Starting phenix.real_space_refine on Thu Jun 26 11:17:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utp_26786/06_2025/7utp_26786.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utp_26786/06_2025/7utp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7utp_26786/06_2025/7utp_26786.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utp_26786/06_2025/7utp_26786.map" model { file = "/net/cci-nas-00/data/ceres_data/7utp_26786/06_2025/7utp_26786.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utp_26786/06_2025/7utp_26786.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 20.11, per 1000 atoms: 0.65 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: 7.83 Conformation dependent library (CDL) restraints added in 3.9 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: 4.52 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: 12.51 Time building geometry restraints manager: 9.38 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: 0.770 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: 0.060 Extract box with map and model: 1.410 Check model and map are aligned: 0.250 Set scattering table: 0.300 Process input model: 72.870 Find NCS groups from input model: 4.140 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.039 0.002 TRP F 109 HIS 0.020 0.002 HIS F 102 PHE 0.068 0.004 PHE E 243 TYR 0.098 0.003 TYR E 464 ARG 0.017 0.002 ARG F 481 Details of bonding type rmsd hydrogen bonds : bond 0.28350 ( 295) hydrogen bonds : angle 9.56841 ( 567) SS BOND : bond 0.02517 ( 7) SS BOND : angle 3.12519 ( 14) covalent geometry : bond 0.00694 (31929) covalent geometry : angle 1.10438 (43660) *********************** 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 : 3.227 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: 0.6982 (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: 0.6622 (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: 0.7491 (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: 0.7481 (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: 0.8119 (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: 0.7004 (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: 0.8074 (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: 0.6926 (mm-40) REVERT: I 538 LYS cc_start: 0.8088 (tppt) cc_final: 0.7777 (mmtt) REVERT: C 67 ARG cc_start: 0.6816 (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: 0.6989 (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: 0.7947 (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: 0.7813 (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: 0.5473 time to fit residues: 1308.1074 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 : 3.637 ------------------------------------------------------------------------------- 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 331 optimal weight: 0.0970 chunk 297 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 228 optimal weight: 10.0000 chunk 355 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 234 HIS A 242 GLN A 277 HIS A 302 ASN A 426 ASN A 491 GLN A 546 ASN ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 GLN ** 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 F 497 GLN F 565 ASN E 48 GLN E 143 GLN E 493 ASN E 543 HIS I 383 GLN I 483 HIS C 102 HIS B 115 ASN B 468 GLN B 493 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108598 restraints weight = 52417.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.112912 restraints weight = 24243.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115683 restraints weight = 13583.724| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 31936 Z= 0.136 Angle : 0.615 8.725 43674 Z= 0.314 Chirality : 0.044 0.200 4764 Planarity : 0.005 0.101 5732 Dihedral : 6.233 84.163 4257 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.64 % Allowed : 21.09 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 3686 helix: -1.61 (0.43), residues: 100 sheet: -0.76 (0.17), residues: 871 loop : -0.51 (0.12), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 58 HIS 0.010 0.001 HIS F 403 PHE 0.033 0.002 PHE A 197 TYR 0.028 0.001 TYR A 561 ARG 0.012 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 295) hydrogen bonds : angle 6.41518 ( 567) SS BOND : bond 0.00538 ( 7) SS BOND : angle 1.27520 ( 14) covalent geometry : bond 0.00310 (31929) covalent geometry : angle 0.61516 (43660) *********************** 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 1660 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1540 time to evaluate : 5.104 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 47 ASN cc_start: 0.8020 (t0) cc_final: 0.7776 (t0) REVERT: A 60 GLU cc_start: 0.7343 (tt0) cc_final: 0.7038 (tp30) REVERT: A 104 GLN cc_start: 0.8227 (pt0) cc_final: 0.7786 (pt0) REVERT: A 177 LEU cc_start: 0.8505 (tt) cc_final: 0.8282 (tp) REVERT: A 200 TRP cc_start: 0.8299 (p90) cc_final: 0.8023 (p90) REVERT: A 214 TRP cc_start: 0.8429 (p90) cc_final: 0.7563 (p90) REVERT: A 215 ASP cc_start: 0.7332 (m-30) cc_final: 0.7014 (m-30) REVERT: A 237 ASP cc_start: 0.7895 (t0) cc_final: 0.7390 (t0) REVERT: A 256 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7709 (mmt90) REVERT: A 260 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7063 (tt0) REVERT: A 302 ASN cc_start: 0.8082 (m-40) cc_final: 0.7539 (m110) REVERT: A 312 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8182 (mtmt) REVERT: A 331 MET cc_start: 0.7653 (ttm) cc_final: 0.7432 (ttm) REVERT: A 335 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6248 (tm-30) REVERT: A 350 GLN cc_start: 0.7512 (mt0) cc_final: 0.7092 (mp10) REVERT: A 380 PHE cc_start: 0.7584 (p90) cc_final: 0.7282 (p90) REVERT: A 396 GLU cc_start: 0.7474 (tt0) cc_final: 0.7117 (tt0) REVERT: A 414 TRP cc_start: 0.7952 (p90) cc_final: 0.7496 (p90) REVERT: A 425 THR cc_start: 0.8175 (p) cc_final: 0.7965 (p) REVERT: A 446 ASN cc_start: 0.8163 (m110) cc_final: 0.7957 (m110) REVERT: A 473 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 501 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8339 (ttpt) REVERT: A 530 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7910 (ttpp) REVERT: A 540 ARG cc_start: 0.8234 (ptm-80) cc_final: 0.7932 (ptm160) REVERT: A 569 MET cc_start: 0.6816 (mmm) cc_final: 0.6235 (tpp) REVERT: G 50 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6601 (mp0) REVERT: G 54 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8402 (mt) REVERT: G 62 THR cc_start: 0.8427 (m) cc_final: 0.7836 (t) REVERT: G 109 TRP cc_start: 0.8418 (m100) cc_final: 0.7935 (m100) REVERT: G 174 MET cc_start: 0.7762 (mtp) cc_final: 0.7103 (mtp) REVERT: G 193 GLU cc_start: 0.7236 (mp0) cc_final: 0.6796 (mp0) REVERT: G 213 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7131 (tm-30) REVERT: G 246 ILE cc_start: 0.8569 (mm) cc_final: 0.8281 (mm) REVERT: G 283 ARG cc_start: 0.8485 (mtp180) cc_final: 0.8176 (mtp180) REVERT: G 327 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6832 (mm-30) REVERT: G 335 GLU cc_start: 0.7287 (tt0) cc_final: 0.6929 (tt0) REVERT: G 342 TYR cc_start: 0.7722 (p90) cc_final: 0.7142 (p90) REVERT: G 345 PHE cc_start: 0.8019 (m-80) cc_final: 0.7486 (m-80) REVERT: G 398 PHE cc_start: 0.8769 (p90) cc_final: 0.8396 (p90) REVERT: G 464 TYR cc_start: 0.8048 (t80) cc_final: 0.7795 (t80) REVERT: G 479 LYS cc_start: 0.8720 (mmtm) cc_final: 0.8377 (mmtm) REVERT: G 501 LYS cc_start: 0.8498 (ttpp) cc_final: 0.7940 (ttpp) REVERT: G 518 MET cc_start: 0.7801 (ptp) cc_final: 0.7491 (ptp) REVERT: G 530 LYS cc_start: 0.8182 (ttpp) cc_final: 0.7886 (ttpp) REVERT: G 560 ASN cc_start: 0.8264 (m-40) cc_final: 0.7928 (m-40) REVERT: F 73 MET cc_start: 0.7869 (ttp) cc_final: 0.7332 (ttt) REVERT: F 80 ARG cc_start: 0.3800 (tpt90) cc_final: 0.1737 (tpt170) REVERT: F 109 TRP cc_start: 0.8509 (m100) cc_final: 0.8122 (m100) REVERT: F 120 TRP cc_start: 0.8417 (m100) cc_final: 0.7764 (m100) REVERT: F 135 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: F 144 GLU cc_start: 0.7189 (pm20) cc_final: 0.6975 (pm20) REVERT: F 151 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7747 (mmmm) REVERT: F 165 TYR cc_start: 0.8582 (m-80) cc_final: 0.8332 (m-80) REVERT: F 167 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7962 (m-40) REVERT: F 197 PHE cc_start: 0.8223 (m-10) cc_final: 0.7573 (m-80) REVERT: F 201 LYS cc_start: 0.8131 (mmpt) cc_final: 0.7727 (mmpt) REVERT: F 216 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7925 (ptm160) REVERT: F 266 PHE cc_start: 0.8293 (t80) cc_final: 0.7785 (t80) REVERT: F 279 TRP cc_start: 0.8429 (p-90) cc_final: 0.8216 (p-90) REVERT: F 296 GLN cc_start: 0.7266 (mp10) cc_final: 0.7057 (mp10) REVERT: F 302 ASN cc_start: 0.8036 (m-40) cc_final: 0.7209 (p0) REVERT: F 308 VAL cc_start: 0.8795 (p) cc_final: 0.8592 (m) REVERT: F 335 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6668 (tp30) REVERT: F 346 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6783 (mt-10) REVERT: F 386 GLN cc_start: 0.7226 (tt0) cc_final: 0.7009 (tt0) REVERT: F 409 TYR cc_start: 0.8322 (t80) cc_final: 0.7973 (t80) REVERT: F 451 TYR cc_start: 0.8497 (t80) cc_final: 0.8087 (t80) REVERT: F 470 TRP cc_start: 0.8074 (p90) cc_final: 0.7835 (p90) REVERT: F 520 ARG cc_start: 0.7553 (mtt90) cc_final: 0.7128 (mtt90) REVERT: F 532 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8045 (ttmm) REVERT: F 533 LEU cc_start: 0.8464 (tp) cc_final: 0.7269 (tp) REVERT: F 551 MET cc_start: 0.7357 (ttt) cc_final: 0.6966 (ttt) REVERT: F 562 VAL cc_start: 0.8634 (p) cc_final: 0.8407 (m) REVERT: F 565 ASN cc_start: 0.7783 (m-40) cc_final: 0.7501 (m-40) REVERT: F 575 LYS cc_start: 0.7519 (mmtt) cc_final: 0.7018 (mmtt) REVERT: D 48 GLN cc_start: 0.8044 (mt0) cc_final: 0.7810 (mt0) REVERT: D 49 THR cc_start: 0.7849 (m) cc_final: 0.7435 (p) REVERT: D 50 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6607 (tm-30) REVERT: D 67 ARG cc_start: 0.7857 (mmt-90) cc_final: 0.7627 (mmt-90) REVERT: D 73 MET cc_start: 0.8182 (ptt) cc_final: 0.7550 (ptp) REVERT: D 174 MET cc_start: 0.7666 (mtp) cc_final: 0.7228 (mtp) REVERT: D 256 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7757 (mtm-85) REVERT: D 510 TYR cc_start: 0.8425 (t80) cc_final: 0.8127 (t80) REVERT: E 51 PHE cc_start: 0.8439 (m-80) cc_final: 0.8184 (m-80) REVERT: E 60 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6807 (tm-30) REVERT: E 106 VAL cc_start: 0.7988 (t) cc_final: 0.7616 (p) REVERT: E 113 ASP cc_start: 0.6970 (t0) cc_final: 0.6729 (t0) REVERT: E 142 GLU cc_start: 0.7735 (pt0) cc_final: 0.6832 (pt0) REVERT: E 163 LYS cc_start: 0.7737 (mppt) cc_final: 0.7236 (mppt) REVERT: E 210 TYR cc_start: 0.8590 (p90) cc_final: 0.8182 (p90) REVERT: E 213 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7785 (tm-30) REVERT: E 236 THR cc_start: 0.8221 (t) cc_final: 0.8010 (t) REVERT: E 237 ASP cc_start: 0.7722 (t0) cc_final: 0.7414 (t0) REVERT: E 240 ASP cc_start: 0.7302 (m-30) cc_final: 0.7094 (m-30) REVERT: E 245 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7941 (p) REVERT: E 247 GLU cc_start: 0.7607 (mp0) cc_final: 0.7173 (mp0) REVERT: E 266 PHE cc_start: 0.8173 (t80) cc_final: 0.7931 (t80) REVERT: E 302 ASN cc_start: 0.8414 (t0) cc_final: 0.8153 (p0) REVERT: E 342 TYR cc_start: 0.7257 (p90) cc_final: 0.6906 (p90) REVERT: E 387 LYS cc_start: 0.8687 (tptm) cc_final: 0.8205 (tptm) REVERT: E 400 TYR cc_start: 0.8084 (t80) cc_final: 0.7299 (t80) REVERT: E 464 TYR cc_start: 0.7888 (t80) cc_final: 0.7409 (t80) REVERT: E 471 ASP cc_start: 0.6151 (t0) cc_final: 0.5847 (t0) REVERT: E 479 LYS cc_start: 0.8325 (mptt) cc_final: 0.7963 (mptt) REVERT: E 483 HIS cc_start: 0.7776 (m170) cc_final: 0.6975 (m-70) REVERT: E 501 LYS cc_start: 0.8077 (tttt) cc_final: 0.7274 (tttt) REVERT: E 520 ARG cc_start: 0.7574 (mtp85) cc_final: 0.6987 (mtp85) REVERT: E 530 LYS cc_start: 0.7956 (tmtt) cc_final: 0.7354 (tttt) REVERT: E 532 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7701 (ttpt) REVERT: E 538 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7625 (ttmm) REVERT: E 582 LYS cc_start: 0.6450 (pmtt) cc_final: 0.6062 (pmtt) REVERT: I 95 ASN cc_start: 0.8302 (m-40) cc_final: 0.8055 (m-40) REVERT: I 96 MET cc_start: 0.4611 (OUTLIER) cc_final: 0.4224 (ptt) REVERT: I 101 ILE cc_start: 0.8410 (mt) cc_final: 0.8151 (mt) REVERT: I 145 ILE cc_start: 0.8867 (mm) cc_final: 0.8547 (mm) REVERT: I 237 ASP cc_start: 0.7274 (t0) cc_final: 0.6844 (t0) REVERT: I 265 THR cc_start: 0.7446 (p) cc_final: 0.7189 (p) REVERT: I 269 ASP cc_start: 0.6891 (p0) cc_final: 0.6300 (p0) REVERT: I 318 GLN cc_start: 0.8549 (mt0) cc_final: 0.8124 (mm-40) REVERT: I 485 ASN cc_start: 0.7145 (p0) cc_final: 0.6475 (p0) REVERT: I 491 GLN cc_start: 0.7358 (mm-40) cc_final: 0.6753 (mm-40) REVERT: I 529 TRP cc_start: 0.7850 (t60) cc_final: 0.7610 (t60) REVERT: I 565 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7824 (t0) REVERT: C 68 LEU cc_start: 0.8034 (tp) cc_final: 0.7563 (tp) REVERT: C 73 MET cc_start: 0.8104 (ptt) cc_final: 0.7712 (ptt) REVERT: C 77 GLU cc_start: 0.6797 (tp30) cc_final: 0.6225 (tp30) REVERT: C 115 ASN cc_start: 0.7668 (t0) cc_final: 0.6480 (t0) REVERT: C 147 ASN cc_start: 0.8373 (t0) cc_final: 0.7971 (t0) REVERT: C 193 GLU cc_start: 0.6835 (tp30) cc_final: 0.6193 (tp30) REVERT: C 200 TRP cc_start: 0.8616 (p90) cc_final: 0.8346 (p90) REVERT: C 509 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6958 (tm-30) REVERT: C 528 TRP cc_start: 0.8565 (m100) cc_final: 0.7956 (m100) REVERT: C 529 TRP cc_start: 0.8845 (t60) cc_final: 0.8643 (t60) REVERT: B 53 PHE cc_start: 0.8208 (m-80) cc_final: 0.7815 (p90) REVERT: B 80 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7614 (mmm-85) REVERT: B 117 TRP cc_start: 0.8073 (m100) cc_final: 0.7609 (m100) REVERT: B 125 ASP cc_start: 0.7311 (m-30) cc_final: 0.7047 (m-30) REVERT: B 152 THR cc_start: 0.8525 (m) cc_final: 0.8001 (p) REVERT: B 193 GLU cc_start: 0.7552 (tt0) cc_final: 0.6930 (tt0) REVERT: B 216 ARG cc_start: 0.7767 (tpt-90) cc_final: 0.7411 (tpt-90) REVERT: B 240 ASP cc_start: 0.7187 (m-30) cc_final: 0.6957 (m-30) REVERT: B 256 ARG cc_start: 0.7874 (mtp180) cc_final: 0.7497 (mtp85) REVERT: B 400 TYR cc_start: 0.7743 (t80) cc_final: 0.7433 (t80) REVERT: B 415 ILE cc_start: 0.8365 (mt) cc_final: 0.8117 (mt) REVERT: B 416 GLN cc_start: 0.7939 (tt0) cc_final: 0.7652 (mp10) REVERT: B 417 ASN cc_start: 0.7936 (t0) cc_final: 0.7612 (t0) REVERT: B 491 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7204 (mm-40) REVERT: B 510 TYR cc_start: 0.8853 (t80) cc_final: 0.8571 (t80) REVERT: B 569 MET cc_start: 0.7067 (mmm) cc_final: 0.6760 (mmm) REVERT: B 575 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7449 (mmtt) outliers start: 120 outliers final: 68 residues processed: 1565 average time/residue: 0.6742 time to fit residues: 1650.3414 Evaluate side-chains 1579 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1498 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 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 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 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 497 GLN Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 54 LEU 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 206 THR Chi-restraints excluded: chain G residue 225 THR 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 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 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 167 ASN Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS 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 50 GLU Chi-restraints excluded: chain E residue 70 HIS Chi-restraints excluded: chain E residue 82 VAL 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 319 MET 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 206 THR Chi-restraints excluded: chain I residue 232 ILE Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 335 GLU 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 565 ASN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 509 GLU 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 549 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 170 optimal weight: 0.0670 chunk 68 optimal weight: 20.0000 chunk 348 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 353 optimal weight: 9.9990 chunk 219 optimal weight: 0.9980 chunk 194 optimal weight: 0.0170 chunk 232 optimal weight: 30.0000 chunk 139 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 overall best weight: 3.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 282 ASN A 384 HIS ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 ASN G 468 GLN G 497 GLN G 505 ASN F 93 ASN ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN E 403 HIS I 48 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 403 HIS C 147 ASN ** C 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 HIS B 549 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106737 restraints weight = 52643.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111038 restraints weight = 24418.