 (mt0) cc_final: 0.7871 (mt0) REVERT: I 582 LYS cc_start: 0.8267 (pttm) cc_final: 0.7966 (pttm) REVERT: C 193 GLU cc_start: 0.7126 (tp30) cc_final: 0.6646 (tp30) REVERT: C 378 TYR cc_start: 0.2838 (OUTLIER) cc_final: 0.0978 (m-80) REVERT: C 501 LYS cc_start: 0.8648 (tttp) cc_final: 0.8085 (tttm) REVERT: C 509 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: C 564 SER cc_start: 0.7855 (t) cc_final: 0.7574 (t) REVERT: B 52 LYS cc_start: 0.8327 (ttmm) cc_final: 0.8008 (ttmm) REVERT: B 53 PHE cc_start: 0.8378 (m-80) cc_final: 0.7777 (p90) REVERT: B 117 TRP cc_start: 0.7935 (m100) cc_final: 0.7397 (m100) REVERT: B 133 MET cc_start: 0.6911 (mmt) cc_final: 0.6630 (mmt) REVERT: B 142 GLU cc_start: 0.7657 (pp20) cc_final: 0.7364 (pp20) REVERT: B 151 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8326 (mttm) REVERT: B 167 ASN cc_start: 0.7826 (m-40) cc_final: 0.7585 (m-40) REVERT: B 201 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8539 (mtmt) REVERT: B 255 LEU cc_start: 0.8466 (mt) cc_final: 0.8257 (mm) REVERT: B 256 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7370 (mtp85) REVERT: B 266 PHE cc_start: 0.8230 (t80) cc_final: 0.8018 (t80) REVERT: B 268 PHE cc_start: 0.8439 (m-80) cc_final: 0.8062 (m-10) REVERT: B 397 ARG cc_start: 0.8521 (ptp-170) cc_final: 0.8193 (mtp180) REVERT: B 424 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7784 (m) REVERT: B 430 LEU cc_start: 0.8446 (tp) cc_final: 0.8111 (tp) REVERT: B 449 ASN cc_start: 0.8214 (t0) cc_final: 0.7992 (t0) REVERT: B 463 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7781 (m) REVERT: B 479 LYS cc_start: 0.8304 (mttm) cc_final: 0.8040 (mttm) REVERT: B 491 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7022 (mm-40) REVERT: B 501 LYS cc_start: 0.8841 (tttm) cc_final: 0.8640 (pttp) REVERT: B 506 LEU cc_start: 0.8644 (mp) cc_final: 0.8331 (mm) REVERT: B 535 PHE cc_start: 0.8078 (m-80) cc_final: 0.7870 (m-80) REVERT: B 569 MET cc_start: 0.6990 (mmm) cc_final: 0.6700 (mmm) outliers start: 142 outliers final: 100 residues processed: 1562 average time/residue: 0.2085 time to fit residues: 511.8827 Evaluate side-chains 1640 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1515 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 558 GLN Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 404 GLN Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 520 ARG Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 518 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 493 ASN Chi-restraints excluded: chain E residue 520 ARG Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 444 TYR Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 518 MET Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain I residue 551 MET Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 0.0010 chunk 216 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 177 optimal weight: 0.0050 chunk 304 optimal weight: 7.9990 chunk 273 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 446 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN G 104 GLN ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 HIS ** F 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 ASN E 127 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN C 468 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.130036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111973 restraints weight = 52601.