Starting phenix.real_space_refine on Sat Feb 7 09:25:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7utv_26790/02_2026/7utv_26790.cif Found real_map, /net/cci-nas-00/data/ceres_data/7utv_26790/02_2026/7utv_26790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7utv_26790/02_2026/7utv_26790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7utv_26790/02_2026/7utv_26790.map" model { file = "/net/cci-nas-00/data/ceres_data/7utv_26790/02_2026/7utv_26790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7utv_26790/02_2026/7utv_26790.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.077 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 122 5.16 5 C 20703 2.51 5 N 5570 2.21 5 O 6151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32546 Number of models: 1 Model: "" Number of chains: 10 Chain: "L" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 456 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 91 Planarities with less than four sites: {'UNK:plan-1': 90} Unresolved non-hydrogen planarities: 90 Chain: "H" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 501 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'CIS': 1, 'TRANS': 98} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 99} Unresolved non-hydrogen planarities: 99 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: "B" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3780 Classifications: {'peptide': 472} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 437} Chain breaks: 3 Chain: "C" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3216 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 372} Chain breaks: 5 Chain: "D" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3449 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 398} Chain breaks: 4 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: "F" 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: "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: "I" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4192 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 487} Chain breaks: 3 Time building chain proxies: 7.21, per 1000 atoms: 0.22 Number of scatterers: 32546 At special positions: 0 Unit cell: (182.6, 202.4, 128.7, 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 122 16.00 O 6151 8.00 N 5570 7.00 C 20703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 494 " distance=2.04 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 494 " distance=2.03 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 494 " distance=2.04 Simple disulfide: pdb=" SG CYS D 490 " - pdb=" SG CYS D 494 " distance=2.04 Simple disulfide: pdb=" SG CYS E 490 " - pdb=" SG CYS E 494 " distance=2.04 Simple disulfide: pdb=" SG CYS F 490 " - pdb=" SG CYS F 494 " distance=2.04 Simple disulfide: pdb=" SG CYS G 490 " - pdb=" SG CYS G 494 " distance=2.04 Simple disulfide: pdb=" SG CYS I 490 " - pdb=" SG CYS I 494 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7766 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 72 sheets defined 13.2% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'H' and resid 34 through 38 Processing helix chain 'A' and resid 86 through 92 removed outlier: 4.138A pdb=" N VAL A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.833A pdb=" N THR A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.668A pdb=" N MET A 190 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.590A pdb=" N VAL A 241 " --> pdb=" O PRO A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.791A pdb=" N PHE A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 561 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 121 removed outlier: 4.098A pdb=" N TRP B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 187 through 191 removed outlier: 3.504A pdb=" N MET B 190 " --> pdb=" O PRO B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 3.814A pdb=" N VAL B 241 " --> pdb=" O PRO B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 removed outlier: 3.502A pdb=" N SER B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 443 through 448 removed outlier: 4.269A pdb=" N ILE B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 95 through 99 removed outlier: 3.817A pdb=" N ASP C 99 " --> pdb=" O MET C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 237 through 241 removed outlier: 3.737A pdb=" N VAL C 241 " --> pdb=" O PRO C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 557 through 562 removed outlier: 3.519A pdb=" N TYR C 561 " --> pdb=" O GLN C 558 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 562 " --> pdb=" O PHE C 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 3.964A pdb=" N VAL D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 237 through 241 removed outlier: 3.516A pdb=" N VAL D 241 " --> pdb=" O PRO D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 557 through 561 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.588A pdb=" N MET E 190 " --> pdb=" O PRO E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 removed outlier: 3.515A pdb=" N VAL E 241 " --> pdb=" O PRO E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 309 through 313 removed outlier: 3.779A pdb=" N ARG E 313 " --> pdb=" O GLN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 Processing helix chain 'E' and resid 443 through 447 Processing helix chain 'E' and resid 557 through 561 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 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 237 through 241 removed outlier: 3.561A pdb=" N VAL F 241 " --> pdb=" O PRO F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 250 Processing helix chain 'F' and resid 281 through 285 Processing helix chain 'F' and resid 309 through 313 removed outlier: 3.858A 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 425 through 427 No H-bonds generated for 'chain 'F' and resid 425 through 427' Processing helix chain 'F' and resid 443 through 448 removed outlier: 3.992A pdb=" N ILE F 447 " --> pdb=" O ASN F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 561 removed outlier: 3.601A pdb=" N TYR F 561 " --> pdb=" O GLN F 558 " (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 120 Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.916A pdb=" N MET G 190 " --> pdb=" O PRO G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 241 removed outlier: 3.583A pdb=" N VAL G 241 " --> pdb=" O PRO G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 250 Processing helix chain 'G' and resid 281 through 285 Processing helix chain 'G' and resid 309 through 313 removed outlier: 4.091A pdb=" N ARG G 313 " --> pdb=" O GLN G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 385 removed outlier: 4.087A pdb=" N GLY G 385 " --> pdb=" O ARG G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 Processing helix chain 'G' and resid 425 through 427 No H-bonds generated for 'chain 'G' and resid 425 through 427' Processing helix chain 'G' and resid 443 through 448 Processing helix chain 'G' and resid 557 through 561 Processing helix chain 'I' and resid 86 through 91 Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'I' and resid 116 through 120 Processing helix chain 'I' and resid 122 through 132 Processing helix chain 'I' and resid 187 through 192 removed outlier: 3.510A pdb=" N MET I 190 " --> pdb=" O PRO I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 241 Processing helix chain 'I' and resid 245 through 249 Processing helix chain 'I' and resid 281 through 285 Processing helix chain 'I' and resid 309 through 313 removed outlier: 4.088A pdb=" N ARG I 313 " --> pdb=" O GLN I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 413 Processing helix chain 'I' and resid 425 through 427 No H-bonds generated for 'chain 'I' and resid 425 through 427' Processing helix chain 'I' and resid 443 through 447 Processing helix chain 'I' and resid 557 through 561 removed outlier: 3.530A pdb=" N TYR I 561 " --> pdb=" O GLN I 558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA3, first strand: chain 'H' and resid 49 through 50 removed outlier: 6.429A pdb=" N UNK H 41 " --> pdb=" O UNK H 32 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N UNK H 32 " --> pdb=" O UNK H 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 44 through 45 current: chain 'B' and resid 102 through 112 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 49 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=AA6, first strand: chain 'A' and resid 80 through 84 Processing sheet with id=AA7, first strand: chain 'A' and resid 216 through 218 Processing sheet with id=AA8, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.018A pdb=" N HIS A 277 " --> pdb=" O ARG A 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 319 removed outlier: 4.190A pdb=" N MET A 319 " --> pdb=" O ASN G 375 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASN G 375 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.866A pdb=" N GLU A 335 " --> pdb=" O ALA A 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 351 through 354 removed outlier: 3.738A pdb=" N SER A 348 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 396 through 399 removed outlier: 7.036A pdb=" N ASN A 375 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET F 319 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 429 through 430 removed outlier: 3.628A pdb=" N SER G 348 " --> pdb=" O GLY G 351 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 463 through 464 removed outlier: 4.186A pdb=" N TYR A 464 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 574 " --> pdb=" O TYR A 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 470 through 472 removed outlier: 7.021A pdb=" N ASP A 471 " --> pdb=" O CYS A 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 44 through 45 current: chain 'C' and resid 102 through 112 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, 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=AB9, first strand: chain 'B' and resid 216 through 218 Processing sheet with id=AC1, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.034A pdb=" N HIS B 277 " --> pdb=" O ARG B 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 346 through 348 removed outlier: 3.557A pdb=" N SER B 348 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 396 through 399 removed outlier: 7.044A pdb=" N ASN B 375 " --> pdb=" O MET I 319 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N MET I 319 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AC5, first strand: chain 'B' and resid 463 through 464 removed outlier: 4.127A pdb=" N TYR B 464 " --> pdb=" O GLU B 574 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 574 " --> pdb=" O TYR B 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 470 through 472 removed outlier: 6.698A pdb=" N ASP B 471 " --> pdb=" O CYS B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 44 through 45 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 44 through 45 current: chain 'D' and resid 102 through 112 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 49 through 53 