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113782 restraints weight = 13683.289| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 31936 Z= 0.196 Angle : 0.604 13.059 43674 Z= 0.306 Chirality : 0.045 0.191 4764 Planarity : 0.005 0.073 5732 Dihedral : 5.634 71.975 4241 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.37 % Allowed : 22.40 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.13), residues: 3686 helix: -1.54 (0.39), residues: 124 sheet: -0.63 (0.17), residues: 865 loop : -0.44 (0.12), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 279 HIS 0.006 0.001 HIS B 222 PHE 0.030 0.002 PHE A 266 TYR 0.022 0.002 TYR I 342 ARG 0.007 0.001 ARG F 481 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 295) hydrogen bonds : angle 6.12585 ( 567) SS BOND : bond 0.00608 ( 7) SS BOND : angle 1.28817 ( 14) covalent geometry : bond 0.00422 (31929) covalent geometry : angle 0.60364 (43660) *********************** 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 1686 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1542 time to evaluate : 3.238 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: 0.8057 (OUTLIER) cc_final: 0.7776 (t0) REVERT: A 60 GLU cc_start: 0.7471 (tt0) cc_final: 0.7159 (tp30) REVERT: A 79 TYR cc_start: 0.8399 (m-80) cc_final: 0.7895 (m-80) REVERT: A 104 GLN cc_start: 0.8174 (pt0) cc_final: 0.7595 (pt0) REVERT: A 109 TRP cc_start: 0.8668 (m100) cc_final: 0.8078 (m100) REVERT: A 147 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7923 (t0) REVERT: A 163 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8450 (mmmt) REVERT: A 177 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8277 (tp) REVERT: A 192 SER cc_start: 0.7818 (t) cc_final: 0.7607 (t) REVERT: A 214 TRP cc_start: 0.8546 (p90) cc_final: 0.7400 (p90) REVERT: A 215 ASP cc_start: 0.7481 (m-30) cc_final: 0.7121 (m-30) REVERT: A 216 ARG cc_start: 0.7024 (ttt-90) cc_final: 0.6765 (ttt180) REVERT: A 237 ASP cc_start: 0.7873 (t0) cc_final: 0.7408 (t0) REVERT: A 244 TYR cc_start: 0.7736 (m-80) cc_final: 0.7239 (m-80) REVERT: A 247 GLU cc_start: 0.7677 (mp0) cc_final: 0.7282 (mp0) REVERT: A 259 ASP cc_start: 0.6546 (p0) cc_final: 0.6309 (p0) REVERT: A 260 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: A 302 ASN cc_start: 0.8222 (m-40) cc_final: 0.7523 (m110) REVERT: A 312 LYS cc_start: 0.8487 (mtmt) cc_final: 0.8168 (mtmt) REVERT: A 335 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6145 (tm-30) REVERT: A 350 GLN cc_start: 0.7478 (mt0) cc_final: 0.7188 (mp10) REVERT: A 380 PHE cc_start: 0.7602 (p90) cc_final: 0.7293 (p90) REVERT: A 411 GLU cc_start: 0.7835 (mp0) cc_final: 0.7373 (mp0) REVERT: A 414 TRP cc_start: 0.8066 (p90) cc_final: 0.7655 (p90) REVERT: A 473 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6772 (mm-30) REVERT: A 495 PRO cc_start: 0.7274 (Cg_exo) cc_final: 0.7033 (Cg_endo) REVERT: A 501 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8021 (ttpp) REVERT: A 524 TYR cc_start: 0.8544 (p90) cc_final: 0.8225 (p90) REVERT: G 60 GLU cc_start: 0.7563 (tp30) cc_final: 0.7131 (tp30) REVERT: G 62 THR cc_start: 0.8456 (m) cc_final: 0.7888 (t) REVERT: G 109 TRP cc_start: 0.8431 (m100) cc_final: 0.8096 (m100) REVERT: G 137 HIS cc_start: 0.8573 (m170) cc_final: 0.8361 (m170) REVERT: G 144 GLU cc_start: 0.7470 (pm20) cc_final: 0.7000 (pm20) REVERT: G 174 MET cc_start: 0.7922 (mtp) cc_final: 0.7232 (mtp) REVERT: G 191 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.7770 (mtt180) REVERT: G 193 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6714 (mp0) REVERT: G 200 TRP cc_start: 0.8405 (p90) cc_final: 0.8196 (p90) REVERT: G 213 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7267 (tm-30) REVERT: G 266 PHE cc_start: 0.8226 (t80) cc_final: 0.7932 (t80) REVERT: G 283 ARG cc_start: 0.8551 (mtp180) cc_final: 0.8079 (mtp180) REVERT: G 327 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6985 (mm-30) REVERT: G 335 GLU cc_start: 0.7320 (tt0) cc_final: 0.6951 (tt0) REVERT: G 342 TYR cc_start: 0.7787 (p90) cc_final: 0.7270 (p90) REVERT: G 345 PHE cc_start: 0.8034 (m-80) cc_final: 0.7519 (m-80) REVERT: G 378 TYR cc_start: 0.8112 (m-80) cc_final: 0.7301 (m-80) REVERT: G 398 PHE cc_start: 0.8750 (p90) cc_final: 0.8253 (p90) REVERT: G 425 THR cc_start: 0.8076 (p) cc_final: 0.7838 (p) REVERT: G 464 TYR cc_start: 0.8157 (t80) cc_final: 0.7874 (t80) REVERT: G 479 LYS cc_start: 0.8697 (mmtm) cc_final: 0.8426 (mmtm) REVERT: G 501 LYS cc_start: 0.8472 (ttpp) cc_final: 0.7981 (ttpp) REVERT: G 505 ASN cc_start: 0.7613 (t0) cc_final: 0.6962 (t0) REVERT: G 510 TYR cc_start: 0.8068 (t80) cc_final: 0.7813 (t80) REVERT: G 518 MET cc_start: 0.7791 (ptp) cc_final: 0.7504 (ptp) REVERT: G 521 ILE cc_start: 0.8705 (mt) cc_final: 0.8461 (mt) REVERT: G 530 LYS cc_start: 0.8241 (ttpp) cc_final: 0.7216 (ttpp) REVERT: G 532 LYS cc_start: 0.8232 (ttpp) cc_final: 0.7982 (ttmm) REVERT: G 560 ASN cc_start: 0.8218 (m-40) cc_final: 0.7940 (m-40) REVERT: F 72 ASN cc_start: 0.8297 (t0) cc_final: 0.8056 (t0) REVERT: F 73 MET cc_start: 0.7960 (ttp) cc_final: 0.7322 (ttp) REVERT: F 80 ARG cc_start: 0.4057 (tpt90) cc_final: 0.2408 (tpt170) REVERT: F 81 ARG cc_start: 0.6313 (ptp-170) cc_final: 0.4419 (ptt-90) REVERT: F 120 TRP cc_start: 0.8441 (m100) cc_final: 0.7779 (m100) REVERT: F 135 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: F 137 HIS cc_start: 0.8400 (m90) cc_final: 0.8169 (m170) REVERT: F 144 GLU cc_start: 0.7251 (pm20) cc_final: 0.6998 (pm20) REVERT: F 151 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7866 (mmmm) REVERT: F 193 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7545 (mt-10) REVERT: F 197 PHE cc_start: 0.8202 (m-10) cc_final: 0.7567 (m-80) REVERT: F 201 LYS cc_start: 0.8087 (mmpt) cc_final: 0.7680 (mmpt) REVERT: F 216 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.8087 (tmm-80) REVERT: F 225 THR cc_start: 0.7327 (m) cc_final: 0.7009 (p) REVERT: F 266 PHE cc_start: 0.8328 (t80) cc_final: 0.7764 (t80) REVERT: F 302 ASN cc_start: 0.7996 (m-40) cc_final: 0.7149 (p0) REVERT: F 312 LYS cc_start: 0.8480 (mptt) cc_final: 0.7724 (mptt) REVERT: F 317 THR cc_start: 0.8157 (p) cc_final: 0.7890 (t) REVERT: F 335 GLU cc_start: 0.7197 (tt0) cc_final: 0.6990 (tt0) REVERT: F 346 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6632 (mt-10) REVERT: F 409 TYR cc_start: 0.8362 (t80) cc_final: 0.8006 (t80) REVERT: F 439 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7361 (mmtp) REVERT: F 451 TYR cc_start: 0.8606 (t80) cc_final: 0.8375 (t80) REVERT: F 468 GLN cc_start: 0.7409 (tt0) cc_final: 0.7158 (tt0) REVERT: F 497 GLN cc_start: 0.8445 (mt0) cc_final: 0.8218 (mt0) REVERT: F 501 LYS cc_start: 0.8370 (ttpp) cc_final: 0.8008 (ptmm) REVERT: F 532 LYS cc_start: 0.8526 (ttmm) cc_final: 0.8057 (ttmm) REVERT: F 533 LEU cc_start: 0.8471 (tp) cc_final: 0.7607 (tp) REVERT: F 551 MET cc_start: 0.7184 (ttt) cc_final: 0.6847 (ttt) REVERT: F 562 VAL cc_start: 0.8605 (p) cc_final: 0.8373 (m) REVERT: F 581 ARG cc_start: 0.7301 (ttp-110) cc_final: 0.6989 (ttp80) REVERT: D 48 GLN cc_start: 0.8116 (mt0) cc_final: 0.7824 (mt0) REVERT: D 49 THR cc_start: 0.7975 (m) cc_final: 0.7477 (p) REVERT: D 50 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6658 (tm-30) REVERT: D 70 HIS cc_start: 0.7894 (t-170) cc_final: 0.7638 (t-170) REVERT: D 73 MET cc_start: 0.8234 (ptt) cc_final: 0.7724 (ptm) REVERT: D 174 MET cc_start: 0.7692 (mtp) cc_final: 0.7108 (mtp) REVERT: D 208 TRP cc_start: 0.7808 (t60) cc_final: 0.7149 (t60) REVERT: D 256 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7351 (mtm-85) REVERT: D 510 TYR cc_start: 0.8396 (t80) cc_final: 0.8085 (t80) REVERT: E 95 ASN cc_start: 0.8265 (t0) cc_final: 0.7918 (t0) REVERT: E 106 VAL cc_start: 0.7994 (t) cc_final: 0.7620 (p) REVERT: E 131 ASN cc_start: 0.8428 (m-40) cc_final: 0.7966 (t0) REVERT: E 142 GLU cc_start: 0.7694 (pt0) cc_final: 0.6889 (pt0) REVERT: E 163 LYS cc_start: 0.7803 (mppt) cc_final: 0.7253 (mppt) REVERT: E 170 THR cc_start: 0.8697 (p) cc_final: 0.8480 (m) REVERT: E 210 TYR cc_start: 0.8543 (p90) cc_final: 0.8164 (p90) REVERT: E 237 ASP cc_start: 0.7568 (t0) cc_final: 0.7250 (t0) REVERT: E 240 ASP cc_start: 0.7282 (m-30) cc_final: 0.7049 (m-30) REVERT: E 245 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7699 (p) REVERT: E 247 GLU cc_start: 0.7728 (mp0) cc_final: 0.7205 (mp0) REVERT: E 256 ARG cc_start: 0.7888 (mtp180) cc_final: 0.7496 (mtp85) REVERT: E 266 PHE cc_start: 0.8234 (t80) cc_final: 0.7980 (t80) REVERT: E 302 ASN cc_start: 0.8494 (t0) cc_final: 0.8231 (t0) REVERT: E 335 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6268 (tm-30) REVERT: E 342 TYR cc_start: 0.7209 (p90) cc_final: 0.6937 (p90) REVERT: E 387 LYS cc_start: 0.8707 (tptm) cc_final: 0.8246 (tptm) REVERT: E 400 TYR cc_start: 0.8085 (t80) cc_final: 0.7331 (t80) REVERT: E 464 TYR cc_start: 0.8039 (t80) cc_final: 0.7595 (t80) REVERT: E 471 ASP cc_start: 0.6304 (t0) cc_final: 0.5981 (t0) REVERT: E 472 LYS cc_start: 0.3542 (OUTLIER) cc_final: 0.1361 (tmmt) REVERT: E 479 LYS cc_start: 0.8346 (mptt) cc_final: 0.7974 (mptt) REVERT: E 483 HIS cc_start: 0.7892 (m170) cc_final: 0.7134 (m-70) REVERT: E 501 LYS cc_start: 0.8188 (tttt) cc_final: 0.7407 (tttt) REVERT: E 520 ARG cc_start: 0.7670 (mtp85) cc_final: 0.7232 (mtp85) REVERT: E 530 LYS cc_start: 0.7993 (tmtt) cc_final: 0.7446 (tttt) REVERT: E 532 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7718 (ttpt) REVERT: E 538 LYS cc_start: 0.7997 (ttmm) cc_final: 0.7204 (mtpp) REVERT: I 95 ASN cc_start: 0.8375 (m-40) cc_final: 0.8048 (m-40) REVERT: I 96 MET cc_start: 0.4245 (OUTLIER) cc_final: 0.3922 (ptt) REVERT: I 109 TRP cc_start: 0.8814 (m100) cc_final: 0.7774 (m100) REVERT: I 122 ASN cc_start: 0.8106 (p0) cc_final: 0.7065 (p0) REVERT: I 147 ASN cc_start: 0.8129 (t0) cc_final: 0.7773 (t0) REVERT: I 150 LEU cc_start: 0.8459 (mt) cc_final: 0.8072 (mp) REVERT: I 193 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7157 (mp0) REVERT: I 237 ASP cc_start: 0.7430 (t0) cc_final: 0.6898 (t0) REVERT: I 269 ASP cc_start: 0.6938 (p0) cc_final: 0.6693 (p0) REVERT: I 318 GLN cc_start: 0.8590 (mt0) cc_final: 0.8126 (mm-40) REVERT: I 415 ILE cc_start: 0.8711 (mt) cc_final: 0.8378 (mm) REVERT: I 464 TYR cc_start: 0.7961 (t80) cc_final: 0.7740 (t80) REVERT: I 485 ASN cc_start: 0.7247 (p0) cc_final: 0.6339 (p0) REVERT: I 528 TRP cc_start: 0.8294 (m100) cc_final: 0.7578 (m100) REVERT: I 529 TRP cc_start: 0.7995 (t60) cc_final: 0.7733 (t60) REVERT: I 538 LYS cc_start: 0.8562 (tppt) cc_final: 0.8279 (tppt) REVERT: I 565 ASN cc_start: 0.8157 (t0) cc_final: 0.7870 (t0) REVERT: I 582 LYS cc_start: 0.8290 (pttm) cc_final: 0.7996 (pttm) REVERT: C 46 ASN cc_start: 0.8478 (t0) cc_final: 0.8111 (t0) REVERT: C 67 ARG cc_start: 0.7180 (mmt-90) cc_final: 0.6746 (mmt-90) REVERT: C 73 MET cc_start: 0.8052 (ptt) cc_final: 0.7672 (ptt) REVERT: C 77 GLU cc_start: 0.6859 (tp30) cc_final: 0.6262 (tp30) REVERT: C 509 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: C 528 TRP cc_start: 0.8661 (m100) cc_final: 0.8206 (m100) REVERT: C 529 TRP cc_start: 0.8859 (t60) cc_final: 0.8642 (t60) REVERT: B 46 ASN cc_start: 0.8127 (t0) cc_final: 0.7758 (t0) REVERT: B 53 PHE cc_start: 0.8317 (m-80) cc_final: 0.7856 (p90) REVERT: B 117 TRP cc_start: 0.8017 (m100) cc_final: 0.7502 (m100) REVERT: B 122 ASN cc_start: 0.7675 (p0) cc_final: 0.7386 (p0) REVERT: B 152 THR cc_start: 0.8545 (m) cc_final: 0.8023 (p) REVERT: B 182 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7846 (m) REVERT: B 256 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7593 (mtp180) REVERT: B 268 PHE cc_start: 0.8547 (m-10) cc_final: 0.8185 (m-10) REVERT: B 415 ILE cc_start: 0.8379 (mt) cc_final: 0.8133 (mt) REVERT: B 416 GLN cc_start: 0.7864 (tt0) cc_final: 0.7544 (mp10) REVERT: B 417 ASN cc_start: 0.8003 (t0) cc_final: 0.7736 (t0) REVERT: B 463 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7821 (m) REVERT: B 511 ASP cc_start: 0.8099 (t0) cc_final: 0.7689 (t0) REVERT: B 549 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: B 565 ASN cc_start: 0.8129 (m110) cc_final: 0.7882 (m110) REVERT: B 569 MET cc_start: 0.7064 (mmm) cc_final: 0.6723 (mmm) REVERT: B 575 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7484 (mmtt) outliers start: 144 outliers final: 90 residues processed: 1578 average time/residue: 0.4910 time to fit residues: 1206.1836 Evaluate side-chains 1625 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1519 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 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 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 282 ASN Chi-restraints excluded: chain A residue 335 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 471 ASP Chi-restraints excluded: chain A residue 511 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 87 MET 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 260 GLU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 277 HIS Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 451 TYR Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain F residue 44 THR 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 150 LEU Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 349 THR 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 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 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 70 HIS 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 195 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 468 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 133 MET Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 153 VAL 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 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 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 378 TYR 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 153 VAL Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 182 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 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 549 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 160 optimal weight: 10.0000 chunk 5 optimal weight: 0.0980 chunk 320 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 154 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 282 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 GLN F 95 ASN ** F 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 234 HIS ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN E 403 HIS E 558 GLN I 48 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN I 446 ASN ** C 86 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 446 ASN B 483 HIS B 549 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.124724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106614 restraints weight = 52542.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.110881 restraints weight = 24435.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.113636 restraints weight = 13713.136| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 31936 Z= 0.260 Angle : 0.624 11.807 43674 Z= 0.320 Chirality : 0.046 0.180 4764 Planarity : 0.005 0.062 5732 Dihedral : 5.502 69.695 4238 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 5.13 % Allowed : 23.76 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 3686 helix: -1.54 (0.39), residues: 124 sheet: -0.59 (0.17), residues: 870 loop : -0.47 (0.12), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 279 HIS 0.007 0.001 HIS B 222 PHE 0.034 0.002 PHE A 266 TYR 0.027 0.002 TYR A 210 ARG 0.008 0.001 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 295) hydrogen bonds : angle 6.06708 ( 567) SS BOND : bond 0.00594 ( 7) SS BOND : angle 1.41104 ( 14) covalent geometry : bond 0.00545 (31929) covalent geometry : angle 0.62341 (43660) *********************** 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 1739 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 1570 time to evaluate : 3.315 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 47 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7847 (t0) REVERT: A 60 GLU cc_start: 0.7495 (tt0) cc_final: 0.7138 (tp30) REVERT: A 67 ARG cc_start: 0.8307 (mmt180) cc_final: 0.7998 (mmt180) REVERT: A 79 TYR cc_start: 0.8404 (m-80) cc_final: 0.7829 (m-80) REVERT: A 104 GLN cc_start: 0.8178 (pt0) cc_final: 0.7527 (pt0) REVERT: A 147 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7959 (t0) REVERT: A 163 LYS cc_start: 0.8733 (mmmt) cc_final: 0.8473 (mmmt) REVERT: A 192 SER cc_start: 0.7978 (t) cc_final: 0.7772 (t) REVERT: A 214 TRP cc_start: 0.8610 (p90) cc_final: 0.7420 (p90) REVERT: A 215 ASP cc_start: 0.7483 (m-30) cc_final: 0.7152 (m-30) REVERT: A 216 ARG cc_start: 0.7126 (ttt-90) cc_final: 0.6770 (ttt-90) REVERT: A 237 ASP cc_start: 0.7914 (t0) cc_final: 0.7351 (t0) REVERT: A 247 GLU cc_start: 0.7711 (mp0) cc_final: 0.7383 (mp0) REVERT: A 260 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: A 269 ASP cc_start: 0.7415 (p0) cc_final: 0.7162 (p0) REVERT: A 279 TRP cc_start: 0.8863 (p-90) cc_final: 0.8242 (p-90) REVERT: A 302 ASN cc_start: 0.8263 (m-40) cc_final: 0.7534 (m110) REVERT: A 312 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8156 (mtmt) REVERT: A 335 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6309 (tm-30) REVERT: A 350 GLN cc_start: 0.7442 (mt0) cc_final: 0.7198 (mp10) REVERT: A 380 PHE cc_start: 0.7617 (p90) cc_final: 0.7305 (p90) REVERT: A 382 ARG cc_start: 0.8129 (mtt90) cc_final: 0.7874 (mmt90) REVERT: A 411 GLU cc_start: 0.7802 (mp0) cc_final: 0.7412 (mp0) REVERT: A 413 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6596 (m-30) REVERT: A 414 TRP cc_start: 0.8082 (p90) cc_final: 0.7679 (p90) REVERT: A 473 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 501 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8112 (ttpp) REVERT: A 524 TYR cc_start: 0.8519 (p90) cc_final: 0.8229 (p90) REVERT: A 528 TRP cc_start: 0.8416 (m100) cc_final: 0.8014 (m100) REVERT: G 50 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6651 (mp0) REVERT: G 54 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8540 (mt) REVERT: G 60 GLU cc_start: 0.7560 (tp30) cc_final: 0.7126 (tp30) REVERT: G 62 THR cc_start: 0.8437 (m) cc_final: 0.7950 (t) REVERT: G 67 ARG cc_start: 0.8299 (mtt-85) cc_final: 0.8067 (mmt-90) REVERT: G 109 TRP cc_start: 0.8435 (m100) cc_final: 0.8058 (m100) REVERT: G 120 TRP cc_start: 0.8637 (m100) cc_final: 0.8090 (m100) REVERT: G 144 GLU cc_start: 0.7403 (pm20) cc_final: 0.7164 (pm20) REVERT: G 174 MET cc_start: 0.7944 (mtp) cc_final: 0.7552 (mtp) REVERT: G 185 PHE cc_start: 0.8239 (t80) cc_final: 0.7946 (t80) REVERT: G 193 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: G 213 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7470 (tm-30) REVERT: G 245 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7834 (t) REVERT: G 266 PHE cc_start: 0.8292 (t80) cc_final: 0.7908 (t80) REVERT: G 312 LYS cc_start: 0.8483 (mtpp) cc_final: 0.8210 (mtpp) REVERT: G 327 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7039 (mm-30) REVERT: G 333 PRO cc_start: 0.9042 (Cg_exo) cc_final: 0.8788 (Cg_endo) REVERT: G 335 GLU cc_start: 0.7285 (tt0) cc_final: 0.6920 (tt0) REVERT: G 342 TYR cc_start: 0.7790 (p90) cc_final: 0.7237 (p90) REVERT: G 345 PHE cc_start: 0.8012 (m-80) cc_final: 0.7506 (m-80) REVERT: G 382 ARG cc_start: 0.5590 (mtm180) cc_final: 0.5053 (mtm180) REVERT: G 398 PHE cc_start: 0.8737 (p90) cc_final: 0.8269 (p90) REVERT: G 425 THR cc_start: 0.7965 (p) cc_final: 0.7700 (p) REVERT: G 464 TYR cc_start: 0.8166 (t80) cc_final: 0.7867 (t80) REVERT: G 475 ASP cc_start: 0.7554 (t0) cc_final: 0.7002 (t0) REVERT: G 479 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8388 (mmtm) REVERT: G 505 ASN cc_start: 0.7695 (t0) cc_final: 0.6929 (t0) REVERT: G 518 MET cc_start: 0.7774 (ptp) cc_final: 0.7485 (ptp) REVERT: G 520 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7956 (mtm-85) REVERT: G 521 ILE cc_start: 0.8730 (mt) cc_final: 0.8492 (mt) REVERT: G 530 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7404 (ttpp) REVERT: G 532 LYS cc_start: 0.8210 (ttpp) cc_final: 0.8008 (ttmm) REVERT: F 67 ARG cc_start: 0.8424 (mmt180) cc_final: 0.8021 (mmt90) REVERT: F 72 ASN cc_start: 0.8311 (t0) cc_final: 0.8037 (t0) REVERT: F 73 MET cc_start: 0.8041 (ttp) cc_final: 0.7132 (ttp) REVERT: F 75 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7261 (mm-30) REVERT: F 80 ARG cc_start: 0.4471 (tpt90) cc_final: 0.1858 (mmt180) REVERT: F 120 TRP cc_start: 0.8451 (m100) cc_final: 0.7905 (m100) REVERT: F 125 ASP cc_start: 0.7694 (m-30) cc_final: 0.7436 (m-30) REVERT: F 135 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: F 137 HIS cc_start: 0.8406 (m90) cc_final: 0.8194 (m170) REVERT: F 144 GLU cc_start: 0.7339 (pm20) cc_final: 0.7039 (pm20) REVERT: F 151 LYS cc_start: 0.8300 (mmmm) cc_final: 0.7793 (mmmm) REVERT: F 193 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7548 (mt-10) REVERT: F 194 THR cc_start: 0.8622 (p) cc_final: 0.8392 (t) REVERT: F 197 PHE cc_start: 0.8277 (m-10) cc_final: 0.7496 (m-80) REVERT: F 201 LYS cc_start: 0.8083 (mmpt) cc_final: 0.7686 (mmpt) REVERT: F 213 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7030 (tm-30) REVERT: F 225 THR cc_start: 0.7433 (m) cc_final: 0.7213 (p) REVERT: F 237 ASP cc_start: 0.8092 (t0) cc_final: 0.7849 (t0) REVERT: F 242 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7167 (pp30) REVERT: F 266 PHE cc_start: 0.8382 (t80) cc_final: 0.7779 (t80) REVERT: F 279 TRP cc_start: 0.8313 (p-90) cc_final: 0.8106 (p-90) REVERT: F 302 ASN cc_start: 0.7961 (m-40) cc_final: 0.7734 (m-40) REVERT: F 312 LYS cc_start: 0.8581 (mptt) cc_final: 0.7975 (mptt) REVERT: F 317 THR cc_start: 0.8207 (p) cc_final: 0.7887 (t) REVERT: F 335 GLU cc_start: 0.7320 (tt0) cc_final: 0.7058 (tt0) REVERT: F 346 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6609 (mt-10) REVERT: F 409 TYR cc_start: 0.8439 (t80) cc_final: 0.7974 (t80) REVERT: F 419 ASN cc_start: 0.8444 (m110) cc_final: 0.8110 (m110) REVERT: F 459 ASN cc_start: 0.8125 (m-40) cc_final: 0.7853 (m110) REVERT: F 475 ASP cc_start: 0.7998 (t0) cc_final: 0.7518 (t0) REVERT: F 497 GLN cc_start: 0.8458 (mt0) cc_final: 0.7975 (mt0) REVERT: F 518 MET cc_start: 0.8051 (ptp) cc_final: 0.7524 (ptp) REVERT: F 520 ARG cc_start: 0.7583 (mtt90) cc_final: 0.7041 (mtt90) REVERT: F 532 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8066 (ttmm) REVERT: F 538 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7298 (ttpt) REVERT: F 551 MET cc_start: 0.7141 (ttt) cc_final: 0.6814 (ttt) REVERT: F 562 VAL cc_start: 0.8619 (p) cc_final: 0.8404 (m) REVERT: F 575 LYS cc_start: 0.7720 (mmtt) cc_final: 0.7256 (mmmt) REVERT: D 46 ASN cc_start: 0.7894 (t0) cc_final: 0.7305 (t0) REVERT: D 49 THR cc_start: 0.7991 (m) cc_final: 0.7482 (p) REVERT: D 50 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6689 (tm-30) REVERT: D 73 MET cc_start: 0.8228 (ptt) cc_final: 0.7731 (ptm) REVERT: D 107 THR cc_start: 0.8395 (m) cc_final: 0.7875 (p) REVERT: D 174 MET cc_start: 0.7622 (mtp) cc_final: 0.7141 (mtp) REVERT: D 200 TRP cc_start: 0.8776 (p90) cc_final: 0.8302 (p90) REVERT: D 209 ARG cc_start: 0.4495 (OUTLIER) cc_final: 0.3973 (pmt170) REVERT: D 256 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7251 (mtm-85) REVERT: E 51 PHE cc_start: 0.8470 (m-80) cc_final: 0.8231 (m-80) REVERT: E 95 ASN cc_start: 0.8304 (t0) cc_final: 0.7971 (t0) REVERT: E 142 GLU cc_start: 0.7693 (pt0) cc_final: 0.6830 (pt0) REVERT: E 163 LYS cc_start: 0.7974 (mppt) cc_final: 0.7471 (mppt) REVERT: E 237 ASP cc_start: 0.7598 (t0) cc_final: 0.7188 (t0) REVERT: E 240 ASP cc_start: 0.7260 (m-30) cc_final: 0.7012 (m-30) REVERT: E 256 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7536 (mtp85) REVERT: E 266 PHE cc_start: 0.8290 (t80) cc_final: 0.8058 (t80) REVERT: E 302 ASN cc_start: 0.8497 (t0) cc_final: 0.8187 (t0) REVERT: E 335 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6153 (tm-30) REVERT: E 342 TYR cc_start: 0.7180 (p90) cc_final: 0.6895 (p90) REVERT: E 387 LYS cc_start: 0.8730 (tptm) cc_final: 0.8271 (tptm) REVERT: E 451 TYR cc_start: 0.3683 (OUTLIER) cc_final: 0.3058 (t80) REVERT: E 464 TYR cc_start: 0.8111 (t80) cc_final: 0.7753 (t80) REVERT: E 471 ASP cc_start: 0.6426 (t0) cc_final: 0.6141 (t0) REVERT: E 472 LYS cc_start: 0.3387 (OUTLIER) cc_final: 0.1046 (tmmt) REVERT: E 479 LYS cc_start: 0.8289 (mptt) cc_final: 0.7928 (mptt) REVERT: E 501 LYS cc_start: 0.8185 (tttt) cc_final: 0.7628 (tttt) REVERT: E 508 ASN cc_start: 0.8034 (p0) cc_final: 0.6259 (p0) REVERT: E 509 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7377 (mm-30) REVERT: E 520 ARG cc_start: 0.7690 (mtp85) cc_final: 0.7370 (mtp85) REVERT: E 532 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7736 (ttpt) REVERT: E 581 ARG cc_start: 0.8267 (ttp-170) cc_final: 0.8049 (ttp-170) REVERT: E 582 LYS cc_start: 0.6960 (pmtt) cc_final: 0.6290 (pmtt) REVERT: I 81 ARG cc_start: 0.5896 (ptp90) cc_final: 0.4204 (ptp90) REVERT: I 95 ASN cc_start: 0.8340 (m-40) cc_final: 0.7999 (m-40) REVERT: I 105 ILE cc_start: 0.8666 (mm) cc_final: 0.8432 (mm) REVERT: I 109 TRP cc_start: 0.8773 (m100) cc_final: 0.7871 (m100) REVERT: I 147 ASN cc_start: 0.8169 (t0) cc_final: 0.7744 (t0) REVERT: I 150 LEU cc_start: 0.8483 (mt) cc_final: 0.8101 (mp) REVERT: I 178 ASP cc_start: 0.6717 (t0) cc_final: 0.6452 (t0) REVERT: I 193 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7272 (mp0) REVERT: I 237 ASP cc_start: 0.7460 (t0) cc_final: 0.6919 (t0) REVERT: I 269 ASP cc_start: 0.6951 (p0) cc_final: 0.6688 (p0) REVERT: I 318 GLN cc_start: 0.8561 (mt0) cc_final: 0.8079 (mm-40) REVERT: I 406 THR cc_start: 0.7768 (p) cc_final: 0.7561 (t) REVERT: I 485 ASN cc_start: 0.7356 (p0) cc_final: 0.6614 (p0) REVERT: I 528 TRP cc_start: 0.8372 (m100) cc_final: 0.7616 (m100) REVERT: I 529 TRP cc_start: 0.8136 (t60) cc_final: 0.7805 (t60) REVERT: I 538 LYS cc_start: 0.8632 (tppt) cc_final: 0.8362 (tppt) REVERT: I 550 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7573 (mm-40) REVERT: I 565 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7886 (t0) REVERT: I 577 GLN cc_start: 0.8049 (mt0) cc_final: 0.7802 (mt0) REVERT: I 582 LYS cc_start: 0.8372 (pttm) cc_final: 0.8082 (pttm) REVERT: C 67 ARG cc_start: 0.7145 (mmt-90) cc_final: 0.6776 (mmt-90) REVERT: C 73 MET cc_start: 0.7921 (ptt) cc_final: 0.7681 (ptt) REVERT: C 77 GLU cc_start: 0.6866 (tp30) cc_final: 0.6304 (tp30) REVERT: C 193 GLU cc_start: 0.7076 (tp30) cc_final: 0.6403 (tp30) REVERT: C 509 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: C 528 TRP cc_start: 0.8662 (m100) cc_final: 0.8228 (m100) REVERT: C 564 SER cc_start: 0.7648 (t) cc_final: 0.7424 (t) REVERT: B 53 PHE cc_start: 0.8350 (m-80) cc_final: 0.7804 (p90) REVERT: B 117 TRP cc_start: 0.8043 (m100) cc_final: 0.7517 (m100) REVERT: B 122 ASN cc_start: 0.7684 (p0) cc_final: 0.7430 (p0) REVERT: B 151 LYS cc_start: 0.8625 (mttm) cc_final: 0.8405 (mttm) REVERT: B 182 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.7943 (m) REVERT: B 259 ASP cc_start: 0.6942 (p0) cc_final: 0.6719 (p0) REVERT: B 268 PHE cc_start: 0.8569 (m-10) cc_final: 0.8159 (m-10) REVERT: B 415 ILE cc_start: 0.8451 (mt) cc_final: 0.8166 (mt) REVERT: B 416 GLN cc_start: 0.7894 (tt0) cc_final: 0.7674 (mp-120) REVERT: B 424 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7957 (m) REVERT: B 463 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7846 (m) REVERT: B 511 ASP cc_start: 0.8126 (t0) cc_final: 0.7790 (t0) REVERT: B 535 PHE cc_start: 0.8167 (m-80) cc_final: 0.7912 (m-80) REVERT: B 549 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: B 565 ASN cc_start: 0.8124 (m110) cc_final: 0.7846 (m110) REVERT: B 569 MET cc_start: 0.6955 (mmm) cc_final: 0.6707 (mmm) outliers start: 169 outliers final: 112 residues processed: 1612 average time/residue: 0.5300 time to fit residues: 1333.0285 Evaluate side-chains 1676 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 1543 time to evaluate : 5.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 ASN 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 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 201 LYS 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 326 THR 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 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 54 LEU 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 326 THR Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 383 GLN Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 451 TYR Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 519 SER Chi-restraints excluded: chain G residue 544 THR Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 44 THR 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 216 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 242 GLN Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 448 PHE Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 538 LYS Chi-restraints excluded: chain F residue 552 SER Chi-restraints excluded: chain D residue 41 SER 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 209 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 498 LEU 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 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 260 GLU 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 E residue 506 LEU 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 206 THR Chi-restraints excluded: chain I residue 254 LEU Chi-restraints excluded: chain I residue 306 ILE Chi-restraints excluded: chain I residue 319 MET 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 552 SER Chi-restraints excluded: chain I residue 565 ASN 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 192 SER Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 501 LYS 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 153 VAL Chi-restraints excluded: chain B residue 172 SER 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 260 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 271 LYS 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 549 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 275 optimal weight: 0.0040 chunk 270 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 243 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 385 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 2 optimal weight: 0.0270 chunk 188 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS A 282 ASN ** A 549 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 ASN ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 GLN F 143 GLN F 234 HIS ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 550 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 HIS I 47 ASN I 48 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 446 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 GLN B 137 HIS B 318 GLN B 446 ASN B 468 GLN B 549 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107951 restraints weight = 52047.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112231 restraints weight = 24184.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114992 restraints weight = 13584.496| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31936 Z= 0.098 Angle : 0.569 11.940 43674 Z= 0.284 Chirality : 0.043 0.177 4764 Planarity : 0.005 0.060 5732 Dihedral : 4.932 69.433 4237 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.07 % Allowed : 26.28 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 3686 helix: -1.10 (0.47), residues: 94 sheet: -0.34 (0.17), residues: 891 loop : -0.34 (0.12), residues: 2701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 470 HIS 0.004 0.001 HIS F 234 PHE 0.035 0.001 PHE E 243 TYR 0.024 0.001 TYR A 561 ARG 0.009 0.001 ARG G 216 Details of bonding type rmsd hydrogen bonds : bond 0.02884 ( 295) hydrogen bonds : angle 5.88659 ( 567) SS BOND : bond 0.00700 ( 7) SS BOND : angle 1.06272 ( 14) covalent geometry : bond 0.00228 (31929) covalent geometry : angle 0.56908 (43660) *********************** 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 1663 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1529 time to evaluate : 3.248 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: 0.7229 (tt0) cc_final: 0.6857 (tp30) REVERT: A 79 TYR cc_start: 0.8335 (m-80) cc_final: 0.7787 (m-80) REVERT: A 104 GLN cc_start: 0.8182 (pt0) cc_final: 0.7584 (pt0) REVERT: A 109 TRP cc_start: 0.8651 (m100) cc_final: 0.8336 (m100) REVERT: A 163 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8440 (mmmt) REVERT: A 174 MET cc_start: 0.8378 (mtp) cc_final: 0.8177 (mtp) REVERT: A 183 MET cc_start: 0.7768 (mmm) cc_final: 0.7531 (mmm) REVERT: A 192 SER cc_start: 0.7774 (t) cc_final: 0.7524 (t) REVERT: A 213 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 214 TRP cc_start: 0.8562 (p90) cc_final: 0.7263 (p90) REVERT: A 215 ASP cc_start: 0.7408 (m-30) cc_final: 0.7074 (m-30) REVERT: A 216 ARG cc_start: 0.7059 (ttt-90) cc_final: 0.6792 (ttt180) REVERT: A 237 ASP cc_start: 0.7849 (t0) cc_final: 0.7224 (t0) REVERT: A 244 TYR cc_start: 0.7479 (m-80) cc_final: 0.6995 (m-80) REVERT: A 247 GLU cc_start: 0.7648 (mp0) cc_final: 0.7309 (mp0) REVERT: A 260 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: A 279 TRP cc_start: 0.8809 (p-90) cc_final: 0.8235 (p-90) REVERT: A 302 ASN cc_start: 0.8266 (m-40) cc_final: 0.7693 (m110) REVERT: A 312 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8186 (mtmt) REVERT: A 335 GLU cc_start: 0.7194 (tt0) cc_final: 0.6266 (tm-30) REVERT: A 348 SER cc_start: 0.8535 (t) cc_final: 0.8213 (p) REVERT: A 350 GLN cc_start: 0.7433 (mt0) cc_final: 0.7185 (mp10) REVERT: A 411 GLU cc_start: 0.7719 (mp0) cc_final: 0.7398 (mp0) REVERT: A 414 TRP cc_start: 0.7892 (p90) cc_final: 0.7560 (p90) REVERT: A 446 ASN cc_start: 0.8180 (m110) cc_final: 0.7807 (m110) REVERT: A 473 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6880 (mm-30) REVERT: A 524 TYR cc_start: 0.8518 (p90) cc_final: 0.8251 (p90) REVERT: A 530 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7862 (ttpp) REVERT: A 538 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7785 (ttmt) REVERT: G 48 GLN cc_start: 0.1964 (mm110) cc_final: 0.1424 (mm-40) REVERT: G 50 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6743 (mp0) REVERT: G 54 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8439 (mt) REVERT: G 60 GLU cc_start: 0.7467 (tp30) cc_final: 0.7058 (tp30) REVERT: G 62 THR cc_start: 0.8286 (m) cc_final: 0.7676 (t) REVERT: G 67 ARG cc_start: 0.8322 (mtt-85) cc_final: 0.8084 (mmt-90) REVERT: G 68 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8035 (tt) REVERT: G 109 TRP cc_start: 0.8443 (m100) cc_final: 0.8077 (m100) REVERT: G 115 ASN cc_start: 0.7873 (t0) cc_final: 0.7548 (t0) REVERT: G 120 TRP cc_start: 0.8519 (m100) cc_final: 0.7985 (m100) REVERT: G 174 MET cc_start: 0.7793 (mtp) cc_final: 0.7207 (mtp) REVERT: G 193 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: G 213 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7277 (tm-30) REVERT: G 230 THR cc_start: 0.8243 (p) cc_final: 0.8015 (t) REVERT: G 266 PHE cc_start: 0.8198 (t80) cc_final: 0.7880 (t80) REVERT: G 283 ARG cc_start: 0.8405 (mtp180) cc_final: 0.8086 (mtp180) REVERT: G 303 PHE cc_start: 0.8233 (m-80) cc_final: 0.8023 (m-80) REVERT: G 312 LYS cc_start: 0.8386 (mtpp) cc_final: 0.8136 (mtpp) REVERT: G 327 GLU cc_start: 0.7609 (mm-30) cc_final: 0.6931 (mm-30) REVERT: G 335 GLU cc_start: 0.7329 (tt0) cc_final: 0.7008 (tt0) REVERT: G 342 TYR cc_start: 0.7659 (p90) cc_final: 0.7224 (p90) REVERT: G 345 PHE cc_start: 0.7985 (m-80) cc_final: 0.7488 (m-80) REVERT: G 378 TYR cc_start: 0.7995 (m-80) cc_final: 0.7116 (m-80) REVERT: G 382 ARG cc_start: 0.5246 (mtm180) cc_final: 0.4607 (mtm180) REVERT: G 398 PHE cc_start: 0.8707 (p90) cc_final: 0.8259 (p90) REVERT: G 425 THR cc_start: 0.7889 (p) cc_final: 0.7653 (p) REVERT: G 457 LEU cc_start: 0.8068 (mt) cc_final: 0.7735 (mp) REVERT: G 464 TYR cc_start: 0.8074 (t80) cc_final: 0.7706 (t80) REVERT: G 479 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8333 (mmtm) REVERT: G 501 LYS cc_start: 0.8445 (ttpp) cc_final: 0.8143 (ttpp) REVERT: G 505 ASN cc_start: 0.7679 (t0) cc_final: 0.6953 (t0) REVERT: G 509 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7455 (mm-30) REVERT: G 518 MET cc_start: 0.7757 (ptp) cc_final: 0.7473 (ptp) REVERT: G 521 ILE cc_start: 0.8695 (mt) cc_final: 0.8450 (mt) REVERT: G 528 TRP cc_start: 0.8209 (m100) cc_final: 0.7624 (m100) REVERT: G 530 LYS cc_start: 0.8241 (ttpp) cc_final: 0.7450 (ttpp) REVERT: G 532 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7933 (ttmm) REVERT: G 560 ASN cc_start: 0.8141 (m-40) cc_final: 0.7834 (m-40) REVERT: G 582 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8154 (pttm) REVERT: F 67 ARG cc_start: 0.8387 (mmt180) cc_final: 0.8096 (mmt90) REVERT: F 72 ASN cc_start: 0.8317 (t0) cc_final: 0.8028 (t0) REVERT: F 73 MET cc_start: 0.8050 (ttp) cc_final: 0.7354 (ttp) REVERT: F 75 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7294 (mm-30) REVERT: F 80 ARG cc_start: 0.4400 (tpt90) cc_final: 0.1523 (mmt180) REVERT: F 109 TRP cc_start: 0.8505 (m100) cc_final: 0.8015 (m100) REVERT: F 120 TRP cc_start: 0.8365 (m100) cc_final: 0.7719 (m100) REVERT: F 125 ASP cc_start: 0.7620 (m-30) cc_final: 0.7360 (m-30) REVERT: F 135 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7037 (mp0) REVERT: F 144 GLU cc_start: 0.7362 (pm20) cc_final: 0.7076 (pm20) REVERT: F 150 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8408 (mt) REVERT: F 151 LYS cc_start: 0.8315 (mmmm) cc_final: 0.7798 (mmmm) REVERT: F 191 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7781 (mmt90) REVERT: F 193 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7599 (mt-10) REVERT: F 201 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7654 (mmpt) REVERT: F 213 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7069 (tm-30) REVERT: F 225 THR cc_start: 0.7296 (m) cc_final: 0.7042 (p) REVERT: F 237 ASP cc_start: 0.8065 (t0) cc_final: 0.7805 (t0) REVERT: F 242 GLN cc_start: 0.7577 (pt0) cc_final: 0.7232 (pp30) REVERT: F 266 PHE cc_start: 0.8241 (t80) cc_final: 0.7715 (t80) REVERT: F 302 ASN cc_start: 0.7959 (m-40) cc_final: 0.7148 (p0) REVERT: F 312 LYS cc_start: 0.8545 (mptt) cc_final: 0.7890 (mptt) REVERT: F 317 THR cc_start: 0.8134 (p) cc_final: 0.7748 (t) REVERT: F 346 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6499 (mt-10) REVERT: F 409 TYR cc_start: 0.8273 (t80) cc_final: 0.7979 (t80) REVERT: F 419 ASN cc_start: 0.8415 (m110) cc_final: 0.8118 (m110) REVERT: F 451 TYR cc_start: 0.8473 (t80) cc_final: 0.7980 (t80) REVERT: F 481 ARG cc_start: 0.8275 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: F 518 MET cc_start: 0.8037 (ptp) cc_final: 0.7563 (ptp) REVERT: F 532 LYS cc_start: 0.8522 (ttmm) cc_final: 0.8034 (ttmm) REVERT: F 533 LEU cc_start: 0.8408 (tp) cc_final: 0.7735 (tp) REVERT: F 538 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7283 (ttpt) REVERT: F 550 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7940 (mm110) REVERT: F 551 MET cc_start: 0.7073 (ttt) cc_final: 0.6673 (ttt) REVERT: F 562 VAL cc_start: 0.8670 (p) cc_final: 0.8413 (m) REVERT: D 46 ASN cc_start: 0.8019 (t0) cc_final: 0.7780 (t0) REVERT: D 49 THR cc_start: 0.7983 (m) cc_final: 0.7437 (p) REVERT: D 50 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6621 (tm-30) REVERT: D 73 MET cc_start: 0.8203 (ptt) cc_final: 0.7874 (ptm) REVERT: D 107 THR cc_start: 0.8460 (m) cc_final: 0.7785 (p) REVERT: D 174 MET cc_start: 0.7725 (mtp) cc_final: 0.7173 (mtp) REVERT: D 200 TRP cc_start: 0.8753 (p90) cc_final: 0.8328 (p90) REVERT: D 256 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7108 (mtm-85) REVERT: E 51 PHE cc_start: 0.8493 (m-80) cc_final: 0.8239 (m-80) REVERT: E 95 ASN cc_start: 0.8163 (t0) cc_final: 0.7779 (t0) REVERT: E 113 ASP cc_start: 0.7004 (t0) cc_final: 0.6704 (t0) REVERT: E 127 GLN cc_start: 0.8222 (tt0) cc_final: 0.7817 (tt0) REVERT: E 142 GLU cc_start: 0.7581 (pt0) cc_final: 0.6487 (pt0) REVERT: E 163 LYS cc_start: 0.7893 (mppt) cc_final: 0.7450 (mppt) REVERT: E 210 TYR cc_start: 0.8498 (p90) cc_final: 0.8151 (p90) REVERT: E 213 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7841 (tm-30) REVERT: E 237 ASP cc_start: 0.7527 (t0) cc_final: 0.7118 (t0) REVERT: E 240 ASP cc_start: 0.7228 (m-30) cc_final: 0.7024 (m-30) REVERT: E 256 ARG cc_start: 0.7895 (mtp180) cc_final: 0.7208 (mtp85) REVERT: E 266 PHE cc_start: 0.8181 (t80) cc_final: 0.7940 (t80) REVERT: E 302 ASN cc_start: 0.8499 (t0) cc_final: 0.8185 (t0) REVERT: E 335 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6069 (tm-30) REVERT: E 342 TYR cc_start: 0.7164 (p90) cc_final: 0.6888 (p90) REVERT: E 386 GLN cc_start: 0.8146 (tt0) cc_final: 0.7940 (tt0) REVERT: E 387 LYS cc_start: 0.8701 (tptm) cc_final: 0.8459 (tptm) REVERT: E 396 GLU cc_start: 0.7368 (tt0) cc_final: 0.7045 (tt0) REVERT: E 400 TYR cc_start: 0.8061 (t80) cc_final: 0.7299 (t80) REVERT: E 451 TYR cc_start: 0.3420 (OUTLIER) cc_final: 0.2922 (t80) REVERT: E 464 TYR cc_start: 0.7976 (t80) cc_final: 0.7410 (t80) REVERT: E 471 ASP cc_start: 0.6239 (t0) cc_final: 0.5954 (t0) REVERT: E 472 LYS cc_start: 0.3375 (OUTLIER) cc_final: 0.1238 (tmmt) REVERT: E 479 LYS cc_start: 0.8274 (mptt) cc_final: 0.7882 (mptt) REVERT: E 501 LYS cc_start: 0.8133 (tttt) cc_final: 0.7591 (tttt) REVERT: E 532 LYS cc_start: 0.8302 (ttpt) cc_final: 0.7538 (ttpt) REVERT: E 538 LYS cc_start: 0.7813 (ttmm) cc_final: 0.7351 (mtpp) REVERT: E 550 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7435 (mm-40) REVERT: E 582 LYS cc_start: 0.6699 (pmtt) cc_final: 0.6064 (pmtt) REVERT: I 47 ASN cc_start: 0.8429 (t160) cc_final: 0.7969 (t0) REVERT: I 81 ARG cc_start: 0.5850 (ptp90) cc_final: 0.4197 (ptp90) REVERT: I 82 VAL cc_start: 0.8309 (t) cc_final: 0.7985 (p) REVERT: I 95 ASN cc_start: 0.8294 (m-40) cc_final: 0.7957 (m-40) REVERT: I 96 MET cc_start: 0.3832 (ptt) cc_final: 0.3590 (ptt) REVERT: I 178 ASP cc_start: 0.6765 (t0) cc_final: 0.6450 (t0) REVERT: I 193 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7089 (mp0) REVERT: I 237 ASP cc_start: 0.7322 (t0) cc_final: 0.6738 (t0) REVERT: I 269 ASP cc_start: 0.6937 (p0) cc_final: 0.6622 (p0) REVERT: I 318 GLN cc_start: 0.8497 (mt0) cc_final: 0.7862 (mm-40) REVERT: I 397 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.7720 (mtp180) REVERT: I 415 ILE cc_start: 0.8687 (mt) cc_final: 0.8319 (mm) REVERT: I 485 ASN cc_start: 0.7182 (p0) cc_final: 0.6499 (p0) REVERT: I 501 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8337 (ptpt) REVERT: I 529 TRP cc_start: 0.8062 (t60) cc_final: 0.7689 (t60) REVERT: I 538 LYS cc_start: 0.8631 (tppt) cc_final: 0.8331 (tppt) REVERT: I 577 GLN cc_start: 0.7967 (mt0) cc_final: 0.7763 (mt0) REVERT: I 582 LYS cc_start: 0.8388 (pttm) cc_final: 0.8115 (pttm) REVERT: C 67 ARG cc_start: 0.7020 (mmt-90) cc_final: 0.6720 (mmt-90) REVERT: C 115 ASN cc_start: 0.7682 (t0) cc_final: 0.6629 (t0) REVERT: C 193 GLU cc_start: 0.6994 (tp30) cc_final: 0.6654 (tp30) REVERT: C 211 TYR cc_start: 0.7006 (m-80) cc_final: 0.6482 (m-80) REVERT: C 509 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: C 528 TRP cc_start: 0.8533 (m100) cc_final: 0.8201 (m100) REVERT: C 564 SER cc_start: 0.7569 (t) cc_final: 0.7357 (t) REVERT: B 53 PHE cc_start: 0.8362 (m-80) cc_final: 0.7778 (p90) REVERT: B 117 TRP cc_start: 0.7975 (m100) cc_final: 0.7406 (m100) REVERT: B 151 LYS cc_start: 0.8662 (mttm) cc_final: 0.8442 (mttm) REVERT: B 167 ASN cc_start: 0.7874 (m-40) cc_final: 0.7531 (m-40) REVERT: B 201 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8491 (mmmt) REVERT: B 255 LEU cc_start: 0.8279 (mt) cc_final: 0.8062 (mm) REVERT: B 268 PHE cc_start: 0.8539 (m-10) cc_final: 0.8312 (m-10) REVERT: B 279 TRP cc_start: 0.5970 (p-90) cc_final: 0.5657 (p-90) REVERT: B 380 PHE cc_start: 0.7559 (p90) cc_final: 0.7295 (p90) REVERT: B 424 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7833 (m) REVERT: B 463 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7691 (m) REVERT: B 491 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7084 (mm-40) REVERT: B 506 LEU cc_start: 0.8593 (mt) cc_final: 0.8241 (mp) REVERT: B 539 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8400 (mm) REVERT: B 549 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: B 569 MET cc_start: 0.6995 (mmm) cc_final: 0.6703 (mmm) REVERT: B 575 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7485 (mmtt) outliers start: 134 outliers final: 82 residues processed: 1567 average time/residue: 0.6897 time to fit residues: 1695.5753 Evaluate side-chains 1609 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 1508 time to evaluate : 6.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 119 VAL 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 226 SER Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 ASN 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 521 ILE Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 383 GLN 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 562 VAL Chi-restraints excluded: chain G residue 571 ILE 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 150 LEU Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 472 LYS Chi-restraints excluded: chain F residue 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 538 LYS Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 119 VAL 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 50 GLU 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 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 254 LEU Chi-restraints excluded: chain E residue 279 TRP Chi-restraints excluded: chain E residue 294 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 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 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 418 ILE 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 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 378 TYR Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 GLU 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 190 MET 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 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 539 LEU Chi-restraints excluded: chain B residue 549 GLN Chi-restraints excluded: chain B residue 558 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 187 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 169 optimal weight: 7.9990 chunk 348 optimal weight: 0.9980 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 426 ASN A 549 GLN G 127 GLN G 181 ASN ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 GLN G 458 ASN G 468 GLN G 497 GLN ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 HIS E 181 ASN E 426 ASN I 47 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 HIS I 234 HIS ** I 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 565 ASN C 46 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104498 restraints weight = 52871.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108698 restraints weight = 24683.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111420 restraints weight = 13895.274| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.132 31936 Z= 0.415 Angle : 0.711 11.590 43674 Z= 0.370 Chirality : 0.049 0.237 4764 Planarity : 0.006 0.092 5732 Dihedral : 5.664 71.284 4237 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.77 % Allowed : 26.10 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3686 helix: -1.36 (0.40), residues: 124 sheet: -0.60 (0.17), residues: 872 loop : -0.56 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 279 HIS 0.008 0.001 HIS B 222 PHE 0.045 0.003 PHE G 53 TYR 0.033 0.003 TYR A 561 ARG 0.010 0.001 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 295) hydrogen bonds : angle 6.21933 ( 567) SS BOND : bond 0.00612 ( 7) SS BOND : angle 1.64316 ( 14) covalent geometry : bond 0.00857 (31929) covalent geometry : angle 0.71045 (43660) *********************** 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 1748 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 1558 time to evaluate : 3.240 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 60 GLU cc_start: 0.7527 (tt0) cc_final: 0.7203 (tp30) REVERT: A 67 ARG cc_start: 0.8292 (mmt180) cc_final: 0.7831 (mmt180) REVERT: A 104 GLN cc_start: 0.8134 (pt0) cc_final: 0.7516 (pt0) REVERT: A 138 LEU cc_start: 0.8431 (mp) cc_final: 0.8194 (mm) REVERT: A 163 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8309 (mmmt) REVERT: A 183 MET cc_start: 0.7876 (mmm) cc_final: 0.7617 (mmm) REVERT: A 214 TRP cc_start: 0.8591 (p90) cc_final: 0.7546 (p90) REVERT: A 216 ARG cc_start: 0.7205 (ttt-90) cc_final: 0.6972 (ttt-90) REVERT: A 237 ASP cc_start: 0.7893 (t0) cc_final: 0.7422 (t0) REVERT: A 244 TYR cc_start: 0.7699 (m-80) cc_final: 0.7475 (m-80) REVERT: A 260 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: A 279 TRP cc_start: 0.8903 (p-90) cc_final: 0.8169 (p-90) REVERT: A 282 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8142 (m110) REVERT: A 302 ASN cc_start: 0.8224 (m-40) cc_final: 0.7551 (m110) REVERT: A 312 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8160 (mtmt) REVERT: A 335 GLU cc_start: 0.7195 (tt0) cc_final: 0.6330 (tm-30) REVERT: A 350 GLN cc_start: 0.7460 (mt0) cc_final: 0.7098 (mp10) REVERT: A 411 GLU cc_start: 0.7886 (mp0) cc_final: 0.7487 (mp0) REVERT: A 413 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: A 414 TRP cc_start: 0.8097 (p90) cc_final: 0.7802 (p90) REVERT: A 427 ASP cc_start: 0.8008 (p0) cc_final: 0.7781 (p0) REVERT: A 428 ASN cc_start: 0.8335 (m-40) cc_final: 0.7797 (m-40) REVERT: A 468 GLN cc_start: 0.7914 (tt0) cc_final: 0.7447 (tt0) REVERT: A 473 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6922 (mm-30) REVERT: A 485 ASN cc_start: 0.7608 (p0) cc_final: 0.7288 (p0) REVERT: A 528 TRP cc_start: 0.8508 (m100) cc_final: 0.8041 (m100) REVERT: A 538 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7747 (ttmt) REVERT: G 50 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: G 60 GLU cc_start: 0.7584 (tp30) cc_final: 0.7147 (tp30) REVERT: G 62 THR cc_start: 0.8519 (m) cc_final: 0.8057 (t) REVERT: G 104 GLN cc_start: 0.8090 (pt0) cc_final: 0.7681 (pt0) REVERT: G 109 TRP cc_start: 0.8457 (m100) cc_final: 0.8035 (m100) REVERT: G 144 GLU cc_start: 0.7466 (pm20) cc_final: 0.7000 (pm20) REVERT: G 174 MET cc_start: 0.7997 (mtp) cc_final: 0.7446 (mtp) REVERT: G 193 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: G 213 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7489 (tm-30) REVERT: G 237 ASP cc_start: 0.7477 (t0) cc_final: 0.6948 (t0) REVERT: G 245 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.6823 (t) REVERT: G 247 GLU cc_start: 0.7722 (mp0) cc_final: 0.6780 (mp0) REVERT: G 248 ASN cc_start: 0.8188 (m110) cc_final: 0.7552 (m110) REVERT: G 263 THR cc_start: 0.8652 (m) cc_final: 0.8200 (p) REVERT: G 266 PHE cc_start: 0.8398 (t80) cc_final: 0.8029 (t80) REVERT: G 312 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8298 (mtpp) REVERT: G 327 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7210 (mm-30) REVERT: G 333 PRO cc_start: 0.9001 (Cg_exo) cc_final: 0.8712 (Cg_endo) REVERT: G 335 GLU cc_start: 0.7306 (tt0) cc_final: 0.6949 (tt0) REVERT: G 345 PHE cc_start: 0.8050 (m-80) cc_final: 0.7583 (m-80) REVERT: G 382 ARG cc_start: 0.5804 (mtm180) cc_final: 0.5288 (mtm110) REVERT: G 398 PHE cc_start: 0.8658 (p90) cc_final: 0.8191 (p90) REVERT: G 425 THR cc_start: 0.8084 (p) cc_final: 0.7838 (p) REVERT: G 434 ASP cc_start: 0.7788 (m-30) cc_final: 0.7414 (t0) REVERT: G 457 LEU cc_start: 0.8329 (mt) cc_final: 0.8060 (mp) REVERT: G 475 ASP cc_start: 0.7636 (t0) cc_final: 0.7087 (t0) REVERT: G 479 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8427 (mmtm) REVERT: G 501 LYS cc_start: 0.8516 (ttpp) cc_final: 0.7256 (ttpp) REVERT: G 505 ASN cc_start: 0.7748 (t0) cc_final: 0.7121 (t0) REVERT: G 518 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7495 (ptp) REVERT: G 530 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7294 (ttpp) REVERT: G 532 LYS cc_start: 0.8230 (ttpp) cc_final: 0.7924 (ttmm) REVERT: F 47 ASN cc_start: 0.8198 (m-40) cc_final: 0.7937 (m-40) REVERT: F 67 ARG cc_start: 0.8433 (mmt180) cc_final: 0.8106 (mmt180) REVERT: F 72 ASN cc_start: 0.8365 (t0) cc_final: 0.8054 (t0) REVERT: F 73 MET cc_start: 0.8148 (ttp) cc_final: 0.7170 (ttp) REVERT: F 80 ARG cc_start: 0.4687 (tpt90) cc_final: 0.4073 (tpt90) REVERT: F 125 ASP cc_start: 0.7718 (m-30) cc_final: 0.7354 (m-30) REVERT: F 135 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: F 144 GLU cc_start: 0.7365 (pm20) cc_final: 0.7021 (pm20) REVERT: F 151 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7509 (mmmm) REVERT: F 167 ASN cc_start: 0.8246 (m110) cc_final: 0.7844 (m-40) REVERT: F 193 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7606 (mt-10) REVERT: F 195 LEU cc_start: 0.7553 (mt) cc_final: 0.7282 (mt) REVERT: F 197 PHE cc_start: 0.8166 (m-10) cc_final: 0.7222 (m-80) REVERT: F 201 LYS cc_start: 0.8077 (mmpt) cc_final: 0.7671 (mmpt) REVERT: F 213 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7161 (tm-30) REVERT: F 237 ASP cc_start: 0.8159 (t0) cc_final: 0.7803 (t0) REVERT: F 242 GLN cc_start: 0.7602 (pt0) cc_final: 0.7242 (pp30) REVERT: F 271 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7961 (mtpp) REVERT: F 279 TRP cc_start: 0.8284 (p-90) cc_final: 0.8010 (p-90) REVERT: F 302 ASN cc_start: 0.7971 (m-40) cc_final: 0.7761 (m-40) REVERT: F 312 LYS cc_start: 0.8639 (mptt) cc_final: 0.7934 (mptt) REVERT: F 335 GLU cc_start: 0.7350 (tt0) cc_final: 0.6815 (tp30) REVERT: F 346 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6696 (mt-10) REVERT: F 409 TYR cc_start: 0.8479 (t80) cc_final: 0.7915 (t80) REVERT: F 419 ASN cc_start: 0.8574 (m110) cc_final: 0.8322 (m110) REVERT: F 468 GLN cc_start: 0.7546 (tt0) cc_final: 0.7337 (mt0) REVERT: F 470 TRP cc_start: 0.8235 (p90) cc_final: 0.8000 (p90) REVERT: F 473 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7378 (tm-30) REVERT: F 474 PHE cc_start: 0.8172 (m-10) cc_final: 0.7629 (m-10) REVERT: F 475 ASP cc_start: 0.8253 (t0) cc_final: 0.7771 (t0) REVERT: F 497 GLN cc_start: 0.8337 (mt0) cc_final: 0.7883 (mt0) REVERT: F 501 LYS cc_start: 0.8509 (ttpp) cc_final: 0.7809 (pttp) REVERT: F 518 MET cc_start: 0.8108 (ptp) cc_final: 0.7628 (ptp) REVERT: F 520 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7162 (mtm110) REVERT: F 532 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8138 (ttmm) REVERT: F 562 VAL cc_start: 0.8613 (p) cc_final: 0.8396 (m) REVERT: D 46 ASN cc_start: 0.7979 (t0) cc_final: 0.7502 (t0) REVERT: D 50 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6679 (tm-30) REVERT: D 67 ARG cc_start: 0.7939 (mmt-90) cc_final: 0.7711 (mmt-90) REVERT: D 68 LEU cc_start: 0.7925 (tp) cc_final: 0.7699 (tp) REVERT: D 70 HIS cc_start: 0.7772 (t-90) cc_final: 0.7277 (t-90) REVERT: D 73 MET cc_start: 0.8295 (ptt) cc_final: 0.7731 (ptm) REVERT: D 144 GLU cc_start: 0.7263 (pm20) cc_final: 0.6607 (pm20) REVERT: D 174 MET cc_start: 0.7649 (mtp) cc_final: 0.7191 (mtp) REVERT: D 190 MET cc_start: 0.7909 (mmm) cc_final: 0.7673 (mmm) REVERT: D 200 TRP cc_start: 0.8779 (p90) cc_final: 0.8375 (p90) REVERT: D 209 ARG cc_start: 0.4817 (OUTLIER) cc_final: 0.4269 (pmt170) REVERT: E 51 PHE cc_start: 0.8500 (m-80) cc_final: 0.8219 (m-80) REVERT: E 95 ASN cc_start: 0.8343 (t0) cc_final: 0.7808 (t0) REVERT: E 142 GLU cc_start: 0.7796 (pt0) cc_final: 0.6783 (pt0) REVERT: E 163 LYS cc_start: 0.8105 (mppt) cc_final: 0.7617 (mppt) REVERT: E 170 THR cc_start: 0.8696 (p) cc_final: 0.8127 (t) REVERT: E 209 ARG cc_start: 0.5211 (OUTLIER) cc_final: 0.4270 (ptt180) REVERT: E 213 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8086 (tm-30) REVERT: E 237 ASP cc_start: 0.7544 (t0) cc_final: 0.7282 (t0) REVERT: E 247 GLU cc_start: 0.7737 (mp0) cc_final: 0.7234 (mp0) REVERT: E 266 PHE cc_start: 0.8359 (t80) cc_final: 0.8116 (t80) REVERT: E 335 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6157 (tm-30) REVERT: E 342 TYR cc_start: 0.7167 (p90) cc_final: 0.6879 (p90) REVERT: E 382 ARG cc_start: 0.7912 (mtt90) cc_final: 0.7553 (mtt90) REVERT: E 387 LYS cc_start: 0.8776 (tptm) cc_final: 0.8538 (tptm) REVERT: E 396 GLU cc_start: 0.7370 (tt0) cc_final: 0.7035 (tt0) REVERT: E 430 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7654 (tt) REVERT: E 451 TYR cc_start: 0.4019 (OUTLIER) cc_final: 0.3363 (t80) REVERT: E 464 TYR cc_start: 0.8224 (t80) cc_final: 0.7957 (t80) REVERT: E 471 ASP cc_start: 0.6643 (t0) cc_final: 0.6275 (t0) REVERT: E 472 LYS cc_start: 0.3794 (OUTLIER) cc_final: 0.1448 (tmmt) REVERT: E 479 LYS cc_start: 0.8338 (mptt) cc_final: 0.7970 (mptt) REVERT: E 483 HIS cc_start: 0.7893 (m170) cc_final: 0.7289 (m-70) REVERT: E 501 LYS