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116271 restraints weight = 24342.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119045 restraints weight = 13612.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120817 restraints weight = 8629.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122020 restraints weight = 6037.599| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31936 Z= 0.111 Angle : 0.616 18.004 43674 Z= 0.301 Chirality : 0.043 0.225 4764 Planarity : 0.005 0.057 5732 Dihedral : 4.701 64.599 4237 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.01 % Allowed : 30.86 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3686 helix: -0.91 (0.51), residues: 88 sheet: -0.23 (0.18), residues: 858 loop : -0.30 (0.12), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 67 TYR 0.060 0.002 TYR A 561 PHE 0.033 0.001 PHE G 303 TRP 0.053 0.001 TRP C 528 HIS 0.004 0.001 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00259 (31929) covalent geometry : angle 0.61617 (43660) SS BOND : bond 0.00390 ( 7) SS BOND : angle 0.88644 ( 14) hydrogen bonds : bond 0.02736 ( 295) hydrogen bonds : angle 5.78452 ( 567) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7372 Ramachandran restraints generated. 3686 Oldfield, 0 Emsley, 3686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1658 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1526 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7230 (tt0) cc_final: 0.6879 (tp30) REVERT: A 67 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7737 (mmt180) REVERT: A 104 GLN cc_start: 0.8089 (pt0) cc_final: 0.7321 (pt0) REVERT: A 109 TRP cc_start: 0.8572 (m100) cc_final: 0.8305 (m100) REVERT: A 165 TYR cc_start: 0.8175 (m-80) cc_final: 0.7652 (m-80) REVERT: A 182 THR cc_start: 0.8423 (m) cc_final: 0.8095 (t) REVERT: A 192 SER cc_start: 0.7820 (t) cc_final: 0.7580 (t) REVERT: A 200 TRP cc_start: 0.8398 (p90) cc_final: 0.8181 (p90) REVERT: A 207 PRO cc_start: 0.8778 (Cg_exo) cc_final: 0.8549 (Cg_endo) REVERT: A 237 ASP cc_start: 0.7743 (t0) cc_final: 0.7317 (t0) REVERT: A 260 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: A 302 ASN cc_start: 0.8182 (m-40) cc_final: 0.7585 (m110) REVERT: A 312 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8235 (mtmt) REVERT: A 335 GLU cc_start: 0.7111 (tt0) cc_final: 0.6073 (tm-30) REVERT: A 346 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6616 (mt-10) REVERT: A 350 GLN cc_start: 0.7415 (mt0) cc_final: 0.7151 (mp10) REVERT: A 411 GLU cc_start: 0.7654 (mp0) cc_final: 0.7330 (mp0) REVERT: A 414 TRP cc_start: 0.8078 (p90) cc_final: 0.7772 (p90) REVERT: A 443 ASN cc_start: 0.8090 (p0) cc_final: 0.7546 (p0) REVERT: A 446 ASN cc_start: 0.8060 (m110) cc_final: 0.7715 (m110) REVERT: A 473 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6858 (mm-30) REVERT: A 502 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8677 (m) REVERT: A 530 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7817 (ttpp) REVERT: A 554 ASN cc_start: 0.7652 (p0) cc_final: 0.7327 (p0) REVERT: G 50 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: G 51 PHE cc_start: 0.7740 (m-10) cc_final: 0.7472 (m-10) REVERT: G 53 PHE cc_start: 0.5423 (p90) cc_final: 0.4799 (p90) REVERT: G 60 GLU cc_start: 0.7385 (tp30) cc_final: 0.7031 (tp30) REVERT: G 68 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8035 (tt) REVERT: G 83 VAL cc_start: 0.8782 (t) cc_final: 0.8427 (m) REVERT: G 90 THR cc_start: 