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 72 current: chain 'C' and resid 261 through 262 Processing sheet with id=AC9, first strand: chain 'C' and resid 216 through 218 Processing sheet with id=AD1, first strand: chain 'C' and resid 345 through 347 Processing sheet with id=AD2, first strand: chain 'C' and resid 377 through 380 Processing sheet with id=AD3, first strand: chain 'C' and resid 470 through 472 removed outlier: 6.607A pdb=" N ASP C 471 " --> pdb=" O CYS C 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 49 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 58 through 72 current: chain 'D' and resid 164 through 167 Processing sheet with id=AD5, first strand: chain 'D' and resid 216 through 218 Processing sheet with id=AD6, first strand: chain 'D' and resid 276 through 278 removed outlier: 5.998A pdb=" N HIS D 277 " --> pdb=" O ARG D 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 345 through 348 removed outlier: 3.988A pdb=" N SER D 348 " --> pdb=" O GLY D 351 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 377 through 380 Processing sheet with id=AD9, first strand: chain 'D' and resid 463 through 464 removed outlier: 4.213A pdb=" N TYR D 464 " --> pdb=" O GLU D 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 470 through 472 removed outlier: 6.805A pdb=" N ASP D 471 " --> pdb=" O CYS D 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 49 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=AE3, first strand: chain 'E' and resid 80 through 84 Processing sheet with id=AE4, first strand: chain 'E' and resid 215 through 218 removed outlier: 4.024A pdb=" N GLY E 235 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR E 217 " --> pdb=" O TYR E 233 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 233 " --> pdb=" O THR E 217 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 276 through 278 Processing sheet with id=AE6, first strand: chain 'E' and resid 335 through 336 removed outlier: 6.648A pdb=" N GLU E 335 " --> pdb=" O ALA E 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 345 through 348 removed outlier: 3.972A pdb=" N SER E 348 " --> pdb=" O GLY E 351 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 377 through 380 Processing sheet with id=AE9, first strand: chain 'E' and resid 415 through 416 Processing sheet with id=AF1, first strand: chain 'E' and resid 463 through 464 removed outlier: 4.270A pdb=" N TYR E 464 " --> pdb=" O GLU E 574 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU E 574 " --> pdb=" O TYR E 464 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 470 through 472 removed outlier: 6.935A pdb=" N ASP E 471 " --> pdb=" O CYS E 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 49 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=AF4, first strand: chain 'F' and resid 80 through 84 Processing sheet with id=AF5, first strand: chain 'F' and resid 215 through 218 removed outlier: 3.871A pdb=" N GLY F 235 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR F 217 " --> pdb=" O TYR F 233 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N TYR F 233 " --> pdb=" O THR F 217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 276 through 278 removed outlier: 5.788A pdb=" N HIS F 277 " --> pdb=" O ARG F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'F' and resid 335 through 336 removed outlier: 6.657A pdb=" N GLU F 335 " --> pdb=" O ALA F 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'F' and resid 351 through 354 removed outlier: 3.710A pdb=" N GLY F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 396 through 399 removed outlier: 7.226A pdb=" N ASN F 375 " --> pdb=" O MET G 319 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET G 319 " --> pdb=" O ASN F 375 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 463 through 464 removed outlier: 3.861A pdb=" N TYR F 464 " --> pdb=" O GLU F 574 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 470 through 472 removed outlier: 6.931A pdb=" N ASP F 471 " --> pdb=" O CYS F 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'G' and resid 49 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=AG4, first strand: chain 'G' and resid 80 through 84 Processing sheet with id=AG5, first strand: chain 'G' and resid 215 through 218 removed outlier: 6.253A pdb=" N ASP G 215 " --> pdb=" O HIS G 234 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 276 through 278 removed outlier: 6.267A pdb=" N HIS G 277 " --> pdb=" O ARG G 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'G' and resid 335 through 336 removed outlier: 6.671A pdb=" N GLU G 335 " --> pdb=" O ALA G 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'G' and resid 470 through 472 removed outlier: 6.674A pdb=" N ASP G 471 " --> pdb=" O CYS G 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, 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=AH1, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AH2, first strand: chain 'I' and resid 215 through 218 removed outlier: 6.507A pdb=" N ASP I 215 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 276 through 278 removed outlier: 6.127A pdb=" N HIS I 277 " --> pdb=" O ARG I 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'I' and resid 335 through 336 removed outlier: 6.828A pdb=" N GLU I 335 " --> pdb=" O ALA I 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'I' and resid 345 through 347 Processing sheet with id=AH6, first strand: chain 'I' and resid 377 through 380 Processing sheet with id=AH7, first strand: chain 'I' and resid 415 through 416 Processing sheet with id=AH8, first strand: chain 'I' and resid 463 through 464 removed outlier: 4.044A pdb=" N TYR I 464 " --> pdb=" O GLU I 574 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 470 through 472 removed outlier: 6.816A pdb=" N ASP I 471 " --> pdb=" O CYS I 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 386 hydrogen bonds defined for protein. 702 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: 5.95 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10686 1.35 - 1.47: 9169 1.47 - 1.60: 13411 1.60 - 1.73: 0 1.73 - 1.85: 212 Bond restraints: 33478 Sorted by residual: bond pdb=" N GLY F 37 " pdb=" CA GLY F 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.18e+00 bond pdb=" N GLY G 37 " pdb=" CA GLY G 37 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.10e+00 bond pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.79e+00 bond pdb=" N GLY D 37 " pdb=" CA GLY D 37 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.63e+00 bond pdb=" N GLY B 37 " pdb=" CA GLY B 37 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.58e+00 ... (remaining 33473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 45029 2.85 - 5.70: 659 5.70 - 8.55: 96 8.55 - 11.40: 3 11.40 - 14.25: 1 Bond angle restraints: 45788 Sorted by residual: angle pdb=" CA UNK L 57 " pdb=" C UNK L 57 " pdb=" N UNK L 58 " ideal model delta sigma weight residual 116.20 127.29 -11.09 2.00e+00 2.50e-01 3.07e+01 angle pdb=" CA VAL I 562 " pdb=" C VAL I 562 " pdb=" N PRO I 563 " ideal model delta sigma weight residual 116.57 121.31 -4.74 9.80e-01 1.04e+00 2.34e+01 angle pdb=" N UNK L 57 " pdb=" CA UNK L 57 " pdb=" C UNK L 57 " ideal model delta sigma weight residual 110.74 124.99 -14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" C UNK L 57 " pdb=" N UNK L 58 " pdb=" CA UNK L 58 " ideal model delta sigma weight residual 121.70 129.70 -8.00 1.80e+00 3.09e-01 1.97e+01 angle pdb=" N LEU A 255 " pdb=" CA LEU A 255 " pdb=" C LEU A 255 " ideal model delta sigma weight residual 111.28 116.10 -4.82 1.09e+00 8.42e-01 1.96e+01 ... (remaining 45783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18341 17.98 - 35.96: 955 35.96 - 53.94: 198 53.94 - 71.92: 60 71.92 - 89.90: 51 Dihedral angle restraints: 19605 sinusoidal: 7563 harmonic: 12042 Sorted by residual: dihedral pdb=" CA ASN G 421 " pdb=" C ASN G 421 " pdb=" N LEU G 422 " pdb=" CA LEU G 422 " ideal model delta harmonic sigma weight residual -180.00 -149.25 -30.75 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA GLU D 55 " pdb=" C GLU D 55 " pdb=" N ASN D 56 " pdb=" CA ASN D 56 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PRO E 272 " pdb=" C PRO E 272 " pdb=" N CYS E 273 " pdb=" CA CYS E 273 " ideal model delta harmonic sigma weight residual 180.00 155.01 24.99 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 19602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3300 0.048 - 0.096: 1270 0.096 - 0.144: 381 0.144 - 0.192: 27 0.192 - 0.240: 2 Chirality restraints: 4980 Sorted by residual: chirality pdb=" CA UNK L 57 " pdb=" N UNK L 57 " pdb=" C UNK L 57 " pdb=" CB UNK L 57 " both_signs ideal model delta sigma weight residual False 2.52 2.28 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA LEU G 422 " pdb=" N LEU G 422 " pdb=" C LEU G 422 " pdb=" CB LEU G 422 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA VAL I 562 " pdb=" N VAL I 562 " pdb=" C VAL I 562 " pdb=" CB VAL I 562 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 4977 not shown) Planarity restraints: 6021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 45 " 0.015 2.00e-02 2.50e+03 1.75e-02 5.33e+00 pdb=" CG PHE D 45 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE D 45 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 45 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE D 45 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE D 45 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 45 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 198 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 199 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 198 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO C 199 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 199 " -0.030 5.00e-02 4.00e+02 ... (remaining 6018 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5784 2.77 - 3.30: 30454 3.30 - 3.83: 53768 3.83 - 4.37: 66200 4.37 - 4.90: 113532 Nonbonded interactions: 269738 Sorted by model distance: nonbonded pdb=" OG SER F 339 " pdb=" OG1 THR F 450 " model vdw 2.234 3.040 nonbonded pdb=" OG1 THR D 278 " pdb=" OD1 ASN D 458 " model vdw 2.270 3.040 nonbonded pdb=" O SER B 192 " pdb=" OG SER B 192 " model vdw 2.305 3.040 nonbonded pdb=" OG1 THR G 152 " pdb=" OD2 ASP G 168 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR F 343 " pdb=" OD1 ASN G 321 " model vdw 2.321 3.040 ... (remaining 269733 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 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'B' and (resid 37 through 509 or resid 516 through 584)) selection = (chain 'E' and (resid 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'F' and (resid 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'G' and (resid 37 through 284 or resid 345 through 509 or resid 516 throu \ gh 584)) selection = (chain 'I' and (resid 37 through 284 or resid 345 through 584)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 37 through 277 or resid 341 through 361 or resid 373 throu \ gh 404 or resid 458 through 540 or resid 550 through 579)) } ncs_group { reference = (chain 