cc_start: 0.8155 (tttt) cc_final: 0.7730 (tttt) REVERT: E 508 ASN cc_start: 0.8150 (p0) cc_final: 0.6360 (p0) REVERT: E 509 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7384 (mm-30) REVERT: E 526 ASP cc_start: 0.6581 (p0) cc_final: 0.6171 (p0) REVERT: E 530 LYS cc_start: 0.8121 (tmtt) cc_final: 0.7561 (tttt) REVERT: E 532 LYS cc_start: 0.8356 (ttpt) cc_final: 0.7639 (ttpt) REVERT: E 582 LYS cc_start: 0.7207 (pmtt) cc_final: 0.6504 (pmtt) REVERT: I 67 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7892 (mmt90) REVERT: I 95 ASN cc_start: 0.8373 (m-40) cc_final: 0.7952 (m-40) REVERT: I 109 TRP cc_start: 0.8746 (m100) cc_final: 0.7864 (m100) REVERT: I 144 GLU cc_start: 0.7767 (pt0) cc_final: 0.7345 (pt0) REVERT: I 146 PHE cc_start: 0.8414 (p90) cc_final: 0.8173 (p90) REVERT: I 178 ASP cc_start: 0.6804 (t0) cc_final: 0.6431 (t0) REVERT: I 183 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6884 (mmm) REVERT: I 185 PHE cc_start: 0.8175 (t80) cc_final: 0.7943 (t80) REVERT: I 193 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7339 (mp0) REVERT: I 214 TRP cc_start: -0.1073 (OUTLIER) cc_final: -0.3579 (p90) REVERT: I 237 ASP cc_start: 0.7555 (t0) cc_final: 0.6847 (t0) REVERT: I 269 ASP cc_start: 0.6979 (p0) cc_final: 0.6724 (p0) REVERT: I 318 GLN cc_start: 0.8596 (mt0) cc_final: 0.8061 (mm-40) REVERT: I 386 GLN cc_start: 0.7715 (tt0) cc_final: 0.7326 (tt0) REVERT: I 464 TYR cc_start: 0.8051 (t80) cc_final: 0.7712 (t80) REVERT: I 485 ASN cc_start: 0.7421 (p0) cc_final: 0.6966 (p0) REVERT: I 529 TRP cc_start: 0.8268 (t60) cc_final: 0.7971 (t60) REVERT: I 532 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8267 (ttpp) REVERT: I 577 GLN cc_start: 0.8187 (mt0) cc_final: 0.7926 (mt0) REVERT: I 582 LYS cc_start: 0.8390 (pttm) cc_final: 0.8084 (pttm) REVERT: C 67 ARG cc_start: 0.7238 (mmt-90) cc_final: 0.6796 (mmt-90) REVERT: C 164 VAL cc_start: 0.8677 (p) cc_final: 0.8436 (m) REVERT: C 193 GLU cc_start: 0.7240 (tp30) cc_final: 0.6823 (tp30) REVERT: C 378 TYR cc_start: 0.2332 (OUTLIER) cc_final: 0.0618 (m-80) REVERT: C 509 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: C 528 TRP cc_start: 0.8668 (m100) cc_final: 0.8092 (m100) REVERT: C 564 SER cc_start: 0.7795 (t) cc_final: 0.7590 (t) REVERT: B 52 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7968 (ttmm) REVERT: B 53 PHE cc_start: 0.8382 (m-80) cc_final: 0.7854 (p90) REVERT: B 68 LEU cc_start: 0.8550 (tp) cc_final: 0.8328 (tp) REVERT: B 82 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8316 (m) REVERT: B 115 ASN cc_start: 0.7593 (t0) cc_final: 0.7259 (t0) REVERT: B 117 TRP cc_start: 0.7997 (m100) cc_final: 0.7459 (m100) REVERT: B 201 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8604 (mmmt) REVERT: B 212 PHE cc_start: 0.7861 (t80) cc_final: 0.7535 (t80) REVERT: B 255 LEU cc_start: 0.8240 (mt) cc_final: 0.7794 (mm) REVERT: B 259 ASP cc_start: 0.6950 (p0) cc_final: 0.6480 (p0) REVERT: B 332 ARG cc_start: 0.8043 (mmt90) cc_final: 0.7817 (mtt90) REVERT: B 344 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8587 (p) REVERT: B 463 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7874 (m) REVERT: B 528 TRP cc_start: 0.8705 (m100) cc_final: 0.8404 (m100) REVERT: B 535 PHE cc_start: 0.8162 (m-80) cc_final: 0.7922 (m-80) REVERT: B 539 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8379 (mm) REVERT: B 550 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6948 (mm-40) REVERT: B 569 MET cc_start: 0.7057 (mmm) cc_final: 0.6800 (mmm) REVERT: B 574 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7045 (mm-30) REVERT: B 575 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7578 (mmtt) outliers start: 190 outliers final: 131 residues processed: 1612 average time/residue: 0.4569 time to fit residues: 1146.3720 Evaluate side-chains 1680 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1526 time to evaluate : 3.544 ------------------------------------------------------------------------------- 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 144 GLU 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 203 THR 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 273 CYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 317 THR 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 436 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 511 ASP 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 A residue 572 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 87 MET 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 255 LEU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 319 MET Chi-restraints excluded: chain G residue 326 THR Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 451 TYR Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 518 MET Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 571 ILE Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain G residue 583 LEU Chi-restraints excluded: chain F residue 44 THR 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 206 THR Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 349 THR 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 494 CYS Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 520 ARG 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 394 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 68 LEU 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 195 LEU Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 241 VAL 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 281 THR 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 506 LEU 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 183 MET Chi-restraints excluded: chain I residue 206 THR Chi-restraints excluded: chain I residue 214 TRP Chi-restraints excluded: chain I residue 230 THR 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 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 551 MET Chi-restraints excluded: chain I residue 558 GLN Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 244 TYR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 378 TYR Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 82 VAL 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 195 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 344 SER 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 476 THR Chi-restraints excluded: chain B residue 497 GLN Chi-restraints excluded: chain B residue 539 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 288 optimal weight: 0.0270 chunk 119 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 126 optimal weight: 0.0470 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 147 ASN A 282 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN G 143 GLN G 181 ASN G 384 HIS G 386 GLN G 458 ASN G 468 GLN G 497 GLN F 95 ASN F 234 HIS F 321 ASN F 350 GLN ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 550 GLN I 48 GLN I 147 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 446 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111274 restraints weight = 52389.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115567 restraints weight = 24364.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118299 restraints weight = 13693.001| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31936 Z= 0.113 Angle : 0.601 9.805 43674 Z= 0.302 Chirality : 0.043 0.191 4764 Planarity : 0.005 0.078 5732 Dihedral : 5.113 72.676 4237 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.13 % Allowed : 28.56 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3686 helix: -1.36 (0.45), residues: 100 sheet: -0.38 (0.18), residues: 834 loop : -0.37 (0.12), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 470 HIS 0.005 0.001 HIS B 222 PHE 0.027 0.001 PHE G 303 TYR 0.034 0.001 TYR F 211 ARG 0.009 0.001 ARG A 520 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 295) hydrogen bonds : angle 5.96429 ( 567) SS BOND : bond 0.00343 ( 7) SS BOND : angle 1.33956 ( 14) covalent geometry : bond 0.00260 (31929) covalent geometry : angle 0.60065 (43660) *********************** 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 1656 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1520 time to evaluate : 3.471 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: 0.7246 (tt0) cc_final: 0.6898 (tp30) REVERT: A 79 TYR cc_start: 0.8267 (m-80) cc_final: 0.7810 (m-80) REVERT: A 104 GLN cc_start: 0.8120 (pt0) cc_final: 0.7494 (pt0) REVERT: A 163 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8346 (mmmt) REVERT: A 177 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8159 (tp) REVERT: A 216 ARG cc_start: 0.7173 (ttt-90) cc_final: 0.6968 (ttt-90) REVERT: A 230 THR cc_start: 0.8593 (p) cc_final: 0.8290 (t) REVERT: A 237 ASP cc_start: 0.7759 (t0) cc_final: 0.7148 (t0) REVERT: A 244 TYR cc_start: 0.7581 (m-80) cc_final: 0.7248 (m-80) REVERT: A 260 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: A 269 ASP cc_start: 0.7315 (p0) cc_final: 0.7112 (p0) REVERT: A 279 TRP cc_start: 0.8864 (p-90) cc_final: 0.8199 (p-90) REVERT: A 312 LYS cc_start: 0.8462 (mtmt) cc_final: 0.8169 (mtmt) REVERT: A 335 GLU cc_start: 0.7042 (tt0) cc_final: 0.6206 (tm-30) REVERT: A 350 GLN cc_start: 0.7363 (mt0) cc_final: 0.7097 (mp10) REVERT: A 380 PHE cc_start: 0.7614 (p90) cc_final: 0.7334 (p90) REVERT: A 411 GLU cc_start: 0.7787 (mp0) cc_final: 0.7495 (mp0) REVERT: A 413 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6630 (m-30) REVERT: A 414 TRP cc_start: 0.8084 (p90) cc_final: 0.7750 (p90) REVERT: A 427 ASP cc_start: 0.7922 (p0) cc_final: 0.7686 (p0) REVERT: A 428 ASN cc_start: 0.8254 (m-40) cc_final: 0.7727 (m-40) REVERT: A 443 ASN cc_start: 0.8281 (p0) cc_final: 0.7643 (p0) REVERT: A 446 ASN cc_start: 0.8182 (m110) cc_final: 0.7885 (m110) REVERT: A 468 GLN cc_start: 0.7820 (tt0) cc_final: 0.7520 (tt0) REVERT: A 473 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6872 (mm-30) REVERT: A 495 PRO cc_start: 0.7282 (Cg_exo) cc_final: 0.6767 (Cg_endo) REVERT: A 538 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7793 (ttmt) REVERT: G 50 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: G 53 PHE cc_start: 0.5257 (p90) cc_final: 0.4739 (p90) REVERT: G 60 GLU cc_start: 0.7517 (tp30) cc_final: 0.7091 (tp30) REVERT: G 62 THR cc_start: 0.8335 (m) cc_final: 0.7718 (t) REVERT: G 68 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8062 (tt) REVERT: G 80 ARG cc_start: 0.7883 (tpp80) cc_final: 0.7589 (ttm-80) REVERT: G 109 TRP cc_start: 0.8471 (m100) cc_final: 0.8149 (m100) REVERT: G 115 ASN cc_start: 0.7616 (t0) cc_final: 0.7327 (t0) REVERT: G 120 TRP cc_start: 0.8514 (m100) cc_final: 0.8124 (m100) REVERT: G 136 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8144 (tp) REVERT: G 137 HIS cc_start: 0.8511 (m90) cc_final: 0.8280 (m170) REVERT: G 144 GLU cc_start: 0.7400 (pm20) cc_final: 0.7024 (pm20) REVERT: G 174 MET cc_start: 0.7817 (mtp) cc_final: 0.7295 (mtp) REVERT: G 193 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: G 213 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7315 (tm-30) REVERT: G 237 ASP cc_start: 0.7388 (t0) cc_final: 0.6907 (t0) REVERT: G 242 GLN cc_start: 0.7846 (mt0) cc_final: 0.7573 (mt0) REVERT: G 266 PHE cc_start: 0.8289 (t80) cc_final: 0.7930 (t80) REVERT: G 268 PHE cc_start: 0.8131 (m-10) cc_final: 0.7840 (m-10) REVERT: G 283 ARG cc_start: 0.8362 (mtp180) cc_final: 0.8124 (mtp180) REVERT: G 312 LYS cc_start: 0.8440 (mtpp) cc_final: 0.8190 (mtpp) REVERT: G 327 GLU cc_start: 0.7551 (mm-30) cc_final: 0.6853 (mm-30) REVERT: G 335 GLU cc_start: 0.7356 (tt0) cc_final: 0.6921 (tt0) REVERT: G 342 TYR cc_start: 0.7620 (p90) cc_final: 0.7266 (p90) REVERT: G 345 PHE cc_start: 0.8008 (m-80) cc_final: 0.7491 (m-80) REVERT: G 382 ARG cc_start: 0.5295 (mtm180) cc_final: 0.4711 (mtp180) REVERT: G 386 GLN cc_start: 0.7697 (mt0) cc_final: 0.7426 (mm-40) REVERT: G 398 PHE cc_start: 0.8654 (p90) cc_final: 0.8286 (p90) REVERT: G 425 THR cc_start: 0.8057 (p) cc_final: 0.7830 (p) REVERT: G 457 LEU cc_start: 0.8228 (mt) cc_final: 0.7913 (mp) REVERT: G 464 TYR cc_start: 0.8022 (t80) cc_final: 0.7760 (t80) REVERT: G 475 ASP cc_start: 0.7556 (t0) cc_final: 0.6954 (t0) REVERT: G 479 LYS cc_start: 0.8643 (mmtm) cc_final: 0.8361 (mmtm) REVERT: G 501 LYS cc_start: 0.8484 (ttpp) cc_final: 0.7989 (ttpp) REVERT: G 505 ASN cc_start: 0.7715 (t0) cc_final: 0.7059 (t0) REVERT: G 510 TYR cc_start: 0.7954 (t80) cc_final: 0.7730 (t80) REVERT: G 518 MET cc_start: 0.7734 (ptp) cc_final: 0.7451 (ptp) REVERT: G 528 TRP cc_start: 0.8213 (m100) cc_final: 0.7596 (m100) REVERT: G 530 LYS cc_start: 0.8138 (ttpp) cc_final: 0.7241 (ttpp) REVERT: G 532 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7958 (ttmm) REVERT: F 67 ARG cc_start: 0.8371 (mmt180) cc_final: 0.8159 (mmt180) REVERT: F 72 ASN cc_start: 0.8317 (t0) cc_final: 0.8070 (t0) REVERT: F 73 MET cc_start: 0.8149 (ttp) cc_final: 0.7323 (ttt) REVERT: F 80 ARG cc_start: 0.4402 (tpt90) cc_final: 0.2119 (mmt180) REVERT: F 95 ASN cc_start: 0.7033 (m110) cc_final: 0.6726 (m-40) REVERT: F 109 TRP cc_start: 0.8474 (m100) cc_final: 0.8099 (m100) REVERT: F 125 ASP cc_start: 0.7592 (m-30) cc_final: 0.7210 (m-30) REVERT: F 135 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: F 144 GLU cc_start: 0.7394 (pm20) cc_final: 0.7149 (pm20) REVERT: F 151 LYS cc_start: 0.8256 (mmmm) cc_final: 0.7548 (mmmm) REVERT: F 167 ASN cc_start: 0.8219 (m110) cc_final: 0.7839 (m-40) REVERT: F 193 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7547 (mt-10) REVERT: F 195 LEU cc_start: 0.7531 (mt) cc_final: 0.7291 (mt) REVERT: F 201 LYS cc_start: 0.8033 (mmpt) cc_final: 0.7621 (mmpt) REVERT: F 213 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7061 (tm-30) REVERT: F 237 ASP cc_start: 0.8163 (t0) cc_final: 0.7785 (t0) REVERT: F 242 GLN cc_start: 0.7643 (pt0) cc_final: 0.7281 (pp30) REVERT: F 266 PHE cc_start: 0.8285 (t80) cc_final: 0.7866 (t80) REVERT: F 271 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7893 (mtpp) REVERT: F 279 TRP cc_start: 0.8261 (p-90) cc_final: 0.7937 (p-90) REVERT: F 312 LYS cc_start: 0.8653 (mptt) cc_final: 0.8084 (mptt) REVERT: F 317 THR cc_start: 0.8156 (p) cc_final: 0.7805 (t) REVERT: F 353 PHE cc_start: 0.7299 (p90) cc_final: 0.6889 (p90) REVERT: F 409 TYR cc_start: 0.8386 (t80) cc_final: 0.8018 (t80) REVERT: F 417 ASN cc_start: 0.7783 (t0) cc_final: 0.7242 (p0) REVERT: F 419 ASN cc_start: 0.8383 (m110) cc_final: 0.7768 (m-40) REVERT: F 451 TYR cc_start: 0.8455 (t80) cc_final: 0.7926 (t80) REVERT: F 473 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7243 (tm-30) REVERT: F 475 ASP cc_start: 0.8152 (t0) cc_final: 0.7644 (t0) REVERT: F 497 GLN cc_start: 0.8357 (mt0) cc_final: 0.7919 (mt0) REVERT: F 501 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8139 (pttp) REVERT: F 518 MET cc_start: 0.8082 (ptp) cc_final: 0.7543 (ptp) REVERT: F 520 ARG cc_start: 0.8001 (mtt90) cc_final: 0.6984 (mtm110) REVERT: F 532 LYS cc_start: 0.8466 (ttmm) cc_final: 0.8030 (ttmm) REVERT: F 562 VAL cc_start: 0.8640 (p) cc_final: 0.8391 (m) REVERT: D 46 ASN cc_start: 0.7966 (t0) cc_final: 0.7398 (t0) REVERT: D 50 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6600 (tm-30) REVERT: D 73 MET cc_start: 0.8285 (ptt) cc_final: 0.7871 (ptm) REVERT: D 107 THR cc_start: 0.8450 (m) cc_final: 0.7849 (p) REVERT: D 174 MET cc_start: 0.7722 (mtp) cc_final: 0.7191 (mtp) REVERT: D 190 MET cc_start: 0.7847 (mmm) cc_final: 0.7618 (mmm) REVERT: D 256 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7582 (mtm-85) REVERT: D 261 PHE cc_start: 0.8634 (t80) cc_final: 0.8407 (t80) REVERT: E 45 PHE cc_start: 0.8090 (t80) cc_final: 0.7520 (t80) REVERT: E 95 ASN cc_start: 0.8205 (t0) cc_final: 0.7616 (t0) REVERT: E 142 GLU cc_start: 0.7557 (pt0) cc_final: 0.6546 (pt0) REVERT: E 163 LYS cc_start: 0.8049 (mppt) cc_final: 0.7591 (mppt) REVERT: E 191 ARG cc_start: 0.5365 (mtt180) cc_final: 0.4583 (mtp180) REVERT: E 209 ARG cc_start: 0.5121 (OUTLIER) cc_final: 0.4289 (ptt180) REVERT: E 210 TYR cc_start: 0.8505 (p90) cc_final: 0.8253 (p90) REVERT: E 213 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7692 (tm-30) REVERT: E 237 ASP cc_start: 0.7460 (t0) cc_final: 0.7127 (t0) REVERT: E 256 ARG cc_start: 0.7911 (mtp180) cc_final: 0.7620 (mtp85) REVERT: E 266 PHE cc_start: 0.8231 (t80) cc_final: 0.7990 (t80) REVERT: E 302 ASN cc_start: 0.8437 (t0) cc_final: 0.8077 (t0) REVERT: E 335 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6145 (tm-30) REVERT: E 342 TYR cc_start: 0.7146 (p90) cc_final: 0.6859 (p90) REVERT: E 377 ARG cc_start: 0.5323 (mtt180) cc_final: 0.4915 (mtt180) REVERT: E 382 ARG cc_start: 0.7878 (mtt90) cc_final: 0.7580 (mtt90) REVERT: E 387 LYS cc_start: 0.8737 (tptm) cc_final: 0.8443 (tptm) REVERT: E 396 GLU cc_start: 0.7301 (tt0) cc_final: 0.6992 (tt0) REVERT: E 400 TYR cc_start: 0.8036 (t80) cc_final: 0.7315 (t80) REVERT: E 451 TYR cc_start: 0.3785 (OUTLIER) cc_final: 0.3410 (t80) REVERT: E 464 TYR cc_start: 0.8037 (t80) cc_final: 0.7639 (t80) REVERT: E 471 ASP cc_start: 0.6379 (t0) cc_final: 0.6032 (t0) REVERT: E 472 LYS cc_start: 0.3426 (OUTLIER) cc_final: 0.1145 (tmmt) REVERT: E 479 LYS cc_start: 0.8282 (mptt) cc_final: 0.7921 (mptt) REVERT: E 501 LYS cc_start: 0.8092 (tttt) cc_final: 0.7685 (tttt) REVERT: E 526 ASP cc_start: 0.6612 (p0) cc_final: 0.6182 (p0) REVERT: E 530 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7396 (tttt) REVERT: E 532 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7628 (ttpt) REVERT: E 538 LYS cc_start: 0.7878 (ttmm) cc_final: 0.7369 (mtpp) REVERT: E 582 LYS cc_start: 0.6896 (pmtt) cc_final: 0.6204 (pmtt) REVERT: I 95 ASN cc_start: 0.7992 (m-40) cc_final: 0.7595 (m-40) REVERT: I 109 TRP cc_start: 0.8760 (m100) cc_final: 0.7674 (m100) REVERT: I 146 PHE cc_start: 0.8334 (p90) cc_final: 0.8127 (p90) REVERT: I 178 ASP cc_start: 0.6646 (t0) cc_final: 0.6341 (t0) REVERT: I 185 PHE cc_start: 0.8102 (t80) cc_final: 0.7881 (t80) REVERT: I 193 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7205 (mp0) REVERT: I 214 TRP cc_start: -0.1383 (OUTLIER) cc_final: -0.3911 (p90) REVERT: I 237 ASP cc_start: 0.7443 (t0) cc_final: 0.6801 (t0) REVERT: I 269 ASP cc_start: 0.6848 (p0) cc_final: 0.6516 (p0) REVERT: I 318 GLN cc_start: 0.8413 (mt0) cc_final: 0.7876 (mm110) REVERT: I 346 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6442 (mm-30) REVERT: I 415 ILE cc_start: 0.8646 (mt) cc_final: 0.8306 (mm) REVERT: I 464 TYR cc_start: 0.7833 (t80) cc_final: 0.7586 (t80) REVERT: I 485 