0.8495 (p) cc_final: 0.8281 (t) REVERT: G 109 TRP cc_start: 0.8416 (m100) cc_final: 0.7997 (m100) REVERT: G 135 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6765 (tp30) REVERT: G 136 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8162 (tp) REVERT: G 137 HIS cc_start: 0.8453 (m90) cc_final: 0.8097 (m170) REVERT: G 144 GLU cc_start: 0.7231 (pm20) cc_final: 0.6963 (pm20) REVERT: G 151 LYS cc_start: 0.7995 (mttm) cc_final: 0.7724 (mmtm) REVERT: G 174 MET cc_start: 0.7795 (mtp) cc_final: 0.7273 (mtp) REVERT: G 185 PHE cc_start: 0.8120 (t80) cc_final: 0.7859 (t80) REVERT: G 193 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6536 (mp0) REVERT: G 213 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7504 (tm-30) REVERT: G 237 ASP cc_start: 0.7417 (t0) cc_final: 0.6941 (t0) REVERT: G 245 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7845 (t) REVERT: G 263 THR cc_start: 0.8562 (m) cc_final: 0.8008 (p) REVERT: G 268 PHE cc_start: 0.8118 (m-80) cc_final: 0.7902 (m-80) REVERT: G 283 ARG cc_start: 0.8296 (mtp180) cc_final: 0.7677 (ptm160) REVERT: G 312 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8202 (mtpp) REVERT: G 327 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6883 (mm-30) REVERT: G 333 PRO cc_start: 0.8881 (Cg_exo) cc_final: 0.8634 (Cg_endo) REVERT: G 335 GLU cc_start: 0.7469 (tt0) cc_final: 0.6929 (tt0) REVERT: G 345 PHE cc_start: 0.7887 (m-80) cc_final: 0.7525 (m-80) REVERT: G 382 ARG cc_start: 0.5344 (mtm180) cc_final: 0.4964 (mtm180) REVERT: G 398 PHE cc_start: 0.8657 (p90) cc_final: 0.8257 (p90) REVERT: G 434 ASP cc_start: 0.7616 (m-30) cc_final: 0.7370 (t0) REVERT: G 453 PRO cc_start: 0.8851 (Cg_exo) cc_final: 0.8574 (Cg_endo) REVERT: G 457 LEU cc_start: 0.8257 (mt) cc_final: 0.8037 (mt) REVERT: G 464 TYR cc_start: 0.7950 (t80) cc_final: 0.7533 (t80) REVERT: G 501 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8140 (ttpp) REVERT: G 505 ASN cc_start: 0.7692 (t0) cc_final: 0.6788 (t0) REVERT: G 509 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7559 (mm-30) REVERT: G 518 MET cc_start: 0.7710 (ptp) cc_final: 0.7427 (ptp) REVERT: G 521 ILE cc_start: 0.8769 (mt) cc_final: 0.8470 (mt) REVERT: G 528 TRP cc_start: 0.8231 (m100) cc_final: 0.7656 (m100) REVERT: G 530 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7301 (ttpp) REVERT: G 556 ASP cc_start: 0.7574 (m-30) cc_final: 0.7309 (t0) REVERT: G 560 ASN cc_start: 0.8171 (m110) cc_final: 0.7879 (m-40) REVERT: F 72 ASN cc_start: 0.8462 (t0) cc_final: 0.8133 (t0) REVERT: F 73 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7044 (ttp) REVERT: F 80 ARG cc_start: 0.4135 (tpt90) cc_final: 0.1525 (mmt180) REVERT: F 81 ARG cc_start: 0.5507 (ptp-170) cc_final: 0.4929 (ptp-170) REVERT: F 109 TRP cc_start: 0.8368 (m100) cc_final: 0.7881 (m100) REVERT: F 120 TRP cc_start: 0.8419 (m100) cc_final: 0.7872 (m100) REVERT: F 125 ASP cc_start: 0.7560 (m-30) cc_final: 0.7156 (m-30) REVERT: F 135 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: F 143 GLN cc_start: 0.8084 (mt0) cc_final: 0.7831 (mt0) REVERT: F 144 GLU cc_start: 0.7332 (pm20) cc_final: 0.7013 (pm20) REVERT: F 151 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7538 (mmmm) REVERT: F 167 ASN cc_start: 0.8309 (m110) cc_final: 0.7911 (m-40) REVERT: F 193 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: F 201 LYS cc_start: 0.8029 (mmpt) cc_final: 0.7616 (mmpt) REVERT: F 213 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7168 (tm-30) REVERT: F 237 ASP cc_start: 0.8149 (t0) cc_final: 0.7909 (t0) REVERT: F 245 THR cc_start: 0.7957 (t) cc_final: 0.7609 (p) REVERT: F 266 PHE cc_start: 0.8235 (t80) cc_final: 0.7924 (t80) REVERT: F 279 TRP cc_start: 0.8393 (p-90) cc_final: 0.8030 (p-90) REVERT: F 327 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7133 (mm-30) REVERT: F 336 VAL cc_start: 0.8782 (t) cc_final: 0.8392 (p) REVERT: F 353 PHE cc_start: 0.7326 (p90) cc_final: 0.7083 (p90) REVERT: F 419 ASN cc_start: 0.8526 (m110) cc_final: 0.8203 (m110) REVERT: F 439 LYS cc_start: 0.7953 (mmtp) cc_final: 0.7535 (mmtp) REVERT: F 473 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7164 (tm-30) REVERT: F 474 PHE cc_start: 0.8044 (m-10) cc_final: 0.7412 (m-10) REVERT: F 475 ASP cc_start: 0.8030 (t0) cc_final: 0.7273 (t0) REVERT: F 492 ASN cc_start: 0.8687 (p0) cc_final: 0.8368 (p0) REVERT: F 497 GLN cc_start: 0.8368 (mt0) cc_final: 0.8003 (mt0) REVERT: F 501 LYS cc_start: 0.8555 (ttpp) cc_final: 0.7995 (pttp) REVERT: F 518 MET cc_start: 0.7720 (ptp) cc_final: 0.7387 (ptp) REVERT: F 520 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7413 (mtm110) REVERT: F 532 LYS cc_start: 0.8494 (ttmm) cc_final: 0.8062 (ttmm) REVERT: F 533 LEU cc_start: 0.8353 (tp) cc_final: 0.7914 (tp) REVERT: F 562 VAL cc_start: 0.8634 (p) cc_final: 0.8412 (m) REVERT: F 577 GLN cc_start: 0.8031 (mt0) cc_final: 0.7662 (mt0) REVERT: D 46 ASN cc_start: 0.8012 (t0) cc_final: 0.7459 (t0) REVERT: D 50 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6506 (tm-30) REVERT: D 70 HIS cc_start: 0.7703 (t-90) cc_final: 0.7467 (t-90) REVERT: D 73 MET cc_start: 0.8219 (ptt) cc_final: 0.7930 (ptm) REVERT: D 107 THR cc_start: 0.8442 (m) cc_final: 0.7777 (p) REVERT: D 142 GLU cc_start: 0.7648 (pt0) cc_final: 0.7413 (pt0) REVERT: D 144 GLU cc_start: 0.7231 (pm20) cc_final: 0.6593 (pm20) REVERT: D 174 MET cc_start: 0.7615 (mtp) cc_final: 0.7115 (mtp) REVERT: D 190 MET cc_start: 0.7828 (mmm) cc_final: 0.7499 (mmm) REVERT: D 209 ARG cc_start: 0.4082 (OUTLIER) cc_final: 0.3018 (pmt170) REVERT: D 256 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7682 (mtm-85) REVERT: D 565 ASN cc_start: 0.7784 (m-40) cc_final: 0.7583 (m-40) REVERT: E 95 ASN cc_start: 0.8037 (t0) cc_final: 0.7633 (t0) REVERT: E 126 TRP cc_start: 0.8684 (t-100) cc_final: 0.8432 (t-100) REVERT: E 142 GLU cc_start: 0.7571 (pt0) cc_final: 0.6545 (pt0) REVERT: E 163 LYS cc_start: 0.7973 (mppt) cc_final: 0.7543 (mppt) REVERT: E 209 ARG cc_start: 0.5089 (OUTLIER) cc_final: 0.4478 (ptt180) REVERT: E 210 TYR cc_start: 0.8522 (p90) cc_final: 0.8254 (p90) REVERT: E 213 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7705 (tm-30) REVERT: E 237 ASP cc_start: 0.7468 (t0) cc_final: 0.7198 (t0) REVERT: E 256 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7401 (mtp85) REVERT: E 266 PHE cc_start: 0.8196 (t80) cc_final: 0.7851 (t80) REVERT: E 335 GLU cc_start: 0.6870 (tm-30) cc_final: 0.6244 (tm-30) REVERT: E 377 ARG cc_start: 0.5259 (mtt180) cc_final: 0.4878 (mtt180) REVERT: E 387 LYS cc_start: 0.8732 (tptm) cc_final: 0.8416 (tptm) REVERT: E 400 TYR cc_start: 0.8003 (t80) cc_final: 0.7323 (t80) REVERT: E 404 GLN cc_start: 0.8038 (pt0) cc_final: 0.7435 (pt0) REVERT: E 430 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7640 (tt) REVERT: E 451 TYR cc_start: 0.3687 (OUTLIER) cc_final: 0.3316 (t80) REVERT: E 464 TYR cc_start: 0.8060 (t80) cc_final: 