'H' and resid 10 through 100) 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 individual isotropic 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: 0.540 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.480 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.009 0.091 33486 Z= 0.368 Angle : 0.925 14.246 45804 Z= 0.493 Chirality : 0.053 0.240 4980 Planarity : 0.006 0.065 6021 Dihedral : 13.274 89.900 11815 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.54 % Rotamer: Outliers : 1.24 % Allowed : 3.43 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.12), residues: 3895 helix: -1.05 (0.40), residues: 110 sheet: 0.07 (0.16), residues: 916 loop : -0.53 (0.11), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 216 TYR 0.034 0.003 TYR G 342 PHE 0.040 0.003 PHE D 45 TRP 0.020 0.003 TRP G 545 HIS 0.009 0.002 HIS G 137 Details of bonding type rmsd covalent geometry : bond 0.00929 (33478) covalent geometry : angle 0.92286 (45788) SS BOND : bond 0.00615 ( 8) SS BOND : angle 3.21566 ( 16) hydrogen bonds : bond 0.25940 ( 386) hydrogen bonds : angle 8.39753 ( 702) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 1273 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8069 (t0) REVERT: A 48 GLN cc_start: 0.8257 (mt0) cc_final: 0.8020 (mt0) REVERT: A 60 GLU cc_start: 0.7810 (tt0) cc_final: 0.7509 (tt0) REVERT: A 87 MET cc_start: 0.7142 (ttm) cc_final: 0.6847 (ttm) REVERT: A 89 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7976 (ttmt) REVERT: A 100 ASP cc_start: 0.7745 (m-30) cc_final: 0.7446 (m-30) REVERT: A 128 LEU cc_start: 0.8654 (tp) cc_final: 0.8415 (tp) REVERT: A 131 ASN cc_start: 0.8448 (m-40) cc_final: 0.8215 (m-40) REVERT: A 144 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 153 VAL cc_start: 0.8873 (t) cc_final: 0.8478 (m) REVERT: A 167 ASN cc_start: 0.8000 (m-40) cc_final: 0.7776 (m-40) REVERT: A 230 THR cc_start: 0.8518 (p) cc_final: 0.8303 (p) REVERT: A 239 ASP cc_start: 0.8053 (t0) cc_final: 0.7820 (t0) REVERT: A 249 SER cc_start: 0.8160 (p) cc_final: 0.7907 (p) REVERT: A 269 ASP cc_start: 0.7064 (p0) cc_final: 0.6643 (p0) REVERT: A 276 THR cc_start: 0.8823 (p) cc_final: 0.8609 (p) REVERT: A 296 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7695 (mm-40) REVERT: A 401 ILE cc_start: 0.8421 (mm) cc_final: 0.8182 (pp) REVERT: A 439 LYS cc_start: 0.8544 (mmtp) cc_final: 0.7951 (mmtt) REVERT: A 471 ASP cc_start: 0.7651 (t0) cc_final: 0.7439 (t0) REVERT: A 519 SER cc_start: 0.8481 (t) cc_final: 0.8257 (t) REVERT: A 536 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8081 (ttpp) REVERT: A 556 ASP cc_start: 0.8015 (m-30) cc_final: 0.7790 (m-30) REVERT: A 575 LYS cc_start: 0.8625 (mttt) cc_final: 0.8349 (mttt) REVERT: B 47 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8379 (t160) REVERT: B 51 PHE cc_start: 0.8280 (m-80) cc_final: 0.8060 (m-80) REVERT: B 77 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 87 MET cc_start: 0.7536 (ptm) cc_final: 0.7329 (ptm) REVERT: B 109 TRP cc_start: 0.8693 (m100) cc_final: 0.8050 (m100) REVERT: B 113 ASP cc_start: 0.7803 (t0) cc_final: 0.7570 (t0) REVERT: B 145 ILE cc_start: 0.8739 (mt) cc_final: 0.8455 (mp) REVERT: B 180 ASN cc_start: 0.8169 (m-40) cc_final: 0.7940 (m-40) REVERT: B 219 ILE cc_start: 0.8733 (mt) cc_final: 0.8525 (OUTLIER) REVERT: B 221 SER cc_start: 0.8733 (p) cc_final: 0.8435 (p) REVERT: B 234 HIS cc_start: 0.8512 (m170) cc_final: 0.7927 (m-70) REVERT: B 248 ASN cc_start: 0.8436 (m-40) cc_final: 0.8201 (m-40) REVERT: B 271 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7917 (ptmt) REVERT: B 384 HIS cc_start: 0.8683 (m90) cc_final: 0.8355 (m170) REVERT: B 408 ARG cc_start: 0.4888 (mtm110) cc_final: 0.4383 (mtm180) REVERT: B 409 TYR cc_start: 0.8110 (t80) cc_final: 0.7593 (t80) REVERT: B 411 GLU cc_start: 0.7945 (tt0) cc_final: 0.7195 (tt0) REVERT: B 468 GLN cc_start: 0.8578 (mt0) cc_final: 0.7901 (mt0) REVERT: B 475 ASP cc_start: 0.7491 (t0) cc_final: 0.6891 (t0) REVERT: B 479 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8138 (mmtm) REVERT: B 549 GLN cc_start: 0.8069 (tt0) cc_final: 0.7813 (tt0) REVERT: B 569 MET cc_start: 0.8333 (mmm) cc_final: 0.7991 (mmm) REVERT: B 573 TYR cc_start: 0.8164 (p90) cc_final: 0.7525 (p90) REVERT: C 42 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7279 (t) REVERT: C 47 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7895 (t160) REVERT: C 52 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7865 (ttpt) REVERT: C 71 LEU cc_start: 0.8311 (tp) cc_final: 0.8039 (tm) REVERT: C 73 MET cc_start: 0.8129 (mtm) cc_final: 0.7913 (mtm) REVERT: C 77 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7302 (tm-30) REVERT: C 89 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8100 (ttmt) REVERT: C 96 MET cc_start: 0.6499 (ptm) cc_final: 0.5597 (ptm) REVERT: C 125 ASP cc_start: 0.7886 (m-30) cc_final: 0.7590 (m-30) REVERT: C 130 VAL cc_start: 0.8339 (m) cc_final: 0.8101 (t) REVERT: C 133 MET cc_start: 0.8214 (mmt) cc_final: 0.7994 (mmm) REVERT: C 151 LYS cc_start: 0.8335 (mttp) cc_final: 0.8039 (mtpp) REVERT: C 155 GLU cc_start: 0.6999 (pp20) cc_final: 0.6744 (pp20) REVERT: C 183 MET cc_start: 0.8394 (mmm) cc_final: 0.8115 (mmp) REVERT: C 193 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7230 (mt-10) REVERT: C 204 ILE cc_start: 0.8853 (pt) cc_final: 0.8637 (pp) REVERT: C 260 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6199 (mt-10) REVERT: C 271 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7775 (ptmt) REVERT: C 344 SER cc_start: 0.8274 (t) cc_final: 0.7984 (t) REVERT: C 377 ARG cc_start: 0.8686 (ttt90) cc_final: 0.8463 (ttt180) REVERT: C 470 TRP cc_start: 0.8722 (p90) cc_final: 0.8224 (p90) REVERT: C 473 GLU cc_start: 0.7885 (tp30) cc_final: 0.7679 (tp30) REVERT: C 501 LYS cc_start: 0.8569 (tttt) cc_final: 0.8293 (tttt) REVERT: C 511 ASP cc_start: 0.7745 (t0) cc_final: 0.7438 (t0) REVERT: C 530 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8652 (ttpp) REVERT: C 535 PHE cc_start: 0.8629 (m-80) cc_final: 0.8304 (m-80) REVERT: C 561 TYR cc_start: 0.8813 (m-80) cc_final: 0.8611 (m-80) REVERT: C 572 VAL cc_start: 0.8907 (m) cc_final: 0.8380 (p) REVERT: C 574 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7015 (mm-30) REVERT: D 60 GLU cc_start: 0.7852 (tt0) cc_final: 0.7600 (tt0) REVERT: D 77 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7133 (mm-30) REVERT: D 113 ASP cc_start: 0.7523 (t0) cc_final: 0.7304 (t0) REVERT: D 135 GLU cc_start: 0.7967 (pt0) cc_final: 0.7740 (pt0) REVERT: D 209 ARG cc_start: 0.8561 (pmt170) cc_final: 0.6214 (pmt-80) REVERT: D 246 ILE cc_start: 0.8454 (mm) cc_final: 0.8234 (mm) REVERT: D 260 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7128 (mt-10) REVERT: D 269 ASP cc_start: 0.7861 (p0) cc_final: 0.7306 (p0) REVERT: D 387 LYS cc_start: 0.8157 (tptm) cc_final: 0.7953 (tppp) REVERT: D 396 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7412 (mm-30) REVERT: D 400 TYR cc_start: 0.8548 (t80) cc_final: 0.8254 (t80) REVERT: D 472 LYS cc_start: 0.8229 (mmmm) cc_final: 0.8001 (mmmm) REVERT: D 511 ASP cc_start: 0.7956 (t0) cc_final: 0.7606 (t0) REVERT: D 513 ASP cc_start: 0.7796 (t0) cc_final: 0.7381 (t0) REVERT: D 538 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7689 (ttmm) REVERT: D 573 TYR cc_start: 0.7958 (p90) cc_final: 0.7157 (p90) REVERT: E 48 GLN cc_start: 0.8154 (mt0) cc_final: 0.7796 (mt0) REVERT: E 60 GLU cc_start: 0.7429 (tt0) cc_final: 0.7180 (tt0) REVERT: E 77 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7502 (mm-30) REVERT: E 95 ASN cc_start: 0.8024 (m110) cc_final: 0.7814 (m110) REVERT: E 122 ASN cc_start: 0.8221 (p0) cc_final: 0.7907 (p0) REVERT: E 125 ASP cc_start: 0.7706 (m-30) cc_final: 0.7494 (m-30) REVERT: E 144 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7486 (mt-10) REVERT: E 166 ASN cc_start: 0.7475 (m-40) cc_final: 0.7269 (m-40) REVERT: E 167 ASN cc_start: 0.7469 (m-40) cc_final: 0.7246 (m-40) REVERT: E 179 SER cc_start: 0.8404 (p) cc_final: 0.8186 (p) REVERT: E 193 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7309 (mt-10) REVERT: E 240 ASP cc_start: 0.7299 (m-30) cc_final: 0.6992 (m-30) REVERT: E 312 LYS cc_start: 0.5706 (tptp) cc_final: 0.4966 (mtpp) REVERT: E 314 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7333 (mtp180) REVERT: E 325 ILE cc_start: 0.8797 (mt) cc_final: 0.8504 (mp) REVERT: E 353 PHE cc_start: 0.8594 (p90) cc_final: 0.8228 (p90) REVERT: E 411 GLU cc_start: 0.7745 (mp0) cc_final: 0.7225 (mp0) REVERT: E 420 PHE cc_start: 0.8884 (t80) cc_final: 0.8643 (t80) REVERT: E 426 ASN cc_start: 0.8105 (t0) cc_final: 0.7681 (t0) REVERT: E 444 TYR cc_start: 0.8507 (p90) cc_final: 0.8300 (p90) REVERT: E 473 GLU cc_start: 0.7936 (tp30) cc_final: 0.7624 (tp30) REVERT: E 479 LYS cc_start: 0.8720 (mttm) cc_final: 0.8512 (mtpp) REVERT: E 557 ASN cc_start: 0.8320 (p0) cc_final: 0.8118 (p0) REVERT: E 570 LYS cc_start: 0.8667 (ptmt) cc_final: 0.8455 (ptmm) REVERT: E 575 LYS cc_start: 0.8545 (mttp) cc_final: 0.8327 (mttp) REVERT: F 42 THR cc_start: 0.8288 (p) cc_final: 0.7715 (t) REVERT: F 72 ASN cc_start: 0.8623 (m-40) cc_final: 0.8352 (m-40) REVERT: F 77 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7555 (mm-30) REVERT: F 78 ASN cc_start: 0.8511 (m-40) cc_final: 0.8286 (m-40) REVERT: F 135 GLU cc_start: 0.8004 (pt0) cc_final: 0.7722 (pt0) REVERT: F 144 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7692 (mt-10) REVERT: F 163 LYS cc_start: 0.8233 (mttt) cc_final: 0.7953 (mttt) REVERT: F 185 PHE cc_start: 0.8530 (t80) cc_final: 0.8245 (t80) REVERT: F 213 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7907 (tm-30) REVERT: F 239 ASP cc_start: 0.7885 (m-30) cc_final: 0.7589 (m-30) REVERT: F 244 TYR cc_start: 0.8477 (m-80) cc_final: 0.8253 (m-80) REVERT: F 302 ASN cc_start: 0.7749 (m110) cc_final: 0.7426 (m-40) REVERT: F 309 GLN cc_start: 0.7231 (mt0) cc_final: 0.6984 (mt0) REVERT: F 413 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7090 (t0) REVERT: F 434 ASP cc_start: 0.7795 (m-30) cc_final: 0.7407 (m-30) REVERT: F 444 TYR cc_start: 0.8373 (p90) cc_final: 0.8154 (p90) REVERT: F 473 GLU cc_start: 0.7648 (tp30) cc_final: 0.7363 (tp30) REVERT: F 479 LYS cc_start: 0.8592 (mttm) cc_final: 0.8147 (mttm) REVERT: F 481 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8345 (mmm-85) REVERT: F 570 LYS cc_start: 0.8747 (ptpt) cc_final: 0.8371 (ptmm) REVERT: G 60 GLU cc_start: 0.7876 (tt0) cc_final: 0.7576 (tt0) REVERT: G 87 MET cc_start: 0.6876 (ptm) cc_final: 0.6483 (ptm) REVERT: G 115 ASN cc_start: 0.8476 (t0) cc_final: 0.8253 (t0) REVERT: G 151 LYS cc_start: 0.8600 (mttm) cc_final: 0.8326 (mmmm) REVERT: G 177 LEU cc_start: 0.8346 (tp) cc_final: 0.8079 (tm) REVERT: G 204 ILE cc_start: 0.8863 (pt) cc_final: 0.8625 (OUTLIER) REVERT: G 237 ASP cc_start: 0.7747 (t0) cc_final: 0.7430 (t0) REVERT: G 259 ASP cc_start: 0.7236 (m-30) cc_final: 0.6915 (m-30) REVERT: G 274 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7559 (mtp-110) REVERT: G 275 LEU cc_start: 0.8398 (mt) cc_final: 0.8167 (mp) REVERT: G 319 MET cc_start: 0.8462 (mtp) cc_final: 0.8257 (mtp) REVERT: G 375 ASN cc_start: 0.7882 (m110) cc_final: 0.7616 (m110) REVERT: G 382 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.8153 (mtm-85) REVERT: G 396 GLU cc_start: 0.7837 (tp30) cc_final: 0.7607 (tp30) REVERT: G 426 ASN cc_start: 0.8304 (t0) cc_final: 0.8057 (t0) REVERT: G 473 GLU cc_start: 0.7734 (tp30) cc_final: 0.7451 (tp30) REVERT: G 484 VAL cc_start: 0.8915 (m) cc_final: 0.8603 (t) REVERT: G 526 ASP cc_start: 0.7538 (p0) cc_final: 0.7333 (p0) REVERT: G 573 TYR cc_start: 0.8197 (p90) cc_final: 0.7406 (p90) REVERT: I 40 ILE cc_start: 0.8619 (mt) cc_final: 0.8304 (mp) REVERT: I 49 THR cc_start: 0.8310 (p) cc_final: 0.7946 (t) REVERT: I 88 ASP cc_start: 0.7692 (t0) cc_final: 0.7479 (t0) REVERT: I 125 ASP cc_start: 0.7518 (m-30) cc_final: 0.7318 (m-30) REVERT: I 133 MET cc_start: 0.8453 (mmt) cc_final: 0.8232 (mpm) REVERT: I 183 MET cc_start: 0.8330 (mmm) cc_final: 0.8109 (mmm) REVERT: I 193 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7316 (mt-10) REVERT: I 278 THR cc_start: 0.8855 (p) cc_final: 0.8648 (p) REVERT: I 303 PHE cc_start: 0.8310 (m-80) cc_final: 0.7951 (m-10) REVERT: I 311 ASP cc_start: 0.7682 (p0) cc_final: 0.7459 (p0) REVERT: I 312 LYS cc_start: 0.8623 (mttt) cc_final: 0.8291 (mttt) REVERT: I 342 TYR cc_start: 0.7978 (p90) cc_final: 0.7528 (p90) REVERT: I 350 GLN cc_start: 0.8783 (mt0) cc_final: 0.8534 (mt0) REVERT: I 387 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8154 (mmmm) REVERT: I 408 ARG cc_start: 0.8065 (mmt-90) cc_final: 0.7237 (mpt180) REVERT: I 414 TRP cc_start: 0.8717 (p90) cc_final: 0.8491 (p90) REVERT: I 439 LYS cc_start: 0.3149 (mmmt) cc_final: 0.2425 (mmmt) REVERT: I 457 LEU cc_start: 0.8293 (mt) cc_final: 0.8081 (OUTLIER) REVERT: I 501 LYS cc_start: 0.8408 (tttt) cc_final: 0.8111 (tttm) REVERT: I 518 MET cc_start: 0.6797 (ptp) cc_final: 0.6380 (ptp) outliers start: 43 outliers final: 16 residues processed: 1296 average time/residue: 0.5933 time to fit residues: 930.6366 Evaluate side-chains 1155 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 1136 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain B residue 47 ASN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 338 TYR Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 413 ASP Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 387 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 0.0470 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 280 GLN A 384 HIS A 403 HIS A 468 GLN B 48 GLN B 85 ASN B 95 ASN B 181 ASN B 280 GLN B 383 GLN B 404 GLN B 419 ASN C 383 GLN C 508 ASN ** C 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS E 497 GLN F 166 ASN F 180 ASN F 280 GLN F 350 GLN F 493 ASN F 549 GLN F 554 ASN G 47 ASN G 234 HIS ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 419 ASN I 47 ASN I 48 GLN I 147 ASN I 310 GLN I 404 GLN I 459 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108563 restraints weight = 47235.674| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.15 r_work: 0.3242 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33486 Z= 0.122 Angle : 0.570 15.877 45804 Z= 0.289 Chirality : 0.043 0.189 4980 Planarity : 0.005 0.046 6021 Dihedral : 6.323 87.317 4468 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.39 % Allowed : 12.37 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 3895 helix: 0.32 (0.43), residues: 92 sheet: -0.00 (0.16), residues: 1003 loop : -0.24 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 408 TYR 0.028 0.001 TYR G 233 PHE 0.018 0.001 PHE E 448 TRP 0.014 0.001 TRP A 414 HIS 0.006 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00276 (33478) covalent geometry : angle 0.56928 (45788) SS BOND : bond 0.00997 ( 8) SS BOND : angle 1.02908 ( 16) hydrogen bonds : bond 0.03938 ( 386) hydrogen bonds : angle 6.38117 ( 702) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1167 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8268 (t) REVERT: A 47 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8270 (t0) REVERT: A 60 GLU cc_start: 0.7899 (tt0) cc_final: 0.7694 (tt0) REVERT: A 77 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 100 ASP cc_start: 0.7885 (m-30) cc_final: 0.7648 (m-30) REVERT: A 125 ASP cc_start: 0.7749 (m-30) cc_final: 0.7531 (m-30) REVERT: A 131 ASN cc_start: 0.8486 (m-40) cc_final: 0.8124 (m-40) REVERT: A 144 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 239 ASP cc_start: 0.7899 (t0) cc_final: 0.7674 (t0) REVERT: A 296 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7774 (mm-40) REVERT: A 302 ASN cc_start: 0.7378 (m110) cc_final: 0.6927 (m110) REVERT: A 380 PHE cc_start: 0.8388 (p90) cc_final: 0.8177 (p90) REVERT: A 439 LYS cc_start: 0.8478 (mmtp) cc_final: 0.8200 (mttm) REVERT: A 460 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8475 (p) REVERT: A 471 ASP cc_start: 0.7842 (t0) cc_final: 0.7537 (t0) REVERT: A 519 SER cc_start: 0.8611 (t) cc_final: 0.8399 (t) REVERT: A 536 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8138 (ttpp) REVERT: B 51 PHE cc_start: 0.8411 (m-80) cc_final: 0.8170 (m-80) REVERT: B 77 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 82 VAL cc_start: 0.8862 (t) cc_final: 0.8602 (p) REVERT: B 87 MET cc_start: 0.7992 (ptm) cc_final: 0.7750 (ptm) REVERT: B 101 ILE cc_start: 0.8634 (mt) cc_final: 0.8420 (mt) REVERT: B 109 TRP cc_start: 0.8658 (m100) cc_final: 0.7999 (m100) REVERT: B 135 GLU cc_start: 0.8172 (pt0) cc_final: 0.7895 (pt0) REVERT: B 217 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7923 (p) REVERT: B 219 ILE cc_start: 0.8771 (mt) cc_final: 0.8563 (OUTLIER) REVERT: B 221 SER cc_start: 0.8879 (p) cc_final: 0.8614 (p) REVERT: B 271 LYS cc_start: 0.8282 (ptmt) cc_final: 0.7997 (ptmt) REVERT: B 357 ILE cc_start: 0.8205 (mm) cc_final: 0.7959 (mp) REVERT: B 384 HIS cc_start: 0.8714 (m90) cc_final: 0.8510 (m170) REVERT: B 408 ARG cc_start: 0.5349 (mtm110) cc_final: 0.3915 (mtm180) REVERT: B 409 TYR cc_start: 0.7924 (t80) cc_final: 0.7468 (t80) REVERT: B 411 GLU cc_start: 0.8309 (tt0) cc_final: 0.7653 (tt0) REVERT: B 479 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8206 (mmtm) REVERT: B 549 GLN cc_start: 0.8423 (tt0) cc_final: 0.8197 (tt0) REVERT: B 553 ILE cc_start: 0.6494 (mp) cc_final: 0.5977 (tt) REVERT: B 556 ASP cc_start: 0.8115 (m-30) cc_final: 0.7898 (m-30) REVERT: B 559 PHE cc_start: 0.8760 (m-80) cc_final: 0.8534 (m-80) REVERT: B 573 TYR cc_start: 0.8202 (p90) cc_final: 0.7784 (p90) REVERT: B 576 SER cc_start: 0.8489 (t) cc_final: 0.8015 (p) REVERT: C 52 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8071 (ttpt) REVERT: C 71 LEU cc_start: 0.8487 (tp) cc_final: 0.8156 (tm) REVERT: C 73 MET cc_start: 0.8178 (mtm) cc_final: 0.7976 (mtm) REVERT: C 77 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7411 (tm-30) REVERT: C 89 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8333 (ttmt) REVERT: C 96 MET cc_start: 0.6035 (ptm) cc_final: 0.5805 (ptm) REVERT: C 101 ILE cc_start: 0.8708 (mt) cc_final: 0.8504 (mt) REVERT: C 133 MET cc_start: 0.8270 (mmt) cc_final: 0.7992 (mmm) REVERT: C 155 GLU cc_start: 0.7577 (pp20) cc_final: 0.7228 (pp20) REVERT: C 193 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7542 (mt-10) REVERT: C 204 ILE cc_start: 0.9006 (pt) cc_final: 0.8761 (pp) REVERT: C 209 ARG cc_start: 0.8439 (pmt170) cc_final: 0.5166 (pmt-80) REVERT: C 232 ILE cc_start: 0.8460 (pt) cc_final: 0.8259 (pp) REVERT: C 271 LYS cc_start: 0.8105 (ptmt) cc_final: 0.7891 (ptmt) REVERT: C 344 SER cc_start: 0.8225 (t) cc_final: 0.7957 (t) REVERT: C 353 PHE cc_start: 0.8242 (p90) cc_final: 0.7992 (p90) REVERT: C 377 ARG cc_start: 0.8688 (ttt90) cc_final: 0.8450 (ttt180) REVERT: C 382 ARG cc_start: 0.8668 (mtt90) cc_final: 0.8442 (mtt90) REVERT: C 470 TRP cc_start: 0.8694 (p90) cc_final: 0.8213 (p90) REVERT: C 479 LYS cc_start: 0.8656 (mttm) cc_final: 0.8419 (mttm) REVERT: C 501 LYS cc_start: 0.8634 (tttt) cc_final: 0.8423 (tttp) REVERT: C 511 ASP cc_start: 0.7852 (t0) cc_final: 0.7484 (t0) REVERT: C 525 SER cc_start: 0.8693 (t) cc_final: 0.8479 (t) REVERT: C 535 PHE cc_start: 0.8527 (m-80) cc_final: 0.8308 (m-80) REVERT: C 550 GLN cc_start: 0.6346 (mm-40) cc_final: 0.5960 (mp-120) REVERT: C 561 TYR cc_start: 0.8827 (m-80) cc_final: 0.8567 (m-80) REVERT: C 574 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7219 (mm-30) REVERT: D 40 ILE cc_start: 0.8198 (mt) cc_final: 0.7959 (pp) REVERT: D 47 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8327 (t160) REVERT: D 51 PHE cc_start: 0.8306 (m-80) cc_final: 0.7781 (m-80) REVERT: D 60 GLU cc_start: 0.8143 (tt0) cc_final: 0.7921 (tt0) REVERT: D 77 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7308 (mm-30) REVERT: D 80 ARG cc_start: 0.8621 (mtp-110) cc_final: 0.8328 (mtp85) REVERT: D 101 ILE cc_start: 0.8717 (mt) cc_final: 0.8449 (mp) REVERT: D 125 ASP cc_start: 0.7877 (m-30) cc_final: 0.7563 (m-30) REVERT: D 135 GLU cc_start: 0.8200 (pt0) cc_final: 0.7991 (pt0) REVERT: D 260 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7429 (mt-10) REVERT: D 387 LYS cc_start: 0.8327 (tptm) cc_final: 0.8099 (tppp) REVERT: D 396 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 400 TYR cc_start: 0.8620 (t80) cc_final: 0.8297 (t80) REVERT: D 511 ASP cc_start: 0.7958 (t0) cc_final: 0.7609 (t0) REVERT: D 513 ASP cc_start: 0.7940 (t0) cc_final: 0.7575 (t0) REVERT: D 581 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8140 (ttp80) REVERT: E 42 THR cc_start: 0.8215 (m) cc_final: 0.7864 (p) REVERT: E 60 GLU cc_start: 0.7748 (tt0) cc_final: 0.7518 (tt0) REVERT: E 77 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7645 (mm-30) REVERT: E 101 ILE cc_start: 0.8347 (mt) cc_final: 0.8050 (mt) REVERT: E 122 ASN cc_start: 0.8212 (p0) cc_final: 0.7919 (p0) REVERT: E 167 ASN cc_start: 0.7715 (m-40) cc_final: 0.7498 (m-40) REVERT: E 179 SER cc_start: 0.8451 (p) cc_final: 0.8201 (p) REVERT: E 193 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7455 (mt-10) REVERT: E 240 ASP cc_start: 0.7339 (m-30) cc_final: 0.7041 (m-30) REVERT: E 296 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8137 (mm-40) REVERT: E 312 LYS cc_start: 0.5537 (tptp) cc_final: 0.5030 (tptp) REVERT: E 314 ARG cc_start: 0.8531 (mtt90) cc_final: 0.7396 (mtp180) REVERT: E 325 ILE cc_start: 0.8711 (mt) cc_final: 0.8389 (mp) REVERT: E 411 GLU cc_start: 0.8036 (mp0) cc_final: 0.7548 (mp0) REVERT: E 426 ASN cc_start: 0.8100 (t0) cc_final: 0.7621 (t0) REVERT: E 460 VAL cc_start: 0.8567 (p) cc_final: 0.8323 (m) REVERT: E 473 GLU cc_start: 0.7924 (tp30) cc_final: 0.7600 (tp30) REVERT: E 557 ASN cc_start: 0.8502 (p0) cc_final: 0.8165 (p0) REVERT: E 570 LYS cc_start: 0.8791 (ptmt) cc_final: 0.8590 (ptmm) REVERT: F 40 ILE cc_start: 0.8510 (mt) cc_final: 0.8142 (tp) REVERT: F 42 THR cc_start: 0.8282 (p) cc_final: 0.7686 (t) REVERT: F 72 ASN cc_start: 0.8610 (m-40) cc_final: 0.8360 (m-40) REVERT: F 77 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7783 (mm-30) REVERT: F 81 ARG cc_start: 0.8605 (ttp80) cc_final: 0.6788 (pmt-80) REVERT: F 89 LYS cc_start: 0.8346 (tppt) cc_final: 0.7981 (tppt) REVERT: F 163 LYS cc_start: 0.8233 (mttt) cc_final: 0.7924 (mttt) REVERT: F 185 PHE cc_start: 0.8571 (t80) cc_final: 0.8272 (t80) REVERT: F 192 SER cc_start: 0.8302 (t) cc_final: 0.7880 (p) REVERT: F 239 ASP cc_start: 0.7943 (m-30) cc_final: 0.7630 (m-30) REVERT: F 244 TYR cc_start: 0.8503 (m-80) cc_final: 0.8286 (m-80) REVERT: F 411 GLU cc_start: 0.7901 (mp0) cc_final: 0.7645 (mp0) REVERT: F 413 ASP cc_start: 0.7643 (t70) cc_final: 0.7313 (t0) REVERT: F 472 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8183 (ttpp) REVERT: F 475 ASP cc_start: 0.7914 (t70) cc_final: 0.7569 (t70) REVERT: F 479 LYS cc_start: 0.8495 (mttm) cc_final: 0.8287 (mttm) REVERT: F 570 LYS cc_start: 0.8792 (ptpt) cc_final: 0.8442 (ptmm) REVERT: G 49 THR cc_start: 0.8406 (m) cc_final: 0.8073 (p) REVERT: G 60 GLU cc_start: 0.8096 (tt0) cc_final: 0.7862 (tt0) REVERT: G 87 MET cc_start: 0.7371 (ptm) cc_final: 0.7099 (ptm) REVERT: G 89 LYS cc_start: 0.8534 (tttt) cc_final: 0.8267 (ttmm) REVERT: G 101 ILE cc_start: 0.8292 (mt) cc_final: 0.8012 (mt) REVERT: G 115 ASN cc_start: 0.8412 (t0) cc_final: 0.8096 (t0) REVERT: G 151 LYS cc_start: 0.8572 (mttm) cc_final: 0.8291 (mmmm) REVERT: G 177 LEU cc_start: 0.8420 (tp) cc_final: 0.8194 (tm) REVERT: G 204 ILE cc_start: 0.8803 (pt) cc_final: 0.8589 (OUTLIER) REVERT: G 237 ASP cc_start: 0.7437 (t0) cc_final: 0.7124 (t0) REVERT: G 275 LEU cc_start: 0.8370 (mt) cc_final: 0.8156 (mp) REVERT: G 335 GLU cc_start: 0.7815 (tt0) cc_final: 0.7396 (tt0) REVERT: G 349 THR cc_start: 0.8781 (p) cc_final: 0.8557 (p) REVERT: G 375 ASN cc_start: 0.7889 (m110) cc_final: 0.7688 (m110) REVERT: G 382 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8305 (mtm-85) REVERT: G 387 LYS cc_start: 0.8523 (tttt) cc_final: 0.8169 (ttmm) REVERT: G 396 GLU cc_start: 0.7998 (tp30) cc_final: 0.7785 (tp30) REVERT: G 426 ASN cc_start: 0.8437 (t0) cc_final: 0.8157 (t0) REVERT: G 473 GLU cc_start: 0.7842 (tp30) cc_final: 0.7616 (tp30) REVERT: G 475 ASP cc_start: 0.7611 (t70) cc_final: 0.7225 (t70) REVERT: G 484 VAL cc_start: 0.8833 (m) cc_final: 0.8516 (p) REVERT: G 511 ASP cc_start: 0.7875 (t0) cc_final: 0.7643 (t0) REVERT: G 513 ASP cc_start: 0.7447 (m-30) cc_final: 0.7143 (m-30) REVERT: G 549 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7850 (tp40) REVERT: G 573 TYR cc_start: 0.8154 (p90) cc_final: 0.7883 (p90) REVERT: I 40 ILE cc_start: 0.8574 (mt) cc_final: 0.8356 (mp) REVERT: I 88 ASP cc_start: 0.8066 (t0) cc_final: 0.7840 (t0) REVERT: I 151 LYS cc_start: 0.8380 (mtpp) cc_final: 0.8109 (mttp) REVERT: I 183 MET cc_start: 0.8327 (mmm) cc_final: 0.8060 (mmm) REVERT: I 193 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7648 (mt-10) REVERT: I 293 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8188 (p) REVERT: I 303 PHE cc_start: 0.8383 (m-80) cc_final: 0.7984 (m-10) REVERT: I 308 VAL cc_start: 0.8681 (m) cc_final: 0.8462 (p) REVERT: I 312 LYS cc_start: 0.8641 (mttt) cc_final: 0.8322 (mttt) REVERT: I 339 SER cc_start: 0.8437 (m) cc_final: 0.7985 (p) REVERT: I 387 LYS cc_start: 0.8528 (mmmm) cc_final: 0.8178 (mmmm) REVERT: I 439 LYS cc_start: 0.4397 (mmmt) cc_final: 0.4035 (mmtt) REVERT: I 501 LYS cc_start: 0.8690 (tttt) cc_final: 0.8430 (tttm) REVERT: I 518 MET cc_start: 0.6857 (ptp) cc_final: 0.6416 (ptp) outliers start: 83 outliers final: 43 residues processed: 1197 average time/residue: 0.6263 time to fit residues: 899.8474 Evaluate side-chains 1160 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1113 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain D residue 47 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 383 GLN Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 583 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain F residue 506 LEU Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 330 ILE Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 555 VAL Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 377 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 292 optimal weight: 6.9990 chunk 384 optimal weight: 8.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 258 optimal weight: 8.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 403 HIS A 404 GLN A 468 GLN A 554 ASN B 48 GLN B 181 ASN B 383 GLN B 468 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 HIS C 383 GLN D 383 GLN D 508 ASN E 47 ASN E 48 GLN E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 181 ASN E 483 HIS E 497 GLN F 180 ASN F 222 HIS ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 ASN F 549 GLN G 47 ASN G 550 GLN G 577 GLN I 47 ASN I 72 ASN I 147 ASN I 234 HIS I 302 ASN I 318 GLN I 404 GLN I 416 GLN I 459 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106310 restraints weight = 47359.899| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.13 r_work: 0.3215 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 33486 Z= 0.273 Angle : 0.615 16.017 45804 Z= 0.311 Chirality : 0.046 0.185 4980 Planarity : 0.005 0.054 6021 Dihedral : 5.895 88.533 4445 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.20 % Allowed : 15.34 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 3895 helix: -0.29 (0.42), residues: 116 sheet: -0.14 (0.16), residues: 994 loop : -0.35 (0.11), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 382 TYR 0.024 0.002 TYR B 524 PHE 0.025 0.002 PHE F 45 TRP 0.019 0.002 TRP G 545 HIS 0.009 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00623 (33478) covalent geometry : angle 0.61489 (45788) SS BOND : bond 0.00458 ( 8) SS BOND : angle 1.37249 ( 16) hydrogen bonds : bond 0.04302 ( 386) hydrogen bonds : angle 6.11878 ( 702) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1129 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.8548 (t) cc_final: 0.8332 (t) REVERT: A 47 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8197 (t0) REVERT: A 77 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 87 MET cc_start: 0.7852 (ttm) cc_final: 0.7586 (ttm) REVERT: A 89 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8219 (ttmt) REVERT: A 131 ASN cc_start: 0.8457 (m-40) cc_final: 0.8056 (m-40) REVERT: A 144 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 221 SER cc_start: 0.8830 (m) cc_final: 0.8599 (t) REVERT: A 239 ASP cc_start: 0.7972 (t0) cc_final: 0.7717 (t0) REVERT: A 296 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7766 (mm-40) REVERT: A 302 ASN cc_start: 0.7457 (m110) cc_final: 0.6944 (m110) REVERT: A 311 ASP cc_start: 0.7793 (p0) cc_final: 0.7569 (p0) REVERT: A 380 PHE cc_start: 0.8414 (p90) cc_final: 0.8176 (p90) REVERT: A 460 VAL cc_start: 0.8771 (m) cc_final: 0.8469 (p) REVERT: A 471 ASP cc_start: 0.7806 (t0) cc_final: 0.7577 (t0) REVERT: A 519 SER cc_start: 0.8659 (t) cc_final: 0.8456 (t) REVERT: A 536 LYS cc_start: 0.8461 (ttpp) cc_final: 0.8197 (ttpp) REVERT: B 51 PHE cc_start: 0.8497 (m-80) cc_final: 0.8260 (m-80) REVERT: B 77 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7382 (tm-30) REVERT: B 87 MET cc_start: 0.8084 (ptm) cc_final: 0.7782 (ptm) REVERT: B 101 ILE cc_start: 0.8617 (mt) cc_final: 0.8220 (mt) REVERT: B 216 ARG cc_start: 0.8296 (ttt90) cc_final: 0.7863 (ttt90) REVERT: B 221 SER cc_start: 0.8844 (p) cc_final: 0.8535 (p) REVERT: B 271 LYS cc_start: 0.8310 (ptmt) cc_final: 0.8001 (ptmt) REVERT: B 408 ARG cc_start: 0.5470 (mtm110) cc_final: 0.3639 (mtm180) REVERT: B 409 TYR cc_start: 0.8072 (t80) cc_final: 0.7715 (t80) REVERT: B 411 GLU cc_start: 0.8320 (tt0) cc_final: 0.7678 (tt0) REVERT: B 479 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8162 (mmtm) REVERT: B 553 ILE cc_start: 0.6500 (mp) cc_final: 0.5990 (tt) REVERT: B 556 ASP cc_start: 0.8131 (m-30) cc_final: 0.7894 (m-30) REVERT: B 573 TYR cc_start: 0.8164 (p90) cc_final: 0.7718 (p90) REVERT: B 576 SER cc_start: 0.8465 (t) cc_final: 0.8004 (p) REVERT: B 582 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8075 (mtmm) REVERT: C 52 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8076 (ttpt) REVERT: C 71 LEU cc_start: 0.8495 (tp) cc_final: 0.8164 (tm) REVERT: C 77 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 89 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8367 (ttmt) REVERT: C 100 ASP cc_start: 0.7357 (m-30) cc_final: 0.7084 (m-30) REVERT: C 130 VAL cc_start: 0.8329 (t) cc_final: 0.8084 (m) REVERT: C 133 MET cc_start: 0.8235 (mmt) cc_final: 0.7709 (mmm) REVERT: C 155 GLU cc_start: 0.7421 (pp20) cc_final: 0.7106 (pp20) REVERT: C 186 THR cc_start: 0.8254 (m) cc_final: 0.7988 (p) REVERT: C 193 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7500 (mt-10) REVERT: C 204 ILE cc_start: 0.9032 (pt) cc_final: 0.8776 (pp) REVERT: C 271 LYS cc_start: 0.8163 (ptmt) cc_final: 0.7804 (ptmt) REVERT: C 344 SER cc_start: 0.8345 (t) cc_final: 0.8082 (t) REVERT: C 353 PHE cc_start: 0.8276 (p90) cc_final: 0.8000 (p90) REVERT: C 377 ARG cc_start: 0.8687 (ttt90) cc_final: 0.8450 (ttt-90) REVERT: C 470 TRP cc_start: 0.8710 (p90) cc_final: 0.8281 (p90) REVERT: C 471 ASP cc_start: 0.8036 (t0) cc_final: 0.7555 (t0) REVERT: C 479 LYS cc_start: 0.8741 (mttm) cc_final: 0.8506 (mttm) REVERT: C 509 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7014 (mm-30) REVERT: C 511 ASP cc_start: 0.7827 (t0) cc_final: 0.7469 (t0) REVERT: C 550 GLN cc_start: 0.6458 (mm-40) cc_final: 0.6196 (mp-120) REVERT: C 561 TYR cc_start: 0.8839 (m-80) cc_final: 0.8612 (m-80) REVERT: C 574 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7152 (mm-30) REVERT: D 51 PHE cc_start: 0.8355 (m-80) cc_final: 0.7834 (m-80) REVERT: D 77 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7325 (mm-30) REVERT: D 101 ILE cc_start: 0.8703 (mt) cc_final: 0.8456 (mp) REVERT: D 178 ASP cc_start: 0.7890 (t0) cc_final: 0.7439 (t0) REVERT: D 182 THR cc_start: 0.8224 (m) cc_final: 0.8020 (p) REVERT: D 387 LYS cc_start: 0.8364 (tptm) cc_final: 0.8139 (tppp) REVERT: D 396 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 400 TYR cc_start: 0.8659 (t80) cc_final: 0.8334 (t80) REVERT: D 501 LYS cc_start: 0.8544 (tttt) cc_final: 0.8314 (tttm) REVERT: D 511 ASP cc_start: 0.7964 (t0) cc_final: 0.7620 (t0) REVERT: D 513 ASP cc_start: 0.7941 (t0) cc_final: 0.7619 (t0) REVERT: D 581 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8201 (ttp80) REVERT: E 60 GLU cc_start: 0.7726 (tt0) cc_final: 0.7514 (tt0) REVERT: E 77 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 101 ILE cc_start: 0.8524 (mt) cc_final: 0.8192 (mt) REVERT: E 125 ASP cc_start: 0.7817 (m-30) cc_final: 0.7597 (m-30) REVERT: E 135 GLU cc_start: 0.8052 (pt0) cc_final: 0.7785 (pt0) REVERT: E 149 VAL cc_start: 0.8871 (t) cc_final: 0.8358 (p) REVERT: E 179 SER cc_start: 0.8517 (p) cc_final: 0.8293 (p) REVERT: E 193 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7487 (mt-10) REVERT: E 221 SER cc_start: 0.8822 (p) cc_final: 0.8619 (p) REVERT: E 296 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8199 (mm-40) REVERT: E 305 ASP cc_start: 0.8410 (m-30) cc_final: 0.5924 (m-30) REVERT: E 312 LYS cc_start: 0.5706 (tptp) cc_final: 0.4966 (mtpt) REVERT: E 314 ARG cc_start: 0.8526 (mtt90) cc_final: 0.7222 (mtt-85) REVERT: E 325 ILE cc_start: 0.8700 (mt) cc_final: 0.8413 (mp) REVERT: E 411 GLU cc_start: 0.7989 (mp0) cc_final: 