ASN cc_start: 0.7427 (p0) cc_final: 0.6841 (p0) REVERT: I 501 LYS cc_start: 0.8569 (ttpt) cc_final: 0.7769 (ptpt) REVERT: I 529 TRP cc_start: 0.8148 (t60) cc_final: 0.7841 (t60) REVERT: I 532 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8261 (ttpp) REVERT: I 538 LYS cc_start: 0.8548 (tppt) cc_final: 0.8248 (ttmm) REVERT: I 577 GLN cc_start: 0.8129 (mt0) cc_final: 0.7813 (mt0) REVERT: I 582 LYS cc_start: 0.8385 (pttm) cc_final: 0.8091 (pttm) REVERT: C 67 ARG cc_start: 0.7116 (mmt-90) cc_final: 0.6734 (mmt-90) REVERT: C 193 GLU cc_start: 0.7139 (tp30) cc_final: 0.6732 (tp30) REVERT: C 382 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7304 (ttm-80) REVERT: C 509 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: C 528 TRP cc_start: 0.8579 (m100) cc_final: 0.8135 (m100) REVERT: C 564 SER cc_start: 0.7792 (t) cc_final: 0.7577 (t) REVERT: B 52 LYS cc_start: 0.8322 (ttmm) cc_final: 0.7978 (ttmm) REVERT: B 53 PHE cc_start: 0.8374 (m-80) cc_final: 0.7810 (p90) REVERT: B 101 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 109 TRP cc_start: 0.8702 (m100) cc_final: 0.7829 (m100) REVERT: B 142 GLU cc_start: 0.7718 (pp20) cc_final: 0.7344 (pp20) REVERT: B 151 LYS cc_start: 0.8734 (mttm) cc_final: 0.8397 (mttm) REVERT: B 167 ASN cc_start: 0.7882 (m-40) cc_final: 0.7483 (m-40) REVERT: B 174 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7338 (mtp) REVERT: B 201 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8573 (mmmt) REVERT: B 211 TYR cc_start: 0.7764 (m-80) cc_final: 0.7473 (m-10) REVERT: B 332 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7683 (mtt90) REVERT: B 401 ILE cc_start: 0.8959 (mt) cc_final: 0.8574 (mp) REVERT: B 424 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7873 (m) REVERT: B 430 LEU cc_start: 0.8427 (tp) cc_final: 0.8034 (tp) REVERT: B 463 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7820 (m) REVERT: B 473 GLU cc_start: 0.6993 (tt0) cc_final: 0.6757 (tt0) REVERT: B 528 TRP cc_start: 0.8692 (m100) cc_final: 0.8483 (m100) REVERT: B 535 PHE cc_start: 0.8155 (m-80) cc_final: 0.7924 (m-80) REVERT: B 539 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8350 (mm) REVERT: B 550 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7222 (mm-40) REVERT: B 569 MET cc_start: 0.7008 (mmm) cc_final: 0.6708 (mmm) REVERT: B 575 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7464 (mmtt) outliers start: 136 outliers final: 91 residues processed: 1562 average time/residue: 0.4556 time to fit residues: 1105.5549 Evaluate side-chains 1624 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1513 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL 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 275 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 319 MET 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 416 GLN Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 523 THR 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 A residue 572 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 225 THR 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 346 GLU Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 469 ILE 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 216 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 321 ASN Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 396 GLU 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 506 LEU Chi-restraints excluded: chain F residue 550 GLN 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 256 ARG 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 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 166 ASN 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 413 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 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 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 523 THR Chi-restraints excluded: chain C residue 84 VAL 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 378 TYR Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 101 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 174 MET 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 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 539 LEU 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 391 optimal weight: 5.9990 chunk 353 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 307 optimal weight: 0.2980 chunk 93 optimal weight: 8.9990 chunk 242 optimal weight: 0.0770 chunk 210 optimal weight: 10.0000 chunk 390 optimal weight: 6.9990 chunk 365 optimal weight: 9.9990 overall best weight: 3.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 282 ASN ** A 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 ASN G 384 HIS G 468 GLN ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 147 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 ASN C 46 ASN ** C 86 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 = 0.3502 r_free = 0.3502 target = 0.124415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106267 restraints weight = 53082.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.110539 restraints weight = 24557.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113266 restraints weight = 13737.622| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 31936 Z= 0.213 Angle : 0.639 16.938 43674 Z= 0.321 Chirality : 0.045 0.188 4764 Planarity : 0.005 0.078 5732 Dihedral : 5.170 69.892 4237 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.98 % Allowed : 29.29 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3686 helix: -1.42 (0.45), residues: 100 sheet: -0.40 (0.18), residues: 867 loop : -0.42 (0.12), residues: 2719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 529 HIS 0.005 0.001 HIS B 222 PHE 0.025 0.002 PHE F 398 TYR 0.045 0.002 TYR A 561 ARG 0.012 0.001 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 295) hydrogen bonds : angle 5.92101 ( 567) SS BOND : bond 0.00516 ( 7) SS BOND : angle 1.06189 ( 14) covalent geometry : bond 0.00459 (31929) covalent geometry : angle 0.63905 (43660) *********************** 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 1647 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1516 time to evaluate : 3.676 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: 0.7295 (tt0) cc_final: 0.6959 (tp30) REVERT: A 104 GLN cc_start: 0.8094 (pt0) cc_final: 0.7486 (pt0) REVERT: A 163 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8267 (mmmt) REVERT: A 182 THR cc_start: 0.8504 (m) cc_final: 0.8121 (t) REVERT: A 214 TRP cc_start: 0.8544 (p90) cc_final: 0.7469 (p90) REVERT: A 216 ARG cc_start: 0.7218 (ttt-90) cc_final: 0.6949 (ttt-90) REVERT: A 230 THR cc_start: 0.8634 (p) cc_final: 0.8354 (t) REVERT: A 237 ASP cc_start: 0.7767 (t0) cc_final: 0.7456 (t0) REVERT: A 244 TYR cc_start: 0.7625 (m-80) cc_final: 0.7112 (m-80) REVERT: A 260 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: A 279 TRP cc_start: 0.8928 (p-90) cc_final: 0.8281 (p-90) REVERT: A 302 ASN cc_start: 0.8260 (m-40) cc_final: 0.7517 (m110) REVERT: A 312 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8211 (mtmt) REVERT: A 335 GLU cc_start: 0.7123 (tt0) cc_final: 0.6263 (tm-30) REVERT: A 380 PHE cc_start: 0.7677 (p90) cc_final: 0.7397 (p90) REVERT: A 389 THR cc_start: 0.8784 (p) cc_final: 0.8568 (p) REVERT: A 411 GLU cc_start: 0.7857 (mp0) cc_final: 0.7447 (mp0) REVERT: A 413 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6682 (m-30) REVERT: A 414 TRP cc_start: 0.8164 (p90) cc_final: 0.7812 (p90) REVERT: A 428 ASN cc_start: 0.8345 (m-40) cc_final: 0.7824 (m-40) REVERT: A 443 ASN cc_start: 0.8295 (p0) cc_final: 0.7673 (p0) REVERT: A 446 ASN cc_start: 0.8233 (m110) cc_final: 0.7754 (m-40) REVERT: A 468 GLN cc_start: 0.7861 (tt0) cc_final: 0.7477 (tt0) REVERT: A 473 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6883 (mm-30) REVERT: A 495 PRO cc_start: 0.7272 (Cg_exo) cc_final: 0.6990 (Cg_endo) REVERT: A 501 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8071 (ptmm) REVERT: A 538 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7741 (ttmt) REVERT: G 50 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: G 60 GLU cc_start: 0.7574 (tp30) cc_final: 0.7160 (tp30) REVERT: G 62 THR cc_start: 0.8356 (m) cc_final: 0.7741 (t) REVERT: G 67 ARG cc_start: 0.8355 (mtt-85) cc_final: 0.8110 (mtt90) REVERT: G 68 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8080 (tt) REVERT: G 80 ARG cc_start: 0.7963 (tpp80) cc_final: 0.7588 (tpp80) REVERT: G 83 VAL cc_start: 0.8800 (t) cc_final: 0.8405 (m) REVERT: G 104 GLN cc_start: 0.8160 (pt0) cc_final: 0.7906 (pt0) REVERT: G 109 TRP cc_start: 0.8477 (m100) cc_final: 0.8059 (m100) REVERT: G 120 TRP cc_start: 0.8580 (m100) cc_final: 0.8184 (m100) REVERT: G 137 HIS cc_start: 0.8520 (m90) cc_final: 0.8315 (m170) REVERT: G 144 GLU cc_start: 0.7267 (pm20) cc_final: 0.7019 (pm20) REVERT: G 174 MET cc_start: 0.7939 (mtp) cc_final: 0.7571 (mtp) REVERT: G 185 PHE cc_start: 0.8281 (t80) cc_final: 0.7824 (t80) REVERT: G 193 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: G 213 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7394 (tm-30) REVERT: G 237 ASP cc_start: 0.7464 (t0) cc_final: 0.6961 (t0) REVERT: G 242 GLN cc_start: 0.7857 (mt0) cc_final: 0.7562 (mt0) REVERT: G 263 THR cc_start: 0.8564 (m) cc_final: 0.8012 (p) REVERT: G 266 PHE cc_start: 0.8315 (t80) cc_final: 0.8014 (t80) REVERT: G 312 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8226 (mtpp) REVERT: G 327 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6921 (mm-30) REVERT: G 335 GLU cc_start: 0.7489 (tt0) cc_final: 0.6990 (tt0) REVERT: G 342 TYR cc_start: 0.7640 (p90) cc_final: 0.7317 (p90) REVERT: G 345 PHE cc_start: 0.8004 (m-80) cc_final: 0.7527 (m-80) REVERT: G 382 ARG cc_start: 0.5358 (mtm180) cc_final: 0.4605 (mtm110) REVERT: G 386 GLN cc_start: 0.7748 (mt0) cc_final: 0.7516 (mm-40) REVERT: G 398 PHE cc_start: 0.8652 (p90) cc_final: 0.8238 (p90) REVERT: G 464 TYR cc_start: 0.8075 (t80) cc_final: 0.7811 (t80) REVERT: G 475 ASP cc_start: 0.7601 (t0) cc_final: 0.6993 (t0) REVERT: G 479 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8382 (mmtm) REVERT: G 505 ASN cc_start: 0.7708 (t0) cc_final: 0.7038 (t0) REVERT: G 518 MET cc_start: 0.7794 (ptp) cc_final: 0.7528 (ptp) REVERT: G 520 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7923 (mtm-85) REVERT: G 528 TRP cc_start: 0.8163 (m100) cc_final: 0.7560 (m100) REVERT: G 530 LYS cc_start: 0.8115 (ttpp) cc_final: 0.7203 (ttpp) REVERT: G 532 LYS cc_start: 0.8180 (ttpp) cc_final: 0.7954 (ttmm) REVERT: F 47 ASN cc_start: 0.8156 (m-40) cc_final: 0.7846 (m-40) REVERT: F 67 ARG cc_start: 0.8416 (mmt180) cc_final: 0.8108 (mmt90) REVERT: F 72 ASN cc_start: 0.8327 (t0) cc_final: 0.8046 (t0) REVERT: F 73 MET cc_start: 0.8156 (ttp) cc_final: 0.7045 (ttp) REVERT: F 80 ARG cc_start: 0.4313 (tpt90) cc_final: 0.1562 (mmt180) REVERT: F 81 ARG cc_start: 0.6014 (ptp-170) cc_final: 0.5711 (ptp-170) REVERT: F 125 ASP cc_start: 0.7661 (m-30) cc_final: 0.7265 (m-30) REVERT: F 135 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: F 144 GLU cc_start: 0.7398 (pm20) cc_final: 0.7129 (pm20) REVERT: F 151 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7539 (mmmm) REVERT: F 167 ASN cc_start: 0.8237 (m110) cc_final: 0.7857 (m-40) REVERT: F 191 ARG cc_start: 0.8435 (mtt90) cc_final: 0.8221 (mmm-85) REVERT: F 193 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7539 (mt-10) REVERT: F 195 LEU cc_start: 0.7497 (mt) cc_final: 0.7211 (mt) REVERT: F 197 PHE cc_start: 0.8225 (m-10) cc_final: 0.7487 (m-80) REVERT: F 201 LYS cc_start: 0.8065 (mmpt) cc_final: 0.7660 (mmpt) REVERT: F 213 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7121 (tm-30) REVERT: F 237 ASP cc_start: 0.8148 (t0) cc_final: 0.7753 (t0) REVERT: F 271 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7915 (mtpp) REVERT: F 279 TRP cc_start: 0.8246 (p-90) cc_final: 0.7943 (p-90) REVERT: F 312 LYS cc_start: 0.8650 (mptt) cc_final: 0.8042 (mptt) REVERT: F 317 THR cc_start: 0.8192 (p) cc_final: 0.7886 (t) REVERT: F 335 GLU cc_start: 0.7342 (tt0) cc_final: 0.6817 (tp30) REVERT: F 345 PHE cc_start: 0.7216 (m-80) cc_final: 0.6541 (m-10) REVERT: F 409 TYR cc_start: 0.8404 (t80) cc_final: 0.7997 (t80) REVERT: F 419 ASN cc_start: 0.8427 (m110) cc_final: 0.8099 (m-40) REVERT: F 451 TYR cc_start: 0.8479 (t80) cc_final: 0.7965 (t80) REVERT: F 473 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7315 (tm-30) REVERT: F 475 ASP cc_start: 0.8171 (t0) cc_final: 0.7646 (t0) REVERT: F 497 GLN cc_start: 0.8351 (mt0) cc_final: 0.7932 (mt0) REVERT: F 501 LYS cc_start: 0.8520 (ttpp) cc_final: 0.7894 (pttp) REVERT: F 518 MET cc_start: 0.8108 (ptp) cc_final: 0.7561 (ptp) REVERT: F 520 ARG cc_start: 0.8000 (mtt90) cc_final: 0.7157 (mtm110) REVERT: F 532 LYS cc_start: 0.8433 (ttmm) cc_final: 0.7990 (ttmm) REVERT: F 562 VAL cc_start: 0.8643 (p) cc_final: 0.8396 (m) REVERT: D 46 ASN cc_start: 0.7939 (t0) cc_final: 0.7486 (t0) REVERT: D 50 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6637 (tm-30) REVERT: D 73 MET cc_start: 0.8305 (ptt) cc_final: 0.7884 (ptm) REVERT: D 144 GLU cc_start: 0.7266 (pm20) cc_final: 0.6587 (pm20) REVERT: D 174 MET cc_start: 0.7686 (mtp) cc_final: 0.7144 (mtp) REVERT: D 190 MET cc_start: 0.7885 (mmm) cc_final: 0.7651 (mmm) REVERT: D 256 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7587 (mtm-85) REVERT: E 45 PHE cc_start: 0.8187 (t80) cc_final: 0.7687 (t80) REVERT: E 51 PHE cc_start: 0.8461 (m-80) cc_final: 0.8224 (m-80) REVERT: E 95 ASN cc_start: 0.8249 (t0) cc_final: 0.7681 (t0) REVERT: E 142 GLU cc_start: 0.7615 (pt0) cc_final: 0.6591 (pt0) REVERT: E 163 LYS cc_start: 0.8086 (mppt) cc_final: 0.7634 (mppt) REVERT: E 209 ARG cc_start: 0.5047 (OUTLIER) cc_final: 0.4199 (ptt180) REVERT: E 210 TYR cc_start: 0.8567 (p90) cc_final: 0.8292 (p90) REVERT: E 213 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7645 (tm-30) REVERT: E 237 ASP cc_start: 0.7468 (t0) cc_final: 0.7166 (t0) REVERT: E 256 ARG cc_start: 0.7835 (mtp180) cc_final: 0.7538 (mtp85) REVERT: E 266 PHE cc_start: 0.8260 (t80) cc_final: 0.7988 (t80) REVERT: E 302 ASN cc_start: 0.8452 (t0) cc_final: 0.8074 (t0) REVERT: E 335 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6144 (tm-30) REVERT: E 342 TYR cc_start: 0.7174 (p90) cc_final: 0.6909 (p90) REVERT: E 377 ARG cc_start: 0.5441 (mtt180) cc_final: 0.5125 (mtt180) REVERT: E 382 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7567 (mtt90) REVERT: E 387 LYS cc_start: 0.8762 (tptm) cc_final: 0.8491 (tptm) REVERT: E 396 GLU cc_start: 0.7315 (tt0) cc_final: 0.6972 (tt0) REVERT: E 400 TYR cc_start: 0.8045 (t80) cc_final: 0.7364 (t80) REVERT: E 451 TYR cc_start: 0.3845 (OUTLIER) cc_final: 0.3353 (t80) REVERT: E 471 ASP cc_start: 0.6438 (t0) cc_final: 0.6059 (t0) REVERT: E 472 LYS cc_start: 0.3530 (OUTLIER) cc_final: 0.1220 (tmmt) REVERT: E 479 LYS cc_start: 0.8320 (mptt) cc_final: 0.7944 (mptt) REVERT: E 501 LYS cc_start: 0.8080 (tttt) cc_final: 0.7670 (tttt) REVERT: E 508 ASN cc_start: 0.7973 (p0) cc_final: 0.6090 (p0) REVERT: E 509 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7263 (mm-30) REVERT: E 526 ASP cc_start: 0.6629 (p0) cc_final: 0.6214 (p0) REVERT: E 530 LYS cc_start: 0.8048 (tmtt) cc_final: 0.7448 (tttt) REVERT: E 532 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7615 (ttpt) REVERT: E 538 LYS cc_start: 0.7959 (ttmm) cc_final: 0.7505 (mtpp) REVERT: E 581 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7849 (ttp-170) REVERT: E 582 LYS cc_start: 0.6958 (pmtt) cc_final: 0.6235 (pmtt) REVERT: I 95 ASN cc_start: 0.8050 (m-40) cc_final: 0.7668 (m-40) REVERT: I 109 TRP cc_start: 0.8723 (m100) cc_final: 0.7728 (m100) REVERT: I 146 PHE cc_start: 0.8356 (p90) cc_final: 0.8104 (p90) REVERT: I 178 ASP cc_start: 0.6626 (t0) cc_final: 0.6347 (t0) REVERT: I 185 PHE cc_start: 0.8182 (t80) cc_final: 0.7939 (t80) REVERT: I 193 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7282 (mp0) REVERT: I 214 TRP cc_start: -0.1723 (OUTLIER) cc_final: -0.3904 (p90) REVERT: I 237 ASP cc_start: 0.7509 (t0) cc_final: 0.6845 (t0) REVERT: I 269 ASP cc_start: 0.6908 (p0) cc_final: 0.6588 (p0) REVERT: I 318 GLN cc_start: 0.8488 (mt0) cc_final: 0.7922 (mm110) REVERT: I 346 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6457 (mm-30) REVERT: I 386 GLN cc_start: 0.7663 (tt0) cc_final: 0.7261 (tt0) REVERT: I 415 ILE cc_start: 0.8625 (mt) cc_final: 0.8291 (mm) REVERT: I 464 TYR cc_start: 0.7913 (t80) cc_final: 0.7649 (t80) REVERT: I 485 ASN cc_start: 0.7423 (p0) cc_final: 0.6808 (p0) REVERT: I 501 LYS cc_start: 0.8593 (ttpt) cc_final: 0.7508 (ptpt) REVERT: I 529 TRP cc_start: 0.8204 (t60) cc_final: 0.7865 (t60) REVERT: I 532 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8223 (ttpp) REVERT: I 538 LYS cc_start: 0.8512 (tppt) cc_final: 0.7546 (tppt) REVERT: I 577 GLN cc_start: 0.8211 (mt0) cc_final: 0.7911 (mt0) REVERT: I 582 LYS cc_start: 0.8366 (pttm) cc_final: 0.8059 (pttm) REVERT: C 67 ARG cc_start: 0.7161 (mmt-90) cc_final: 0.6746 (mmt-90) REVERT: C 73 MET cc_start: 0.7827 (ptt) cc_final: 0.7540 (ptt) REVERT: C 193 GLU cc_start: 0.7224 (tp30) cc_final: 0.6753 (tp30) REVERT: C 382 ARG cc_start: 0.7819 (ttm170) cc_final: 0.7371 (ttm170) REVERT: C 509 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: C 528 TRP cc_start: 0.8589 (m100) cc_final: 0.8035 (m100) REVERT: C 564 SER cc_start: 0.7819 (t) cc_final: 0.7611 (t) REVERT: B 50 GLU cc_start: 0.6961 (mp0) cc_final: 0.6289 (mp0) REVERT: B 52 LYS cc_start: 0.8315 (ttmm) cc_final: 0.7979 (ttmm) REVERT: B 53 PHE cc_start: 0.8376 (m-80) cc_final: 0.7781 (p90) REVERT: B 101 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8196 (mt) REVERT: B 109 TRP cc_start: 0.8748 (m100) cc_final: 0.7772 (m100) REVERT: B 117 TRP cc_start: 0.7929 (m100) cc_final: 0.7358 (m100) REVERT: B 143 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: B 151 LYS cc_start: 0.8742 (mttm) cc_final: 0.8433 (mttm) REVERT: B 167 ASN cc_start: 0.7938 (m-40) cc_final: 0.7573 (m-40) REVERT: B 174 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7387 (mtp) REVERT: B 201 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8609 (mmmt) REVERT: B 211 TYR cc_start: 0.7778 (m-80) cc_final: 0.7463 (m-10) REVERT: B 332 ARG cc_start: 0.7947 (mmt90) cc_final: 0.7677 (mtt90) REVERT: B 397 ARG cc_start: 0.8533 (ptp-170) cc_final: 0.8277 (ptp-170) REVERT: B 424 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7940 (m) REVERT: B 425 THR cc_start: 0.7485 (p) cc_final: 0.5798 (m) REVERT: B 430 LEU cc_start: 0.8504 (tp) cc_final: 0.8189 (tp) REVERT: B 463 VAL cc_start: 0.8171 (OUTLIER) cc_final: 0.7840 (m) REVERT: B 491 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7005 (mm-40) REVERT: B 535 PHE cc_start: 0.8158 (m-80) cc_final: 0.7904 (m-80) REVERT: B 569 MET cc_start: 0.7019 (mmm) cc_final: 0.6734 (mmm) outliers start: 131 outliers final: 93 residues processed: 1555 average time/residue: 0.4709 time to fit residues: 1139.2300 Evaluate side-chains 1617 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1506 time to evaluate : 3.440 ------------------------------------------------------------------------------- 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 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 282 ASN Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 326 THR 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 471 ASP 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 A residue 572 VAL 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 193 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 319 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 245 THR 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 396 GLU 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 506 LEU 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 256 ARG Chi-restraints excluded: chain D residue 498 LEU 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 111 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 166 ASN 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 413 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 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 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 521 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain C residue 84 VAL 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 378 TYR Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 101 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 174 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 389 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 198 optimal weight: 20.0000 chunk 214 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 307 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 251 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 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 282 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 ASN G 384 HIS G 468 GLN F 143 GLN ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 147 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109601 restraints weight = 52586.