0.7472 (t80) REVERT: E 479 LYS cc_start: 0.8336 (mptt) cc_final: 0.7941 (mptt) REVERT: E 501 LYS cc_start: 0.8089 (tttt) cc_final: 0.7655 (tttt) REVERT: E 520 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7441 (mtp85) REVERT: E 526 ASP cc_start: 0.6505 (p0) cc_final: 0.6080 (p0) REVERT: E 530 LYS cc_start: 0.8056 (tmtt) cc_final: 0.7484 (tttt) REVERT: E 532 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7570 (ttpt) REVERT: E 538 LYS cc_start: 0.7962 (ttmm) cc_final: 0.7664 (mtpp) REVERT: E 552 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7562 (t) REVERT: E 560 ASN cc_start: 0.8300 (m-40) cc_final: 0.8055 (m110) REVERT: I 52 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8103 (ttmm) REVERT: I 82 VAL cc_start: 0.8205 (t) cc_final: 0.7867 (p) REVERT: I 95 ASN cc_start: 0.8246 (m-40) cc_final: 0.7818 (m-40) REVERT: I 109 TRP cc_start: 0.8610 (m100) cc_final: 0.7918 (m100) REVERT: I 144 GLU cc_start: 0.7756 (pt0) cc_final: 0.7463 (pt0) REVERT: I 178 ASP cc_start: 0.6569 (t0) cc_final: 0.6267 (t0) REVERT: I 193 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7034 (mp0) REVERT: I 214 TRP cc_start: -0.1720 (OUTLIER) cc_final: -0.4184 (p90) REVERT: I 269 ASP cc_start: 0.6860 (p0) cc_final: 0.6496 (p0) REVERT: I 274 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.8002 (tpp80) REVERT: I 279 TRP cc_start: 0.8892 (p-90) cc_final: 0.8636 (p-90) REVERT: I 318 GLN cc_start: 0.8471 (mt0) cc_final: 0.8078 (mm110) REVERT: I 346 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6559 (mm-30) REVERT: I 377 ARG cc_start: 0.5023 (mtt180) cc_final: 0.4687 (mtt180) REVERT: I 386 GLN cc_start: 0.7624 (tt0) cc_final: 0.7213 (tt0) REVERT: I 446 ASN cc_start: 0.8399 (m110) cc_final: 0.8149 (m110) REVERT: I 485 ASN cc_start: 0.7294 (p0) cc_final: 0.6869 (p0) REVERT: I 501 LYS cc_start: 0.8594 (ttpt) cc_final: 0.7800 (ttpt) REVERT: I 532 LYS cc_start: 0.8583 (ttmm) cc_final: 0.8232 (ttpp) REVERT: I 577 GLN cc_start: 0.8082 (mt0) cc_final: 0.7802 (mt0) REVERT: I 582 LYS cc_start: 0.8326 (pttm) cc_final: 0.8059 (pttm) REVERT: C 104 GLN cc_start: 0.7933 (pt0) cc_final: 0.7570 (pt0) REVERT: C 193 GLU cc_start: 0.7083 (tp30) cc_final: 0.5990 (tp30) REVERT: C 206 THR cc_start: 0.7888 (t) cc_final: 0.7454 (m) REVERT: C 211 TYR cc_start: 0.6982 (m-80) cc_final: 0.6359 (m-80) REVERT: C 378 TYR cc_start: 0.2796 (OUTLIER) cc_final: 0.0966 (m-80) REVERT: C 501 LYS cc_start: 0.8656 (tttp) cc_final: 0.8078 (tttm) REVERT: C 509 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: C 564 SER cc_start: 0.7904 (t) cc_final: 0.7598 (t) REVERT: B 47 ASN cc_start: 0.8651 (t0) cc_final: 0.8446 (t0) REVERT: B 52 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8008 (ttmm) REVERT: B 53 PHE cc_start: 0.8373 (m-80) cc_final: 0.7760 (p90) REVERT: B 65 SER cc_start: 0.8319 (t) cc_final: 0.7994 (t) REVERT: B 83 VAL cc_start: 0.8773 (t) cc_final: 0.8496 (m) REVERT: B 117 TRP cc_start: 0.7885 (m100) cc_final: 0.7401 (m100) REVERT: B 133 MET cc_start: 0.6871 (mmt) cc_final: 0.6628 (mmt) REVERT: B 151 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8284 (mttm) REVERT: B 182 THR cc_start: 0.8303 (m) cc_final: 0.7978 (p) REVERT: B 201 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8537 (mtmt) REVERT: B 268 PHE cc_start: 0.8414 (m-80) cc_final: 0.8077 (m-10) REVERT: B 397 ARG cc_start: 0.8490 (ptp-170) cc_final: 0.8197 (mtp180) REVERT: B 424 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7719 (m) REVERT: B 430 LEU cc_start: 0.8439 (tp) cc_final: 0.8108 (tp) REVERT: B 449 ASN cc_start: 0.8220 (t0) cc_final: 0.8006 (t0) REVERT: B 463 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7714 (m) REVERT: B 479 LYS cc_start: 0.8276 (mttm) cc_final: 0.8001 (mttm) REVERT: B 491 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7033 (mm-40) REVERT: B 506 LEU cc_start: 0.8599 (mp) cc_final: 0.8299 (mm) REVERT: B 569 MET cc_start: 0.6982 (mmm) cc_final: 0.6709 (mmm) outliers start: 132 outliers final: 84 residues processed: 1569 average time/residue: 0.2053 time to fit residues: 507.7211 Evaluate side-chains 1612 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1502 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 273 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 404 GLN Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain F residue 55 GLU Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 321 ASN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 520 ARG Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 451 TYR Chi-restraints excluded: chain E residue 520 ARG Chi-restraints excluded: chain E residue 552 SER Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 473 GLU Chi-restraints excluded: chain I residue 497 GLN Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 521 ILE Chi-restraints excluded: chain I residue 551 MET Chi-restraints excluded: chain I residue 570 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 151 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 2 optimal weight: 4.9990 chunk 341 optimal weight: 0.7980 chunk 239 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 331 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G 384 HIS G 386 GLN G 416 GLN G 426 ASN ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN E 127 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 ASN I 147 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 GLN ** B 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111965 restraints weight = 52603.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116309 restraints weight = 24457.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119054 restraints weight = 13691.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120849 restraints weight = 8686.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121964 restraints weight = 6063.361| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 31936 Z= 0.169 Angle : 0.721 59.199 43674 Z= 0.386 Chirality : 0.045 0.742 4764 Planarity : 0.005 0.099 5732 Dihedral : 4.704 64.617 4237 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.64 % Allowed : 31.56 % Favored : 64.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3686 helix: -0.91 (0.51), residues: 88 sheet: -0.22 (0.18), residues: 858 loop : -0.31 (0.12), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.041 0.001 ARG A 216 TYR 0.055 0.002 TYR A 561 PHE 0.026 0.002 PHE G 303 TRP 0.044 0.002 TRP C 528 HIS 0.007 0.001 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00370 (31929) covalent geometry : angle 0.72127 (43660) SS BOND : bond 0.00346 ( 7) SS BOND : angle 0.90123 ( 14) hydrogen bonds : bond 0.02763 ( 295) hydrogen bonds : angle 5.77691 ( 567) =============================================================================== Job complete usr+sys time: 8522.56 seconds wall clock time: 146 minutes 50.21 seconds (8810.21 seconds total)