0.7504 (mp0) REVERT: E 460 VAL cc_start: 0.8574 (p) cc_final: 0.8354 (m) REVERT: E 557 ASN cc_start: 0.8508 (p0) cc_final: 0.7969 (p0) REVERT: F 40 ILE cc_start: 0.8504 (mt) cc_final: 0.8115 (tp) REVERT: F 77 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7673 (mm-30) REVERT: F 89 LYS cc_start: 0.8371 (tppt) cc_final: 0.7934 (tppt) REVERT: F 163 LYS cc_start: 0.8250 (mttt) cc_final: 0.7987 (mttt) REVERT: F 173 LEU cc_start: 0.8621 (tp) cc_final: 0.8334 (tt) REVERT: F 185 PHE cc_start: 0.8562 (t80) cc_final: 0.8278 (t80) REVERT: F 192 SER cc_start: 0.8384 (t) cc_final: 0.7913 (p) REVERT: F 222 HIS cc_start: 0.8731 (p90) cc_final: 0.8270 (p-80) REVERT: F 239 ASP cc_start: 0.8033 (m-30) cc_final: 0.7628 (m-30) REVERT: F 244 TYR cc_start: 0.8544 (m-80) cc_final: 0.8324 (m-80) REVERT: F 265 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8215 (p) REVERT: F 297 SER cc_start: 0.8486 (m) cc_final: 0.8166 (p) REVERT: F 411 GLU cc_start: 0.7889 (mp0) cc_final: 0.7607 (mp0) REVERT: F 472 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8159 (ttpp) REVERT: F 479 LYS cc_start: 0.8604 (mttm) cc_final: 0.8400 (mttm) REVERT: F 570 LYS cc_start: 0.8809 (ptpt) cc_final: 0.8436 (ptmm) REVERT: G 49 THR cc_start: 0.8435 (m) cc_final: 0.8061 (p) REVERT: G 77 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7414 (mm-30) REVERT: G 87 MET cc_start: 0.7472 (ptm) cc_final: 0.7177 (ptm) REVERT: G 89 LYS cc_start: 0.8614 (tttt) cc_final: 0.8344 (ttmm) REVERT: G 115 ASN cc_start: 0.8355 (t0) cc_final: 0.8147 (t160) REVERT: G 204 ILE cc_start: 0.8885 (pt) cc_final: 0.8671 (pp) REVERT: G 275 LEU cc_start: 0.8394 (mt) cc_final: 0.8185 (mp) REVERT: G 335 GLU cc_start: 0.7809 (tt0) cc_final: 0.7417 (tt0) REVERT: G 375 ASN cc_start: 0.7889 (m110) cc_final: 0.7584 (m110) REVERT: G 387 LYS cc_start: 0.8463 (tttt) cc_final: 0.8105 (ttmm) REVERT: G 396 GLU cc_start: 0.8019 (tp30) cc_final: 0.7797 (tp30) REVERT: G 426 ASN cc_start: 0.8551 (t0) cc_final: 0.8267 (t0) REVERT: G 473 GLU cc_start: 0.7824 (tp30) cc_final: 0.7611 (tp30) REVERT: G 475 ASP cc_start: 0.7702 (t70) cc_final: 0.7000 (t70) REVERT: G 511 ASP cc_start: 0.8041 (t0) cc_final: 0.7782 (t0) REVERT: G 524 TYR cc_start: 0.8775 (p90) cc_final: 0.8563 (p90) REVERT: G 532 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8496 (ttpp) REVERT: G 549 GLN cc_start: 0.8317 (tp-100) cc_final: 0.7814 (tp40) REVERT: I 40 ILE cc_start: 0.8620 (mt) cc_final: 0.8398 (mp) REVERT: I 41 SER cc_start: 0.8476 (t) cc_final: 0.8150 (p) REVERT: I 88 ASP cc_start: 0.8083 (t0) cc_final: 0.7863 (t0) REVERT: I 100 ASP cc_start: 0.7454 (m-30) cc_final: 0.7192 (m-30) REVERT: I 163 LYS cc_start: 0.8153 (mttp) cc_final: 0.7879 (mttp) REVERT: I 193 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7589 (mt-10) REVERT: I 233 TYR cc_start: 0.8245 (t80) cc_final: 0.7635 (t80) REVERT: I 255 LEU cc_start: 0.8254 (mp) cc_final: 0.8040 (mt) REVERT: I 303 PHE cc_start: 0.8388 (m-80) cc_final: 0.8030 (m-10) REVERT: I 305 ASP cc_start: 0.8395 (m-30) cc_final: 0.8191 (m-30) REVERT: I 312 LYS cc_start: 0.8636 (mttt) cc_final: 0.8383 (mttt) REVERT: I 375 ASN cc_start: 0.7716 (m110) cc_final: 0.7405 (m110) REVERT: I 380 PHE cc_start: 0.8611 (p90) cc_final: 0.8408 (p90) REVERT: I 387 LYS cc_start: 0.8673 (mmmm) cc_final: 0.8407 (mtpp) REVERT: I 439 LYS cc_start: 0.4236 (mmmt) cc_final: 0.2654 (mmmt) REVERT: I 475 ASP cc_start: 0.8114 (m-30) cc_final: 0.7869 (t0) REVERT: I 501 LYS cc_start: 0.8794 (tttt) cc_final: 0.8499 (tttm) REVERT: I 518 MET cc_start: 0.6906 (ptp) cc_final: 0.6480 (ptp) REVERT: I 546 ASN cc_start: 0.8331 (p0) cc_final: 0.8049 (p0) outliers start: 111 outliers final: 63 residues processed: 1169 average time/residue: 0.6181 time to fit residues: 867.3131 Evaluate side-chains 1163 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 1097 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 582 LYS Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain I residue 47 ASN Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 433 THR Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 203 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 393 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 301 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 241 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 230 optimal weight: 0.0270 chunk 170 optimal weight: 0.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 280 GLN A 403 HIS A 446 ASN A 468 GLN A 554 ASN A 558 GLN B 48 GLN B 122 ASN B 181 ASN B 383 GLN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 GLN C 47 ASN C 248 ASN C 383 GLN D 47 ASN D 72 ASN D 350 GLN D 383 GLN D 459 ASN E 47 ASN E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 417 ASN E 419 ASN E 483 HIS E 497 GLN F 180 ASN F 505 ASN G 47 ASN G 166 ASN G 577 GLN I 47 ASN I 72 ASN I 147 ASN I 234 HIS I 302 ASN I 310 GLN I 404 GLN I 459 ASN ** I 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 549 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108464 restraints weight = 46927.795| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.14 r_work: 0.3239 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 33486 Z= 0.110 Angle : 0.537 15.513 45804 Z= 0.267 Chirality : 0.042 0.185 4980 Planarity : 0.004 0.050 6021 Dihedral : 5.460 87.260 4445 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.26 % Allowed : 17.47 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 3895 helix: -0.14 (0.42), residues: 110 sheet: -0.05 (0.16), residues: 964 loop : -0.24 (0.11), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 382 TYR 0.022 0.001 TYR G 233 PHE 0.024 0.001 PHE I 266 TRP 0.012 0.001 TRP G 414 HIS 0.008 0.001 HIS B 234 Details of bonding type rmsd covalent geometry : bond 0.00246 (33478) covalent geometry : angle 0.53625 (45788) SS BOND : bond 0.01532 ( 8) SS BOND : angle 1.04443 ( 16) hydrogen bonds : bond 0.03395 ( 386) hydrogen bonds : angle 5.90862 ( 702) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1130 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8225 (t0) REVERT: A 77 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7620 (mm-30) REVERT: A 131 ASN cc_start: 0.8448 (m-40) cc_final: 0.8154 (m-40) REVERT: A 144 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 221 SER cc_start: 0.8879 (m) cc_final: 0.8613 (t) REVERT: A 239 ASP cc_start: 0.7877 (t0) cc_final: 0.7605 (t0) REVERT: A 296 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7725 (mm-40) REVERT: A 302 ASN cc_start: 0.7350 (m110) cc_final: 0.6848 (m110) REVERT: A 339 SER cc_start: 0.8666 (m) cc_final: 0.8162 (p) REVERT: A 380 PHE cc_start: 0.8327 (p90) cc_final: 0.8114 (p90) REVERT: A 460 VAL cc_start: 0.8810 (m) cc_final: 0.8515 (p) REVERT: A 471 ASP cc_start: 0.7809 (t0) cc_final: 0.7565 (t0) REVERT: A 519 SER cc_start: 0.8655 (t) cc_final: 0.8436 (t) REVERT: B 51 PHE cc_start: 0.8443 (m-80) cc_final: 0.8137 (m-80) REVERT: B 53 PHE cc_start: 0.8575 (m-80) cc_final: 0.8195 (m-80) REVERT: B 77 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7251 (tm-30) REVERT: B 87 MET cc_start: 0.8109 (ptm) cc_final: 0.7804 (ptm) REVERT: B 96 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8081 (ptp) REVERT: B 101 ILE cc_start: 0.8574 (mt) cc_final: 0.8189 (mt) REVERT: B 154 SER cc_start: 0.8726 (m) cc_final: 0.8188 (t) REVERT: B 178 ASP cc_start: 0.7596 (t0) cc_final: 0.7373 (t0) REVERT: B 216 ARG cc_start: 0.8179 (ttt90) cc_final: 0.7767 (ttt90) REVERT: B 219 ILE cc_start: 0.8768 (mt) cc_final: 0.8526 (mm) REVERT: B 221 SER cc_start: 0.8795 (p) cc_final: 0.8202 (p) REVERT: B 271 LYS cc_start: 0.8289 (ptmt) cc_final: 0.7975 (ptmt) REVERT: B 408 ARG cc_start: 0.5350 (mtm110) cc_final: 0.4527 (mtm180) REVERT: B 409 TYR cc_start: 0.7912 (t80) cc_final: 0.7546 (t80) REVERT: B 411 GLU cc_start: 0.8281 (tt0) cc_final: 0.7622 (tt0) REVERT: B 479 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8140 (mmtm) REVERT: B 553 ILE cc_start: 0.6492 (mp) cc_final: 0.5973 (tt) REVERT: B 573 TYR cc_start: 0.8135 (p90) cc_final: 0.7862 (p90) REVERT: B 576 SER cc_start: 0.8393 (t) cc_final: 0.8023 (p) REVERT: C 52 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8004 (ttpt) REVERT: C 71 LEU cc_start: 0.8478 (tp) cc_final: 0.8130 (tm) REVERT: C 77 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7303 (tm-30) REVERT: C 99 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.7099 (t0) REVERT: C 133 MET cc_start: 0.8100 (mmt) cc_final: 0.7524 (mmm) REVERT: C 155 GLU cc_start: 0.7368 (pp20) cc_final: 0.7041 (pp20) REVERT: C 168 ASP cc_start: 0.6978 (t0) cc_final: 0.6482 (t0) REVERT: C 186 THR cc_start: 0.8207 (m) cc_final: 0.8001 (p) REVERT: C 193 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7299 (mt-10) REVERT: C 204 ILE cc_start: 0.9026 (pt) cc_final: 0.8775 (pp) REVERT: C 209 ARG cc_start: 0.8403 (pmt170) cc_final: 0.7991 (pmt170) REVERT: C 232 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8299 (pp) REVERT: C 260 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7110 (mt-10) REVERT: C 271 LYS cc_start: 0.8111 (ptmt) cc_final: 0.7896 (ptmt) REVERT: C 344 SER cc_start: 0.8326 (t) cc_final: 0.8071 (t) REVERT: C 377 ARG cc_start: 0.8679 (ttt90) cc_final: 0.8441 (ttt-90) REVERT: C 397 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7392 (mtm-85) REVERT: C 404 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7260 (pp30) REVERT: C 470 TRP cc_start: 0.8684 (p90) cc_final: 0.8335 (p90) REVERT: C 479 LYS cc_start: 0.8729 (mttm) cc_final: 0.8524 (mttm) REVERT: C 509 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6928 (mm-30) REVERT: C 511 ASP cc_start: 0.7803 (t0) cc_final: 0.7449 (t0) REVERT: C 525 SER cc_start: 0.8698 (t) cc_final: 0.8470 (t) REVERT: C 550 GLN cc_start: 0.5329 (mm-40) cc_final: 0.4820 (tp40) REVERT: C 561 TYR cc_start: 0.8815 (m-80) cc_final: 0.8615 (m-80) REVERT: C 574 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7128 (mm-30) REVERT: D 51 PHE cc_start: 0.8332 (m-80) cc_final: 0.7853 (m-80) REVERT: D 101 ILE cc_start: 0.8661 (mt) cc_final: 0.8379 (mp) REVERT: D 387 LYS cc_start: 0.8275 (tptm) cc_final: 0.8031 (tppp) REVERT: D 396 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7605 (mm-30) REVERT: D 400 TYR cc_start: 0.8648 (t80) cc_final: 0.8323 (t80) REVERT: D 501 LYS cc_start: 0.8510 (tttt) cc_final: 0.8231 (tttm) REVERT: D 511 ASP cc_start: 0.7845 (t0) cc_final: 0.7484 (t0) REVERT: D 513 ASP cc_start: 0.7955 (t0) cc_final: 0.7650 (t0) REVERT: D 532 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8383 (ttpp) REVERT: D 551 MET cc_start: 0.7938 (ttt) cc_final: 0.7633 (ttt) REVERT: D 570 LYS cc_start: 0.8635 (ptmt) cc_final: 0.8408 (ptmt) REVERT: D 574 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7483 (mm-30) REVERT: D 581 ARG cc_start: 0.8419 (ttp80) cc_final: 0.8169 (ttp80) REVERT: E 42 THR cc_start: 0.8113 (m) cc_final: 0.7797 (p) REVERT: E 53 PHE cc_start: 0.8423 (m-80) cc_final: 0.8208 (m-80) REVERT: E 60 GLU cc_start: 0.7628 (tt0) cc_final: 0.7415 (tt0) REVERT: E 77 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7591 (mm-30) REVERT: E 96 MET cc_start: 0.7965 (pmm) cc_final: 0.6707 (ptt) REVERT: E 101 ILE cc_start: 0.8512 (mt) cc_final: 0.8082 (mt) REVERT: E 133 MET cc_start: 0.8322 (mpp) cc_final: 0.7899 (mpp) REVERT: E 146 PHE cc_start: 0.8360 (p90) cc_final: 0.7983 (p90) REVERT: E 149 VAL cc_start: 0.8886 (t) cc_final: 0.8395 (p) REVERT: E 179 SER cc_start: 0.8466 (p) cc_final: 0.8210 (p) REVERT: E 193 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7454 (mt-10) REVERT: E 255 LEU cc_start: 0.8271 (mp) cc_final: 0.8024 (mm) REVERT: E 296 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8156 (mm-40) REVERT: E 305 ASP cc_start: 0.8389 (m-30) cc_final: 0.5794 (m-30) REVERT: E 314 ARG cc_start: 0.8496 (mtt90) cc_final: 0.7371 (mtt-85) REVERT: E 325 ILE cc_start: 0.8660 (mt) cc_final: 0.8370 (mp) REVERT: E 327 GLU cc_start: 0.6099 (OUTLIER) cc_final: 0.5840 (mt-10) REVERT: E 332 ARG cc_start: 0.8583 (mmt180) cc_final: 0.8303 (mpt180) REVERT: E 411 GLU cc_start: 0.7977 (mp0) cc_final: 0.7494 (mp0) REVERT: E 426 ASN cc_start: 0.8110 (t0) cc_final: 0.7646 (t0) REVERT: F 40 ILE cc_start: 0.8431 (mt) cc_final: 0.8050 (tp) REVERT: F 42 THR cc_start: 0.8268 (p) cc_final: 0.7672 (t) REVERT: F 77 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7601 (mm-30) REVERT: F 163 LYS cc_start: 0.8237 (mttt) cc_final: 0.7972 (mttt) REVERT: F 185 PHE cc_start: 0.8580 (t80) cc_final: 0.8318 (t80) REVERT: F 192 SER cc_start: 0.8349 (t) cc_final: 0.7890 (p) REVERT: F 222 HIS cc_start: 0.8828 (p90) cc_final: 0.8339 (p-80) REVERT: F 239 ASP cc_start: 0.8005 (m-30) cc_final: 0.7620 (m-30) REVERT: F 244 TYR cc_start: 0.8552 (m-80) cc_final: 0.8333 (m-80) REVERT: F 249 SER cc_start: 0.8863 (t) cc_final: 0.8449 (t) REVERT: F 297 SER cc_start: 0.8471 (m) cc_final: 0.8150 (p) REVERT: F 411 GLU cc_start: 0.7832 (mp0) cc_final: 0.7532 (mp0) REVERT: F 472 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8126 (ttpp) REVERT: F 475 ASP cc_start: 0.7851 (t70) cc_final: 0.7561 (t70) REVERT: F 479 LYS cc_start: 0.8569 (mttm) cc_final: 0.8342 (mttm) REVERT: F 566 ILE cc_start: 0.9168 (pt) cc_final: 0.8935 (pp) REVERT: F 570 LYS cc_start: 0.8794 (ptpt) cc_final: 0.8433 (ptmm) REVERT: G 49 THR cc_start: 0.8443 (m) cc_final: 0.8059 (p) REVERT: G 87 MET cc_start: 0.7429 (ptm) cc_final: 0.7111 (ptm) REVERT: G 89 LYS cc_start: 0.8592 (tttt) cc_final: 0.8317 (ttmm) REVERT: G 115 ASN cc_start: 0.8347 (t0) cc_final: 0.8107 (t160) REVERT: G 177 LEU cc_start: 0.8525 (tm) cc_final: 0.8304 (tm) REVERT: G 204 ILE cc_start: 0.8832 (pt) cc_final: 0.8615 (pp) REVERT: G 335 GLU cc_start: 0.7794 (tt0) cc_final: 0.7389 (tt0) REVERT: G 375 ASN cc_start: 0.7880 (m110) cc_final: 0.7568 (m110) REVERT: G 387 LYS cc_start: 0.8427 (tttt) cc_final: 0.8069 (tppp) REVERT: G 396 GLU cc_start: 0.8026 (tp30) cc_final: 0.7807 (tp30) REVERT: G 400 TYR cc_start: 0.8293 (t80) cc_final: 0.7869 (t80) REVERT: G 426 ASN cc_start: 0.8534 (t0) cc_final: 0.8247 (t0) REVERT: G 473 GLU cc_start: 0.7857 (tp30) cc_final: 0.7647 (tp30) REVERT: G 475 ASP cc_start: 0.7691 (t70) cc_final: 0.7058 (t70) REVERT: G 511 ASP cc_start: 0.7939 (t0) cc_final: 0.7702 (t0) REVERT: G 524 TYR cc_start: 0.8776 (p90) cc_final: 0.8546 (p90) REVERT: G 532 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8492 (ttpp) REVERT: G 549 GLN cc_start: 0.8325 (tp-100) cc_final: 0.7903 (tp40) REVERT: I 40 ILE cc_start: 0.8582 (mt) cc_final: 0.8342 (mp) REVERT: I 41 SER cc_start: 0.8431 (t) cc_final: 0.8156 (p) REVERT: I 100 ASP cc_start: 0.7370 (m-30) cc_final: 0.7142 (m-30) REVERT: I 163 LYS cc_start: 0.8061 (mttp) cc_final: 0.7811 (mttp) REVERT: I 183 MET cc_start: 0.8258 (mmm) cc_final: 0.8056 (mmm) REVERT: I 193 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7591 (mt-10) REVERT: I 233 TYR cc_start: 0.8060 (t80) cc_final: 0.7633 (t80) REVERT: I 303 PHE cc_start: 0.8340 (m-80) cc_final: 0.7998 (m-10) REVERT: I 305 ASP cc_start: 0.8371 (m-30) cc_final: 0.8161 (m-30) REVERT: I 312 LYS cc_start: 0.8631 (mttt) cc_final: 0.8325 (mttt) REVERT: I 375 ASN cc_start: 0.7701 (m110) cc_final: 0.7371 (m110) REVERT: I 387 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8305 (mtpp) REVERT: I 501 LYS cc_start: 0.8757 (tttt) cc_final: 0.8433 (tttm) REVERT: I 518 MET cc_start: 0.7028 (ptp) cc_final: 0.6587 (ptp) REVERT: I 546 ASN cc_start: 0.8323 (p0) cc_final: 0.8067 (p0) outliers start: 113 outliers final: 58 residues processed: 1165 average time/residue: 0.6173 time to fit residues: 859.7796 Evaluate side-chains 1150 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1085 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 297 SER Chi-restraints excluded: chain I residue 346 GLU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 472 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 194 optimal weight: 3.9990 chunk 308 optimal weight: 0.0050 chunk 23 optimal weight: 0.1980 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 50.0000 chunk 341 optimal weight: 9.9990 chunk 373 optimal weight: 7.9990 chunk 401 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 15 optimal weight: 50.0000 chunk 275 optimal weight: 5.9990 overall best weight: 3.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 309 GLN A 403 HIS A 468 GLN A 554 ASN ** A 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN B 95 ASN B 147 ASN B 234 HIS B 383 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 383 GLN D 47 ASN D 350 GLN D 383 GLN D 459 ASN E 47 ASN E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 383 GLN E 483 HIS E 497 GLN E 558 GLN F 72 ASN F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN F 554 ASN G 318 GLN G 383 GLN G 577 GLN I 47 ASN I 72 ASN I 147 ASN I 234 HIS I 310 GLN I 404 GLN I 459 ASN I 546 ASN I 549 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106578 restraints weight = 47256.617| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.14 r_work: 0.3205 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 33486 Z= 0.240 Angle : 0.586 15.958 45804 Z= 0.293 Chirality : 0.045 0.185 4980 Planarity : 0.005 0.050 6021 Dihedral : 5.533 87.124 4445 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.43 % Allowed : 18.82 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 3895 helix: -0.24 (0.42), residues: 116 sheet: -0.19 (0.16), residues: 988 loop : -0.29 (0.11), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 408 TYR 0.024 0.002 TYR A 444 PHE 0.021 0.002 PHE I 266 TRP 0.017 0.002 TRP G 545 HIS 0.009 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00549 (33478) covalent geometry : angle 0.58548 (45788) SS BOND : bond 0.00466 ( 8) SS BOND : angle 1.13438 ( 16) hydrogen bonds : bond 0.03783 ( 386) hydrogen bonds : angle 5.87076 ( 702) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1124 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8252 (t0) REVERT: A 77 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 131 ASN cc_start: 0.8456 (m-40) cc_final: 0.7995 (m-40) REVERT: A 144 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7627 (mt-10) REVERT: A 221 SER cc_start: 0.8844 (m) cc_final: 0.8602 (t) REVERT: A 239 ASP cc_start: 0.7991 (t0) cc_final: 0.7687 (t0) REVERT: A 296 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7722 (mm-40) REVERT: A 302 ASN cc_start: 0.7443 (m110) cc_final: 0.6920 (m110) REVERT: A 460 VAL cc_start: 0.8820 (m) cc_final: 0.8519 (p) REVERT: A 471 ASP cc_start: 0.7877 (t0) cc_final: 0.7614 (t0) REVERT: A 519 SER cc_start: 0.8634 (t) cc_final: 0.8404 (t) REVERT: A 530 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8383 (ttmt) REVERT: B 51 PHE cc_start: 0.8477 (m-80) cc_final: 0.8176 (m-80) REVERT: B 53 PHE cc_start: 0.8604 (m-80) cc_final: 0.8230 (m-80) REVERT: B 77 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 87 MET cc_start: 0.8108 (ptm) cc_final: 0.7817 (ptm) REVERT: B 96 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8063 (ptp) REVERT: B 101 ILE cc_start: 0.8582 (mt) cc_final: 0.8078 (mt) REVERT: B 135 GLU cc_start: 0.8265 (pt0) cc_final: 0.7997 (pt0) REVERT: B 154 SER cc_start: 0.8733 (m) cc_final: 0.8237 (t) REVERT: B 178 ASP cc_start: 0.7612 (t0) cc_final: 0.7397 (t0) REVERT: B 216 ARG cc_start: 0.8234 (ttt90) cc_final: 0.7618 (ttt90) REVERT: B 221 SER cc_start: 0.8783 (p) cc_final: 0.8161 (p) REVERT: B 271 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8030 (ptmt) REVERT: B 408 ARG cc_start: 0.5417 (mtm180) cc_final: 0.4458 (mtm180) REVERT: B 409 TYR cc_start: 0.8070 (t80) cc_final: 0.7756 (t80) REVERT: B 411 GLU cc_start: 0.8393 (tt0) cc_final: 0.7801 (tt0) REVERT: B 439 LYS cc_start: 0.8573 (mmtm) cc_final: 0.8254 (mmtt) REVERT: B 479 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8134 (mmtm) REVERT: B 553 ILE cc_start: 0.6382 (mp) cc_final: 0.5870 (tt) REVERT: B 576 SER cc_start: 0.8416 (t) cc_final: 0.7956 (p) REVERT: C 52 LYS cc_start: 0.8362 (ttpt) cc_final: 0.7879 (ttpt) REVERT: C 73 MET cc_start: 0.8052 (mtm) cc_final: 0.7771 (mtm) REVERT: C 77 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7327 (tm-30) REVERT: C 133 MET cc_start: 0.8153 (mmt) cc_final: 0.7570 (mmm) REVERT: C 155 GLU cc_start: 0.7601 (pp20) cc_final: 0.7210 (pp20) REVERT: C 193 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7325 (mt-10) REVERT: C 204 ILE cc_start: 0.9029 (pt) cc_final: 0.8788 (pp) REVERT: C 209 ARG cc_start: 0.8470 (pmt170) cc_final: 0.8118 (pmt170) REVERT: C 232 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8303 (pp) REVERT: C 260 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7429 (mt-10) REVERT: C 344 SER cc_start: 0.8342 (t) cc_final: 0.8095 (t) REVERT: C 397 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7440 (mtm-85) REVERT: C 404 GLN cc_start: 0.7834 (pp30) cc_final: 0.7404 (pp30) REVERT: C 470 TRP cc_start: 0.8693 (p90) cc_final: 0.8363 (p90) REVERT: C 479 LYS cc_start: 0.8711 (mttm) cc_final: 0.8484 (mttm) REVERT: C 509 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7085 (mm-30) REVERT: C 511 ASP cc_start: 0.7818 (t0) cc_final: 0.7505 (t0) REVERT: C 525 SER cc_start: 0.8669 (t) cc_final: 0.8424 (t) REVERT: C 550 GLN cc_start: 0.4569 (mm-40) cc_final: 0.4193 (tp40) REVERT: D 51 PHE cc_start: 0.8373 (m-80) cc_final: 0.7911 (m-80) REVERT: D 101 ILE cc_start: 0.8671 (mt) cc_final: 0.8409 (mp) REVERT: D 178 ASP cc_start: 0.7881 (t0) cc_final: 0.7430 (t0) REVERT: D 232 ILE cc_start: 0.8592 (pt) cc_final: 0.8361 (pp) REVERT: D 257 THR cc_start: 0.7721 (t) cc_final: 0.7300 (m) REVERT: D 345 PHE cc_start: 0.8569 (m-80) cc_final: 0.8179 (m-80) REVERT: D 387 LYS cc_start: 0.8303 (tptm) cc_final: 0.7903 (tppp) REVERT: D 396 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7646 (mm-30) REVERT: D 400 TYR cc_start: 0.8678 (t80) cc_final: 0.8362 (t80) REVERT: D 511 ASP cc_start: 0.7867 (t0) cc_final: 0.7510 (t0) REVERT: D 513 ASP cc_start: 0.7982 (t0) cc_final: 0.7675 (t0) REVERT: D 532 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8560 (ttpp) REVERT: D 581 ARG cc_start: 0.8477 (ttp80) cc_final: 0.8224 (ttp80) REVERT: E 60 GLU cc_start: 0.7693 (tt0) cc_final: 0.7482 (tt0) REVERT: E 77 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7630 (mm-30) REVERT: E 96 MET