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113859 restraints weight = 24488.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116578 restraints weight = 13784.620| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31936 Z= 0.196 Angle : 0.646 15.803 43674 Z= 0.322 Chirality : 0.045 0.201 4764 Planarity : 0.005 0.076 5732 Dihedral : 5.158 69.784 4237 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.13 % Allowed : 29.65 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 3686 helix: -1.45 (0.45), residues: 100 sheet: -0.42 (0.18), residues: 865 loop : -0.44 (0.12), residues: 2721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 528 HIS 0.006 0.001 HIS F 222 PHE 0.038 0.002 PHE G 303 TYR 0.039 0.002 TYR A 561 ARG 0.012 0.001 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 295) hydrogen bonds : angle 5.95445 ( 567) SS BOND : bond 0.00502 ( 7) SS BOND : angle 1.01418 ( 14) covalent geometry : bond 0.00423 (31929) covalent geometry : angle 0.64558 (43660) *********************** 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 1660 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1524 time to evaluate : 3.431 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: A 60 GLU cc_start: 0.7269 (tt0) cc_final: 0.6949 (tp30) REVERT: A 104 GLN cc_start: 0.8083 (pt0) cc_final: 0.7495 (pt0) REVERT: A 163 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8305 (mmmt) REVERT: A 182 THR cc_start: 0.8489 (m) cc_final: 0.8074 (t) REVERT: A 214 TRP cc_start: 0.8490 (p90) cc_final: 0.7438 (p90) REVERT: A 216 ARG cc_start: 0.7167 (ttt-90) cc_final: 0.6905 (ttt-90) REVERT: A 237 ASP cc_start: 0.7918 (t0) cc_final: 0.7441 (t0) REVERT: A 260 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: A 279 TRP cc_start: 0.8914 (p-90) cc_final: 0.8278 (p-90) REVERT: A 302 ASN cc_start: 0.8191 (m-40) cc_final: 0.7532 (m110) REVERT: A 312 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8165 (mtmt) REVERT: A 335 GLU cc_start: 0.7102 (tt0) cc_final: 0.6241 (tm-30) REVERT: A 380 PHE cc_start: 0.7686 (p90) cc_final: 0.7364 (p90) REVERT: A 389 THR cc_start: 0.8762 (p) cc_final: 0.8556 (p) REVERT: A 411 GLU cc_start: 0.7849 (mp0) cc_final: 0.7456 (mp0) REVERT: A 413 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6694 (m-30) REVERT: A 414 TRP cc_start: 0.8147 (p90) cc_final: 0.7785 (p90) REVERT: A 443 ASN cc_start: 0.8289 (p0) cc_final: 0.7675 (p0) REVERT: A 446 ASN cc_start: 0.8209 (m110) cc_final: 0.7895 (m110) REVERT: A 468 GLN cc_start: 0.7850 (tt0) cc_final: 0.7519 (tt0) REVERT: A 473 GLU cc_start: 0.7381 (mm-30) cc_final: 0.6867 (mm-30) REVERT: A 501 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8194 (ttpp) REVERT: G 50 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6671 (mp0) REVERT: G 54 LEU cc_start: 0.8610 (mt) cc_final: 0.8058 (mp) REVERT: G 60 GLU cc_start: 0.7516 (tp30) cc_final: 0.7097 (tp30) REVERT: G 62 THR cc_start: 0.8318 (m) cc_final: 0.7720 (t) REVERT: G 67 ARG cc_start: 0.8345 (mtt-85) cc_final: 0.8101 (mtt90) REVERT: G 68 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8090 (tt) REVERT: G 80 ARG cc_start: 0.7962 (tpp80) cc_final: 0.7584 (tpp80) REVERT: G 109 TRP cc_start: 0.8466 (m100) cc_final: 0.7902 (m100) REVERT: G 115 ASN cc_start: 0.7491 (t0) cc_final: 0.7224 (t0) REVERT: G 120 TRP cc_start: 0.8540 (m100) cc_final: 0.8194 (m100) REVERT: G 144 GLU cc_start: 0.7219 (pm20) cc_final: 0.6927 (pm20) REVERT: G 174 MET cc_start: 0.7946 (mtp) cc_final: 0.7418 (mtp) REVERT: G 185 PHE cc_start: 0.8263 (t80) cc_final: 0.7861 (t80) REVERT: G 193 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: G 213 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7485 (tm-30) REVERT: G 237 ASP cc_start: 0.7453 (t0) cc_final: 0.7001 (t0) REVERT: G 242 GLN cc_start: 0.7842 (mt0) cc_final: 0.7574 (mt0) REVERT: G 263 THR cc_start: 0.8567 (m) cc_final: 0.8028 (p) REVERT: G 266 PHE cc_start: 0.8315 (t80) cc_final: 0.7966 (t80) REVERT: G 268 PHE cc_start: 0.8160 (m-10) cc_final: 0.7803 (m-10) REVERT: G 312 LYS cc_start: 0.8553 (mtpp) cc_final: 0.8289 (mtpp) REVERT: G 327 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6811 (mm-30) REVERT: G 335 GLU cc_start: 0.7430 (tt0) cc_final: 0.6955 (tt0) REVERT: G 342 TYR cc_start: 0.7607 (p90) cc_final: 0.7314 (p90) REVERT: G 345 PHE cc_start: 0.8017 (m-80) cc_final: 0.7500 (m-80) REVERT: G 382 ARG cc_start: 0.5388 (mtm180) cc_final: 0.4627 (mtm180) REVERT: G 386 GLN cc_start: 0.7776 (mt0) cc_final: 0.7548 (mm-40) REVERT: G 398 PHE cc_start: 0.8649 (p90) cc_final: 0.8266 (p90) REVERT: G 434 ASP cc_start: 0.7892 (t0) cc_final: 0.7586 (t0) REVERT: G 475 ASP cc_start: 0.7603 (t0) cc_final: 0.7007 (t0) REVERT: G 479 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8374 (mmtm) REVERT: G 501 LYS cc_start: 0.8532 (ttpp) cc_final: 0.7448 (ttpp) REVERT: G 505 ASN cc_start: 0.7719 (t0) cc_final: 0.7077 (t0) REVERT: G 518 MET cc_start: 0.7747 (ptp) cc_final: 0.7492 (ptp) REVERT: G 520 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7943 (mtm-85) REVERT: G 528 TRP cc_start: 0.8193 (m100) cc_final: 0.7618 (m100) REVERT: G 530 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7179 (ttpp) REVERT: G 532 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7969 (ttmm) REVERT: F 47 ASN cc_start: 0.8126 (m-40) cc_final: 0.7831 (m-40) REVERT: F 72 ASN cc_start: 0.8321 (t0) cc_final: 0.8036 (t0) REVERT: F 73 MET cc_start: 0.8146 (ttp) cc_final: 0.7034 (ttp) REVERT: F 80 ARG cc_start: 0.4476 (tpt90) cc_final: 0.1389 (mmt180) REVERT: F 81 ARG cc_start: 0.6135 (ptp-170) cc_final: 0.5852 (ptp-170) REVERT: F 125 ASP cc_start: 0.7605 (m-30) cc_final: 0.7213 (m-30) REVERT: F 135 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: F 144 GLU cc_start: 0.7396 (pm20) cc_final: 0.7154 (pm20) REVERT: F 151 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7775 (mmmm) REVERT: F 193 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7526 (mt-10) REVERT: F 195 LEU cc_start: 0.7499 (mt) cc_final: 0.7195 (mt) REVERT: F 197 PHE cc_start: 0.8220 (m-10) cc_final: 0.7471 (m-80) REVERT: F 201 LYS cc_start: 0.8027 (mmpt) cc_final: 0.7617 (mmpt) REVERT: F 213 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7069 (tm-30) REVERT: F 237 ASP cc_start: 0.8234 (t0) cc_final: 0.7859 (t0) REVERT: F 242 GLN cc_start: 0.7690 (pt0) cc_final: 0.7462 (pp30) REVERT: F 271 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7895 (mtpp) REVERT: F 279 TRP cc_start: 0.8253 (p-90) cc_final: 0.7882 (p-90) REVERT: F 312 LYS cc_start: 0.8663 (mptt) cc_final: 0.8077 (mptt) REVERT: F 335 GLU cc_start: 0.7408 (tt0) cc_final: 0.6853 (tp30) REVERT: F 345 PHE cc_start: 0.7313 (m-80) cc_final: 0.6721 (m-10) REVERT: F 409 TYR cc_start: 0.8399 (t80) cc_final: 0.7988 (t80) REVERT: F 419 ASN cc_start: 0.8513 (m110) cc_final: 0.8133 (m-40) REVERT: F 451 TYR cc_start: 0.8476 (t80) cc_final: 0.7952 (t80) REVERT: F 459 ASN cc_start: 0.8050 (m-40) cc_final: 0.7762 (m110) REVERT: F 473 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7325 (tm-30) REVERT: F 475 ASP cc_start: 0.8160 (t0) cc_final: 0.7662 (t0) REVERT: F 497 GLN cc_start: 0.8366 (mt0) cc_final: 0.7915 (mt0) REVERT: F 501 LYS cc_start: 0.8539 (ttpp) cc_final: 0.8034 (pttp) REVERT: F 518 MET cc_start: 0.8095 (ptp) cc_final: 0.7562 (ptp) REVERT: F 520 ARG cc_start: 0.7977 (mtt90) cc_final: 0.7117 (mtm110) REVERT: F 532 LYS cc_start: 0.8466 (ttmm) cc_final: 0.8028 (ttmm) REVERT: F 557 ASN cc_start: 0.8065 (p0) cc_final: 0.7688 (p0) REVERT: F 562 VAL cc_start: 0.8660 (p) cc_final: 0.8417 (m) REVERT: D 46 ASN cc_start: 0.7986 (t0) cc_final: 0.7501 (t0) REVERT: D 50 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6623 (tm-30) REVERT: D 73 MET cc_start: 0.8302 (ptt) cc_final: 0.7927 (ptm) REVERT: D 107 THR cc_start: 0.8384 (m) cc_final: 0.7749 (p) REVERT: D 142 GLU cc_start: 0.7937 (pt0) cc_final: 0.7341 (pm20) REVERT: D 144 GLU cc_start: 0.7281 (pm20) cc_final: 0.6649 (pm20) REVERT: D 174 MET cc_start: 0.7662 (mtp) cc_final: 0.7141 (mtp) REVERT: D 190 MET cc_start: 0.7862 (mmm) cc_final: 0.7620 (mmm) REVERT: D 256 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7589 (mtm-85) REVERT: E 51 PHE cc_start: 0.8452 (m-80) cc_final: 0.8216 (m-80) REVERT: E 95 ASN cc_start: 0.8212 (t0) cc_final: 0.7657 (t0) REVERT: E 142 GLU cc_start: 0.7698 (pt0) cc_final: 0.6693 (pt0) REVERT: E 163 LYS cc_start: 0.8105 (mppt) cc_final: 0.7660 (mppt) REVERT: E 209 ARG cc_start: 0.4989 (OUTLIER) cc_final: 0.4117 (ptt180) REVERT: E 210 TYR cc_start: 0.8521 (p90) cc_final: 0.8234 (p90) REVERT: E 213 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7657 (tm-30) REVERT: E 237 ASP cc_start: 0.7477 (t0) cc_final: 0.7172 (t0) REVERT: E 256 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7550 (mtp85) REVERT: E 266 PHE cc_start: 0.8251 (t80) cc_final: 0.7988 (t80) REVERT: E 302 ASN cc_start: 0.8447 (t0) cc_final: 0.8066 (t0) REVERT: E 335 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6185 (tm-30) REVERT: E 342 TYR cc_start: 0.7166 (p90) cc_final: 0.6878 (p90) REVERT: E 377 ARG cc_start: 0.5447 (mtt180) cc_final: 0.5116 (mtt180) REVERT: E 382 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7581 (mtt90) REVERT: E 387 LYS cc_start: 0.8759 (tptm) cc_final: 0.8513 (tptm) REVERT: E 400 TYR cc_start: 0.8002 (t80) cc_final: 0.7335 (t80) REVERT: E 404 GLN cc_start: 0.8083 (pt0) cc_final: 0.7382 (pt0) REVERT: E 430 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7617 (tt) REVERT: E 451 TYR cc_start: 0.3850 (OUTLIER) cc_final: 0.3370 (t80) REVERT: E 464 TYR cc_start: 0.8029 (t80) cc_final: 0.7733 (t80) REVERT: E 471 ASP cc_start: 0.6417 (t0) cc_final: 0.6050 (t0) REVERT: E 472 LYS cc_start: 0.3424 (OUTLIER) cc_final: 0.1110 (tmmt) REVERT: E 479 LYS cc_start: 0.8280 (mptt) cc_final: 0.7917 (mptt) REVERT: E 501 LYS cc_start: 0.8124 (tttt) cc_final: 0.7770 (tttt) REVERT: E 526 ASP cc_start: 0.6570 (p0) cc_final: 0.6144 (p0) REVERT: E 530 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7475 (tttt) REVERT: E 532 LYS cc_start: 0.8328 (ttpt) cc_final: 0.7612 (ttpt) REVERT: E 538 LYS cc_start: 0.8013 (ttmm) cc_final: 0.7578 (mtpp) REVERT: E 581 ARG cc_start: 0.8270 (ttp80) cc_final: 0.7817 (ttp-170) REVERT: E 582 LYS cc_start: 0.6943 (pmtt) cc_final: 0.6221 (pmtt) REVERT: I 95 ASN cc_start: 0.8042 (m-40) cc_final: 0.7641 (m-40) REVERT: I 109 TRP cc_start: 0.8720 (m100) cc_final: 0.7744 (m100) REVERT: I 146 PHE cc_start: 0.8361 (p90) cc_final: 0.8115 (p90) REVERT: I 178 ASP cc_start: 0.6655 (t0) cc_final: 0.6336 (t0) REVERT: I 193 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7256 (mp0) REVERT: I 214 TRP cc_start: -0.1633 (OUTLIER) cc_final: -0.3898 (p90) REVERT: I 237 ASP cc_start: 0.7493 (t0) cc_final: 0.6859 (t0) REVERT: I 269 ASP cc_start: 0.6889 (p0) cc_final: 0.6569 (p0) REVERT: I 318 GLN cc_start: 0.8471 (mt0) cc_final: 0.7915 (mm110) REVERT: I 346 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6447 (mm-30) REVERT: I 386 GLN cc_start: 0.7649 (tt0) cc_final: 0.7281 (tt0) REVERT: I 415 ILE cc_start: 0.8651 (mt) cc_final: 0.8317 (mm) REVERT: I 464 TYR cc_start: 0.7865 (t80) cc_final: 0.7561 (t80) REVERT: I 485 ASN cc_start: 0.7412 (p0) cc_final: 0.6783 (p0) REVERT: I 501 LYS cc_start: 0.8616 (ttpt) cc_final: 0.7545 (ptpt) REVERT: I 529 TRP cc_start: 0.8199 (t60) cc_final: 0.7911 (t60) REVERT: I 532 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8209 (ttpp) REVERT: I 538 LYS cc_start: 0.8544 (tppt) cc_final: 0.7575 (tppt) REVERT: I 577 GLN cc_start: 0.8177 (mt0) cc_final: 0.7916 (mt0) REVERT: I 582 LYS cc_start: 0.8406 (pttm) cc_final: 0.8130 (pttm) REVERT: C 67 ARG cc_start: 0.7165 (mmt-90) cc_final: 0.6833 (mmt-90) REVERT: C 73 MET cc_start: 0.7774 (ptt) cc_final: 0.7498 (ptt) REVERT: C 193 GLU cc_start: 0.7220 (tp30) cc_final: 0.6741 (tp30) REVERT: C 382 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7432 (ttm170) REVERT: C 509 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: C 528 TRP cc_start: 0.8587 (m100) cc_final: 0.8054 (m100) REVERT: C 564 SER cc_start: 0.7866 (t) cc_final: 0.7657 (t) REVERT: B 52 LYS cc_start: 0.8336 (ttmm) cc_final: 0.8019 (ttmm) REVERT: B 53 PHE cc_start: 0.8354 (m-80) cc_final: 0.7789 (p90) REVERT: B 68 LEU cc_start: 0.8238 (tp) cc_final: 0.7919 (mp) REVERT: B 101 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8204 (mt) REVERT: B 109 TRP cc_start: 0.8723 (m100) cc_final: 0.7769 (m100) REVERT: B 117 TRP cc_start: 0.7890 (m100) cc_final: 0.7376 (m100) REVERT: B 142 GLU cc_start: 0.7695 (pp20) cc_final: 0.7337 (pp20) REVERT: B 151 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8423 (mttm) REVERT: B 167 ASN cc_start: 0.7952 (m-40) cc_final: 0.7599 (m-40) REVERT: B 174 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7373 (mtp) REVERT: B 201 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8524 (mmmt) REVERT: B 211 TYR cc_start: 0.7769 (m-80) cc_final: 0.7473 (m-10) REVERT: B 332 ARG cc_start: 0.7976 (mmt90) cc_final: 0.7733 (mtt90) REVERT: B 397 ARG cc_start: 0.8459 (ptp-170) cc_final: 0.8047 (ptp-170) REVERT: B 424 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7893 (m) REVERT: B 430 LEU cc_start: 0.8511 (tp) cc_final: 0.8197 (tp) REVERT: B 463 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7849 (m) REVERT: B 470 TRP cc_start: 0.8497 (p90) cc_final: 0.8056 (p90) REVERT: B 491 GLN cc_start: 0.7478 (mm-40) cc_final: 0.6901 (mm-40) REVERT: B 528 TRP cc_start: 0.8625 (m100) cc_final: 0.8404 (m100) REVERT: B 535 PHE cc_start: 0.8163 (m-80) cc_final: 0.7878 (m-80) REVERT: B 569 MET cc_start: 0.7044 (mmm) cc_final: 0.6772 (mmm) outliers start: 136 outliers final: 105 residues processed: 1567 average time/residue: 0.4519 time to fit residues: 1100.9053 Evaluate side-chains 1635 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1512 time to evaluate : 3.257 ------------------------------------------------------------------------------- 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 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 282 ASN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 330 ILE 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 471 ASP 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 A residue 572 VAL 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 193 GLU Chi-restraints excluded: chain G residue 225 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 319 MET Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain G residue 416 GLN Chi-restraints excluded: chain G residue 468 GLN Chi-restraints excluded: chain G residue 562 VAL Chi-restraints excluded: chain G residue 582 LYS Chi-restraints excluded: chain F residue 44 THR 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 216 ARG Chi-restraints excluded: chain F residue 245 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 396 GLU Chi-restraints excluded: chain F residue 417 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 506 LEU Chi-restraints excluded: chain F residue 553 ILE 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 256 ARG Chi-restraints excluded: chain D residue 498 LEU 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 111 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 209 ARG Chi-restraints excluded: chain E residue 241 VAL 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 393 GLU 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 I residue 55 GLU 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 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 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 521 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain C residue 84 VAL 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 378 TYR Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 101 ILE 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 174 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 316 VAL Chi-restraints excluded: chain B residue 389 THR 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 224 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 295 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 340 optimal weight: 8.9990 chunk 357 optimal weight: 0.8980 chunk 342 optimal weight: 9.9990 chunk 378 optimal weight: 1.9990 chunk 370 optimal weight: 6.9990 chunk 283 optimal weight: 0.0060 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN A 426 ASN A 446 ASN ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 HIS ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 143 GLN F 234 HIS F 310 GLN F 321 ASN F 419 ASN ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 147 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111421 restraints weight = 52553.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115729 restraints weight = 24465.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118487 restraints weight = 13733.538| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2967 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= 0.117 Angle : 0.633 16.031 43674 Z= 0.313 Chirality : 0.044 0.226 4764 Planarity : 0.005 0.065 5732 Dihedral : 4.929 68.522 4237 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.61 % Allowed : 30.56 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3686 helix: -1.29 (0.47), residues: 96 sheet: -0.27 (0.18), residues: 877 loop : -0.37 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 208 HIS 0.005 0.001 HIS F 222 PHE 0.022 0.001 PHE B 353 TYR 0.034 0.001 TYR A 561 ARG 0.011 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 295) hydrogen bonds : angle 5.88788 ( 567) SS BOND : bond 0.00416 ( 7) SS BOND : angle 0.86540 ( 14) covalent geometry : bond 0.00273 (31929) covalent geometry : angle 0.63271 (43660) ********************** 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 1634 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1515 time to evaluate : 3.703 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: A 60 GLU cc_start: 0.7196 (tt0) cc_final: 0.6855 (tp30) REVERT: A 79 TYR cc_start: 0.8292 (m-80) cc_final: 0.7794 (m-80) REVERT: A 104 GLN cc_start: 0.8098 (pt0) cc_final: 0.7464 (pt0) REVERT: A 163 LYS cc_start: 0.8615 (mmmt) cc_final: 0.8223 (mmmt) REVERT: A 182 THR cc_start: 0.8388 (m) cc_final: 0.8100 (t) REVERT: A 214 TRP cc_start: 0.8525 (p90) cc_final: 0.7431 (p90) REVERT: A 216 ARG cc_start: 0.7083 (ttt-90) cc_final: 0.6832 (ttt-90) REVERT: A 230 THR cc_start: 0.8632 (p) cc_final: 0.8428 (t) REVERT: A 237 ASP cc_start: 0.7864 (t0) cc_final: 0.7363 (t0) REVERT: A 260 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: A 279 TRP cc_start: 0.8866 (p-90) cc_final: 0.8230 (p-90) REVERT: A 312 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8140 (mtmt) REVERT: A 335 GLU cc_start: 0.7048 (tt0) cc_final: 0.6359 (tm-30) REVERT: A 411 GLU cc_start: 0.7778 (mp0) cc_final: 0.7462 (mp0) REVERT: A 413 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6617 (m-30) REVERT: A 414 TRP cc_start: 0.8049 (p90) cc_final: 0.7741 (p90) REVERT: A 443 ASN cc_start: 0.8183 (p0) cc_final: 0.7548 (p0) REVERT: A 446 ASN cc_start: 0.8230 (m-40) cc_final: 0.7804 (m110) REVERT: A 464 TYR cc_start: 0.8153 (t80) cc_final: 0.7848 (t80) REVERT: A 468 GLN cc_start: 0.7787 (tt0) cc_final: 0.7501 (tt0) REVERT: A 473 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6840 (mm-30) REVERT: A 501 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8121 (ttpp) REVERT: A 538 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7744 (ttmt) REVERT: G 50 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: G 53 PHE cc_start: 0.5231 (p90) cc_final: 0.4720 (p90) REVERT: G 54 LEU cc_start: 0.8557 (mt) cc_final: 0.7993 (mp) REVERT: G 60 GLU cc_start: 0.7420 (tp30) cc_final: 0.7031 (tp30) REVERT: G 67 ARG cc_start: 0.8317 (mtt-85) cc_final: 0.8085 (mtt90) REVERT: G 68 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8063 (tt) REVERT: G 80 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7551 (tpp80) REVERT: G 83 VAL cc_start: 0.8773 (t) cc_final: 0.8389 (m) REVERT: G 90 THR cc_start: 0.8570 (p) cc_final: 0.8370 (t) REVERT: G 109 TRP cc_start: 0.8456 (m100) cc_final: 0.7901 (m100) REVERT: G 120 TRP cc_start: 0.8455 (m100) cc_final: 0.8068 (m100) REVERT: G 144 GLU cc_start: 0.7198 (pm20) cc_final: 0.6778 (pm20) REVERT: G 174 MET cc_start: 0.7841 (mtp) cc_final: 0.7366 (mtp) REVERT: G 185 PHE cc_start: 0.8236 (t80) cc_final: 0.7784 (t80) REVERT: G 193 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: G 213 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7361 (tm-30) REVERT: G 237 ASP cc_start: 0.7572 (t0) cc_final: 0.7107 (t0) REVERT: G 242 GLN cc_start: 0.7809 (mt0) cc_final: 0.7555 (mt0) REVERT: G 266 PHE cc_start: 0.8260 (t80) cc_final: 0.7991 (t80) REVERT: G 283 ARG cc_start: 0.8272 (mtp180) cc_final: 0.7666 (ptm160) REVERT: G 312 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8282 (mtpp) REVERT: G 327 GLU cc_start: 0.7439 (mm-30) cc_final: 0.6806 (mm-30) REVERT: G 335 GLU cc_start: 0.7495 (tt0) cc_final: 0.7002 (tt0) REVERT: G 342 TYR cc_start: 0.7479 (p90) cc_final: 0.7268 (p90) REVERT: G 345 PHE cc_start: 0.8001 (m-80) cc_final: 0.7465 (m-80) REVERT: G 346 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6591 (mm-30) REVERT: G 382 ARG cc_start: 0.5287 (mtm180) cc_final: 0.4496 (mtm180) REVERT: G 398 PHE cc_start: 0.8651 (p90) cc_final: 0.8215 (p90) REVERT: G 457 LEU cc_start: 0.8238 (mt) cc_final: 0.7964 (mp) REVERT: G 475 ASP cc_start: 0.7548 (t0) cc_final: 0.6992 (t0) REVERT: G 501 LYS cc_start: 0.8491 (ttpp) cc_final: 0.7638 (ttpp) REVERT: G 505 ASN cc_start: 0.7716 (t0) cc_final: 0.7092 (t0) REVERT: G 518 MET cc_start: 0.7802 (ptp) cc_final: 0.7541 (ptp) REVERT: G 528 TRP cc_start: 0.8233 (m100) cc_final: 0.7630 (m100) REVERT: G 530 LYS cc_start: 0.8063 (ttpp) cc_final: 0.7141 (ttpp) REVERT: G 532 LYS cc_start: 0.8161 (ttpp) cc_final: 0.7877 (ttmm) REVERT: G 543 HIS cc_start: 0.7701 (m90) cc_final: 0.7368 (m90) REVERT: F 65 SER cc_start: 0.8444 (t) cc_final: 0.8158 (p) REVERT: F 72 ASN cc_start: 0.8310 (t0) cc_final: 0.8034 (t0) REVERT: F 73 MET cc_start: 0.8143 (ttp) cc_final: 0.7058 (ttp) REVERT: F 80 ARG cc_start: 0.4287 (tpt90) cc_final: 0.3641 (tpt90) REVERT: F 81 ARG cc_start: 0.6244 (ptp-170) cc_final: 0.5513 (ptp-170) REVERT: F 109 TRP cc_start: 0.8326 (m100) cc_final: 0.7861 (m100) REVERT: F 125 ASP cc_start: 0.7564 (m-30) cc_final: 0.7152 (m-30) REVERT: F 135 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: F 144 GLU cc_start: 0.7387 (pm20) cc_final: 0.7184 (pm20) REVERT: F 151 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7840 (mmmm) REVERT: F 191 ARG cc_start: 0.8401 (mtt90) cc_final: 0.8059 (mtp85) REVERT: F 193 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7491 (mt-10) REVERT: F 195 LEU cc_start: 0.7493 (mt) cc_final: 0.7227 (mt) REVERT: F 197 PHE cc_start: 0.8196 (m-10) cc_final: 0.7519 (m-80) REVERT: F 201 LYS cc_start: 0.8028 (mmpt) cc_final: 0.7634 (mmpt) REVERT: F 237 ASP cc_start: 0.8202 (t0) cc_final: 0.7992 (t0) REVERT: F 242 GLN cc_start: 0.7699 (pt0) cc_final: 0.7493 (pp30) REVERT: F 271 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7880 (mtpp) REVERT: F 279 TRP cc_start: 0.8317 (p-90) cc_final: 0.7920 (p-90) REVERT: F 335 GLU cc_start: 0.7407 (tt0) cc_final: 0.6882 (tp30) REVERT: F 353 PHE cc_start: 0.7316 (p90) cc_final: 0.6999 (p90) REVERT: F 409 TYR cc_start: 0.8354 (t80) cc_final: 0.7988 (t80) REVERT: F 419 ASN cc_start: 0.8455 (m-40) cc_final: 0.8116 (m-40) REVERT: F 451 TYR cc_start: 0.8416 (t80) cc_final: 0.7850 (t80) REVERT: F 473 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7308 (tm-30) REVERT: F 475 ASP cc_start: 0.8112 (t0) cc_final: 0.7560 (t0) REVERT: F 497 GLN cc_start: 0.8340 (mt0) cc_final: 0.7904 (mt0) REVERT: F 501 LYS cc_start: 0.8504 (ttpp) cc_final: 0.8061 (ttpp) REVERT: F 518 MET cc_start: 0.8090 (ptp) cc_final: 0.7566 (ptp) REVERT: F 520 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7080 (mtm110) REVERT: F 532 LYS cc_start: 0.8500 (ttmm) cc_final: 0.8035 (ttmm) REVERT: F 562 VAL cc_start: 0.8664 (p) cc_final: 0.8424 (m) REVERT: D 46 ASN cc_start: 0.7954 (t0) cc_final: 0.7497 (t0) REVERT: D 50 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6565 (tm-30) REVERT: D 73 MET cc_start: 0.8314 (ptt) cc_final: 0.7954 (ptm) REVERT: D 107 THR cc_start: 0.8468 (m) cc_final: 0.7816 (p) REVERT: D 142 GLU cc_start: 0.7834 (pt0) cc_final: 0.7237 (pm20) REVERT: D 144 GLU cc_start: 0.7268 (pm20) cc_final: 0.6647 (pm20) REVERT: D 174 MET cc_start: 0.7695 (mtp) cc_final: 0.7216 (mtp) REVERT: D 190 MET cc_start: 0.7908 (mmm) cc_final: 0.7663 (mmm) REVERT: D 256 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7619 (mtm-85) REVERT: D 532 LYS cc_start: 0.8336 (tttt) cc_final: 0.8044 (tttt) REVERT: E 51 PHE cc_start: 0.8456 (m-80) cc_final: 0.8226 (m-80) REVERT: E 95 ASN cc_start: 0.8143 (t0) cc_final: 0.7553 (t0) REVERT: E 96 MET cc_start: 0.5551 (ptt) cc_final: 0.5274 (ptt) REVERT: E 142 GLU cc_start: 0.7583 (pt0) cc_final: 0.6545 (pt0) REVERT: E 163 LYS cc_start: 0.8079 (mppt) cc_final: 0.7634 (mppt) REVERT: E 209 ARG cc_start: 0.4920 (OUTLIER) cc_final: 0.4467 (ptt180) REVERT: E 210 TYR cc_start: 0.8434 (p90) cc_final: 0.8212 (p90) REVERT: E 213 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8028 (tm-30) REVERT: E 237 ASP cc_start: 0.7448 (t0) cc_final: 0.7213 (t0) REVERT: E 248 ASN cc_start: 0.7825 (m110) cc_final: 0.7620 (m110) REVERT: E 256 ARG cc_start: 0.7886 (mtp180) cc_final: 0.7591 (mtp85) REVERT: E 266 PHE cc_start: 0.8174 (t80) cc_final: 0.7875 (t80) REVERT: E 302 ASN cc_start: 0.8458 (t0) cc_final: 0.8077 (t0) REVERT: E 335 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6165 (tm-30) REVERT: E 342 TYR cc_start: 0.7185 (p90) cc_final: 0.6947 (p90) REVERT: E 377 ARG cc_start: 0.5160 (mtt180) cc_final: 0.4756 (mtt180) REVERT: E 382 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7574 (mtt90) REVERT: E 387 LYS cc_start: 0.8746 (tptm) cc_final: 0.8507 (tptm) REVERT: E 400 TYR cc_start: 0.8007 (t80) cc_final: 0.7340 (t80) REVERT: E 404 GLN cc_start: 0.8045 (pt0) cc_final: 0.7351 (pt0) REVERT: E 430 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7592 (tt) REVERT: E 451 TYR cc_start: 0.3715 (OUTLIER) cc_final: 0.3332 (t80) REVERT: E 464 TYR cc_start: 0.7934 (t80) cc_final: 0.7633 (t80) REVERT: E 471 ASP cc_start: 0.6323 (t0) cc_final: 0.5802 (t0) REVERT: E 472 LYS cc_start: 0.3630 (OUTLIER) cc_final: 0.1374 (tmmt) REVERT: E 479 LYS cc_start: 0.8268 (mptt) cc_final: 0.7909 (mptt) REVERT: E 501 LYS cc_start: 0.8064 (tttt) cc_final: 0.7570 (tttt) REVERT: E 526 ASP cc_start: 0.6520 (p0) cc_final: 0.6071 (p0) REVERT: E 530 LYS cc_start: 0.8080 (tmtt) cc_final: 0.7600 (tttt) REVERT: E 532 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7602 (ttpt) REVERT: E 538 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7635 (mtpp) REVERT: E 581 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7840 (ttp-170) REVERT: E 582 LYS cc_start: 0.6891 (pmtt) cc_final: 0.6096 (pmtt) REVERT: I 82 VAL cc_start: 0.8296 (t) cc_final: 0.7965 (p) REVERT: I 95 ASN cc_start: 0.7988 (m-40) cc_final: 0.7587 (m-40) REVERT: I 109 TRP cc_start: 0.8704 (m100) cc_final: 0.7719 (m100) REVERT: I 178 ASP cc_start: 0.6606 (t0) cc_final: 0.6288 (t0) REVERT: I 193 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7169 (mp0) REVERT: I 214 TRP cc_start: -0.1912 (OUTLIER) cc_final: -0.4310 (p90) REVERT: I 237 ASP cc_start: 0.7431 (t0) cc_final: 0.6810 (t0) REVERT: I 269 ASP cc_start: 0.6859 (p0) cc_final: 0.6511 (p0) REVERT: I 274 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.8026 (tpp80) REVERT: I 279 TRP cc_start: 0.8856 (p-90) cc_final: 0.7786 (p-90) REVERT: I 318 GLN cc_start: 0.8345 (mt0) cc_final: 0.7860 (mm110) REVERT: I 346 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6477 (mm-30) REVERT: I 386 GLN cc_start: 0.7610 (tt0) cc_final: 0.7215 (tt0) REVERT: I 415 ILE cc_start: 0.8665 (mt) cc_final: 0.8302 (mm) REVERT: I 464 TYR cc_start: 0.7721 (t80) cc_final: 0.7464 (t80) REVERT: I 485 ASN cc_start: 0.7423 (p0) cc_final: 0.6867 (p0) REVERT: I 501 LYS cc_start: 0.8563 (ttpt) cc_final: 0.7609 (ptpt) REVERT: I 529 TRP cc_start: 0.8178 (t60) cc_final: 0.7904 (t60) REVERT: I 532 LYS cc_start: 0.8579 (ttmm) cc_final: 0.8236 (ttpp) REVERT: I 538 LYS cc_start: 0.8565 (tppt) cc_final: 0.8244 (tppt) REVERT: I 577 GLN cc_start: 0.8126 (mt0) cc_final: 0.7819 (mt0) REVERT: I 582 LYS cc_start: 0.8311 (pttm) cc_final: 0.8048 (pttm) REVERT: C 67 ARG cc_start: 0.7095 (mmt-90) cc_final: 0.6729 (mmt-90) REVERT: C 73 MET cc_start: 0.7703 (ptt) cc_final: 0.7451 (ptt) REVERT: C 104 GLN cc_start: 0.7934 (pt0) cc_final: 0.7593 (pt0) REVERT: C 193 GLU cc_start: 0.7185 (tp30) cc_final: 0.6688 (tp30) REVERT: C 382 ARG cc_start: 0.7888 (ttm170) cc_final: 0.7454 (ttm170) REVERT: C 509 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: C 564 SER cc_start: 0.7836 (t) cc_final: 0.7344 (t) REVERT: B 52 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8026 (ttmm) REVERT: B 53 PHE cc_start: 0.8349 (m-80) cc_final: 0.7755 (p90) REVERT: B 68 LEU cc_start: 0.8078 (tp) cc_final: 0.7797 (mp) REVERT: B 101 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8191 (mt) REVERT: B 109 TRP cc_start: 0.8737 (m100) cc_final: 0.7772 (m100) REVERT: B 117 TRP cc_start: 0.7871 (m100) cc_final: 0.7400 (m100) REVERT: B 151 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8346 (mttm) REVERT: B 167 ASN cc_start: 0.7943 (m-40) cc_final: 0.7593 (m-40) REVERT: B 174 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7362 (mtp) REVERT: B 201 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8574 (mmmt) REVERT: B 211 TYR cc_start: 0.7748 (m-80) cc_final: 0.7410 (m-10) REVERT: B 266 PHE cc_start: 0.8163 (t80) cc_final: 0.7323 (t80) REVERT: B 424 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7787 (m) REVERT: B 430 LEU cc_start: 0.8524 (tp) cc_final: 0.8211 (tp) REVERT: B 449 ASN cc_start: 0.8227 (t0) cc_final: 0.7991 (t0) REVERT: B 463 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7824 (m) REVERT: B 479 LYS cc_start: 0.8362 (mttm) cc_final: 0.8119 (mttm) REVERT: B 491 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7059 (mm-40) REVERT: B 528 TRP cc_start: 0.8605 (m100) cc_final: 0.8392 (m100) REVERT: B 535 PHE cc_start: 0.8142 (m-80) cc_final: 0.7882 (m-80) REVERT: B 569 MET cc_start: 0.7010 (mmm) cc_final: 0.6731 (mmm) outliers start: 119 outliers final: 88 residues processed: 1550 average time/residue: 0.4649 time to fit residues: 1121.1312 Evaluate side-chains 1618 residues out of total 3295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1510 time to evaluate : 3.342 ------------------------------------------------------------------------------- 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 166 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 319 MET 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 471 ASP Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 536 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 A residue 572 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 129 ILE Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 265 THR Chi-restraints excluded: chain G residue 277 HIS Chi-restraints excluded: chain G residue 346 GLU Chi-restraints excluded: chain G residue 403 HIS 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 216 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 245 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 479 LYS Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain D residue 44 THR 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 111 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 144 GLU 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 331 MET Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 393 GLU 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 I residue 55 GLU 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 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 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 523 THR Chi-restraints excluded: chain C residue 84 VAL 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 378 TYR Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 101 ILE 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 174 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 389 THR 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 208 optimal weight: 10.0000 chunk 356 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 353 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 chunk 351 optimal weight: 0.0270 chunk 148 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 348 optimal weight: 1.9990 chunk 291 optimal weight: 9.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN G 143 GLN G 384 HIS G 386 GLN ** G 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 147 ASN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN C 166 ASN B 222 HIS ** B 550 GLN ** 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 = 0.3577 r_free = 0.3577 target = 0.129492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111440 restraints weight = 52360.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115737 restraints weight = 24345.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118480 restraints weight = 13649.524| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 31936 Z= 0.164 Angle : 0.744 59.196 43674 Z= 0.399 Chirality : 0.045 0.710 4764 Planarity : 0.005 0.063 5732 Dihedral : 4.928 68.519 4237 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.58 % Allowed : 30.80 % Favored : 65.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3686 helix: -1.28 (0.47), residues: 96 sheet: -0.27 (0.18), residues: 877 loop : -0.37 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP E 208 HIS 0.020 0.001 HIS A 222 PHE 0.020 0.001 PHE G 527 TYR 0.050 0.002 TYR A 561 ARG 0.009 0.001 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.02899 ( 295) hydrogen bonds : angle 5.88326 ( 567) SS BOND : bond 0.00347 ( 7) SS BOND : angle 0.78798 ( 14) covalent geometry : bond 0.00392 (31929) covalent geometry : angle 0.74391 (43660) =============================================================================== Job complete usr+sys time: 19190.11 seconds wall clock time: 343 minutes 23.85 seconds (20603.85 seconds total)