cc_start: 0.8006 (pmm) cc_final: 0.6711 (ptt) REVERT: E 101 ILE cc_start: 0.8502 (mt) cc_final: 0.8180 (mt) REVERT: E 135 GLU cc_start: 0.8069 (pt0) cc_final: 0.7820 (pt0) REVERT: E 146 PHE cc_start: 0.8394 (p90) cc_final: 0.8067 (p90) REVERT: E 149 VAL cc_start: 0.8908 (t) cc_final: 0.8480 (p) REVERT: E 179 SER cc_start: 0.8518 (p) cc_final: 0.8292 (p) REVERT: E 193 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7510 (mt-10) REVERT: E 296 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8195 (mm-40) REVERT: E 305 ASP cc_start: 0.8409 (m-30) cc_final: 0.5898 (m-30) REVERT: E 312 LYS cc_start: 0.5786 (tttp) cc_final: 0.5178 (mtpt) REVERT: E 314 ARG cc_start: 0.8529 (mtt90) cc_final: 0.7362 (mtp180) REVERT: E 325 ILE cc_start: 0.8694 (mt) cc_final: 0.8443 (mp) REVERT: E 332 ARG cc_start: 0.8607 (mmt180) cc_final: 0.8375 (mpt180) REVERT: E 411 GLU cc_start: 0.8008 (mp0) cc_final: 0.7504 (mp0) REVERT: F 40 ILE cc_start: 0.8426 (mt) cc_final: 0.8005 (tp) REVERT: F 77 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7589 (mm-30) REVERT: F 89 LYS cc_start: 0.8417 (tppt) cc_final: 0.8034 (tppt) REVERT: F 163 LYS cc_start: 0.8263 (mttt) cc_final: 0.8012 (mttt) REVERT: F 173 LEU cc_start: 0.8593 (tp) cc_final: 0.8286 (tt) REVERT: F 185 PHE cc_start: 0.8577 (t80) cc_final: 0.8327 (t80) REVERT: F 192 SER cc_start: 0.8415 (t) cc_final: 0.7944 (p) REVERT: F 222 HIS cc_start: 0.8883 (p90) cc_final: 0.8349 (p-80) REVERT: F 239 ASP cc_start: 0.8037 (m-30) cc_final: 0.7692 (m-30) REVERT: F 244 TYR cc_start: 0.8569 (m-80) cc_final: 0.8331 (m-80) REVERT: F 249 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8485 (t) REVERT: F 265 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8134 (p) REVERT: F 293 SER cc_start: 0.8349 (t) cc_final: 0.8008 (p) REVERT: F 411 GLU cc_start: 0.7824 (mp0) cc_final: 0.7542 (mp0) REVERT: F 472 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8117 (ttpp) REVERT: F 566 ILE cc_start: 0.9192 (pt) cc_final: 0.8936 (pp) REVERT: F 570 LYS cc_start: 0.8829 (ptpt) cc_final: 0.8450 (ptmm) REVERT: G 49 THR cc_start: 0.8451 (m) cc_final: 0.8058 (p) REVERT: G 77 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7353 (mm-30) REVERT: G 87 MET cc_start: 0.7412 (ptm) cc_final: 0.7145 (ptm) REVERT: G 89 LYS cc_start: 0.8715 (tttt) cc_final: 0.8367 (ttmm) REVERT: G 177 LEU cc_start: 0.8533 (tm) cc_final: 0.8325 (tm) REVERT: G 187 PRO cc_start: 0.8848 (Cg_endo) cc_final: 0.8487 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8930 (pt) cc_final: 0.8690 (pp) REVERT: G 335 GLU cc_start: 0.7818 (tt0) cc_final: 0.7430 (tt0) REVERT: G 375 ASN cc_start: 0.7902 (m110) cc_final: 0.7599 (m110) REVERT: G 393 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7789 (mt-10) REVERT: G 396 GLU cc_start: 0.8032 (tp30) cc_final: 0.7801 (tp30) REVERT: G 400 TYR cc_start: 0.8300 (t80) cc_final: 0.7835 (t80) REVERT: G 401 ILE cc_start: 0.8558 (mm) cc_final: 0.8289 (mp) REVERT: G 426 ASN cc_start: 0.8562 (t0) cc_final: 0.8295 (t0) REVERT: G 473 GLU cc_start: 0.7871 (tp30) cc_final: 0.7600 (tp30) REVERT: G 475 ASP cc_start: 0.7742 (t70) cc_final: 0.7219 (t70) REVERT: G 511 ASP cc_start: 0.7945 (t0) cc_final: 0.7727 (t0) REVERT: G 524 TYR cc_start: 0.8767 (p90) cc_final: 0.8488 (p90) REVERT: G 536 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7890 (ttpp) REVERT: G 549 GLN cc_start: 0.8250 (tp40) cc_final: 0.7766 (tp40) REVERT: I 40 ILE cc_start: 0.8615 (mt) cc_final: 0.8390 (mp) REVERT: I 41 SER cc_start: 0.8464 (t) cc_final: 0.8116 (p) REVERT: I 76 SER cc_start: 0.8365 (p) cc_final: 0.8136 (t) REVERT: I 89 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8265 (ttmt) REVERT: I 96 MET cc_start: 0.7940 (mpp) cc_final: 0.6553 (ppp) REVERT: I 163 LYS cc_start: 0.8069 (mttp) cc_final: 0.7836 (mttp) REVERT: I 193 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7600 (mt-10) REVERT: I 233 TYR cc_start: 0.8231 (t80) cc_final: 0.7592 (t80) REVERT: I 303 PHE cc_start: 0.8376 (m-80) cc_final: 0.8038 (m-10) REVERT: I 305 ASP cc_start: 0.8370 (m-30) cc_final: 0.8159 (m-30) REVERT: I 312 LYS cc_start: 0.8642 (mttt) cc_final: 0.8311 (mttt) REVERT: I 387 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8459 (mtpp) REVERT: I 439 LYS cc_start: 0.4740 (mmtt) cc_final: 0.2816 (mmmt) REVERT: I 501 LYS cc_start: 0.8798 (tttt) cc_final: 0.8489 (tttm) REVERT: I 518 MET cc_start: 0.7003 (ptp) cc_final: 0.6588 (ptp) outliers start: 119 outliers final: 63 residues processed: 1163 average time/residue: 0.6489 time to fit residues: 902.6505 Evaluate side-chains 1151 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1081 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 206 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 272 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 145 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 311 optimal weight: 6.9990 chunk 345 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 400 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 309 GLN A 403 HIS A 468 GLN B 48 GLN B 166 ASN B 383 GLN ** B 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN D 47 ASN D 167 ASN D 350 GLN D 383 GLN E 47 ASN E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 383 GLN E 483 HIS E 558 GLN F 72 ASN F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN G 115 ASN G 242 GLN ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN I 47 ASN I 72 ASN I 147 ASN I 234 HIS I 404 GLN I 459 ASN I 549 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107951 restraints weight = 46779.407| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.13 r_work: 0.3223 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33486 Z= 0.156 Angle : 0.547 15.688 45804 Z= 0.271 Chirality : 0.043 0.184 4980 Planarity : 0.004 0.057 6021 Dihedral : 5.306 85.871 4445 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.17 % Allowed : 19.89 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.13), residues: 3895 helix: 0.70 (0.46), residues: 93 sheet: -0.17 (0.16), residues: 978 loop : -0.21 (0.11), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 408 TYR 0.023 0.001 TYR A 444 PHE 0.022 0.001 PHE G 303 TRP 0.012 0.001 TRP G 545 HIS 0.008 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00358 (33478) covalent geometry : angle 0.54632 (45788) SS BOND : bond 0.00426 ( 8) SS BOND : angle 0.98232 ( 16) hydrogen bonds : bond 0.03425 ( 386) hydrogen bonds : angle 5.78162 ( 702) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1102 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 87 MET cc_start: 0.7559 (ttm) cc_final: 0.7305 (ttm) REVERT: A 131 ASN cc_start: 0.8430 (m-40) cc_final: 0.8150 (m-40) REVERT: A 144 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 221 SER cc_start: 0.8885 (m) cc_final: 0.8618 (t) REVERT: A 239 ASP cc_start: 0.7940 (t0) cc_final: 0.7619 (t0) REVERT: A 296 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7688 (mm-40) REVERT: A 302 ASN cc_start: 0.7479 (m110) cc_final: 0.6975 (m110) REVERT: A 339 SER cc_start: 0.8717 (m) cc_final: 0.8145 (p) REVERT: A 460 VAL cc_start: 0.8823 (m) cc_final: 0.8520 (p) REVERT: A 471 ASP cc_start: 0.7892 (t0) cc_final: 0.7661 (t0) REVERT: A 519 SER cc_start: 0.8663 (t) cc_final: 0.8432 (t) REVERT: B 51 PHE cc_start: 0.8452 (m-80) cc_final: 0.8155 (m-80) REVERT: B 53 PHE cc_start: 0.8578 (m-80) cc_final: 0.8196 (m-80) REVERT: B 77 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7186 (tm-30) REVERT: B 87 MET cc_start: 0.8090 (ptm) cc_final: 0.7801 (ptm) REVERT: B 96 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8070 (ptp) REVERT: B 101 ILE cc_start: 0.8559 (mt) cc_final: 0.8059 (mt) REVERT: B 135 GLU cc_start: 0.8238 (pt0) cc_final: 0.7978 (pt0) REVERT: B 154 SER cc_start: 0.8733 (m) cc_final: 0.8243 (t) REVERT: B 178 ASP cc_start: 0.7584 (t0) cc_final: 0.7368 (t0) REVERT: B 216 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7597 (ttt90) REVERT: B 221 SER cc_start: 0.8751 (p) cc_final: 0.8142 (p) REVERT: B 234 HIS cc_start: 0.8354 (m-70) cc_final: 0.8118 (m170) REVERT: B 271 LYS cc_start: 0.8313 (ptmt) cc_final: 0.7987 (ptmt) REVERT: B 382 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.8001 (mtm-85) REVERT: B 408 ARG cc_start: 0.5391 (mtm180) cc_final: 0.4032 (mtm180) REVERT: B 409 TYR cc_start: 0.8012 (t80) cc_final: 0.7605 (t80) REVERT: B 411 GLU cc_start: 0.8391 (tt0) cc_final: 0.7871 (tt0) REVERT: B 439 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8217 (mmtt) REVERT: B 479 LYS cc_start: 0.8657 (mmtm) cc_final: 0.8129 (mmtm) REVERT: B 553 ILE cc_start: 0.6439 (mp) cc_final: 0.5920 (tt) REVERT: B 576 SER cc_start: 0.8382 (t) cc_final: 0.7911 (p) REVERT: C 50 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 52 LYS cc_start: 0.8343 (ttpt) cc_final: 0.7935 (ttpt) REVERT: C 77 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7307 (tm-30) REVERT: C 99 ASP cc_start: 0.7311 (t0) cc_final: 0.7004 (t70) REVERT: C 133 MET cc_start: 0.8108 (mmt) cc_final: 0.7581 (mmm) REVERT: C 155 GLU cc_start: 0.7583 (pp20) cc_final: 0.7178 (pp20) REVERT: C 168 ASP cc_start: 0.7045 (t0) cc_final: 0.6546 (t0) REVERT: C 193 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7280 (mt-10) REVERT: C 204 ILE cc_start: 0.9013 (pt) cc_final: 0.8776 (pp) REVERT: C 209 ARG cc_start: 0.8421 (pmt170) cc_final: 0.8033 (pmt170) REVERT: C 221 SER cc_start: 0.8886 (p) cc_final: 0.8627 (t) REVERT: C 232 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8308 (pp) REVERT: C 260 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7394 (mt-10) REVERT: C 397 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7405 (mtm-85) REVERT: C 404 GLN cc_start: 0.7793 (pp30) cc_final: 0.7435 (pp30) REVERT: C 470 TRP cc_start: 0.8640 (p90) cc_final: 0.8362 (p90) REVERT: C 479 LYS cc_start: 0.8698 (mttm) cc_final: 0.8454 (mttm) REVERT: C 509 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7060 (mm-30) REVERT: C 511 ASP cc_start: 0.7806 (t0) cc_final: 0.7469 (t0) REVERT: C 550 GLN cc_start: 0.4584 (mm-40) cc_final: 0.4313 (tp40) REVERT: C 574 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7170 (mm-30) REVERT: D 51 PHE cc_start: 0.8374 (m-80) cc_final: 0.7903 (m-80) REVERT: D 101 ILE cc_start: 0.8632 (mt) cc_final: 0.8354 (mp) REVERT: D 232 ILE cc_start: 0.8594 (pt) cc_final: 0.8367 (pp) REVERT: D 257 THR cc_start: 0.7640 (t) cc_final: 0.7227 (m) REVERT: D 387 LYS cc_start: 0.8316 (tptm) cc_final: 0.8063 (tppp) REVERT: D 396 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7659 (tm-30) REVERT: D 400 TYR cc_start: 0.8673 (t80) cc_final: 0.8360 (t80) REVERT: D 511 ASP cc_start: 0.7841 (t0) cc_final: 0.7464 (t0) REVERT: D 513 ASP cc_start: 0.7973 (t0) cc_final: 0.7667 (t0) REVERT: D 532 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8507 (ttpp) REVERT: D 536 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8209 (ttpp) REVERT: D 581 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8233 (ttp80) REVERT: D 583 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7759 (mt) REVERT: E 60 GLU cc_start: 0.7654 (tt0) cc_final: 0.7449 (tt0) REVERT: E 96 MET cc_start: 0.7999 (pmm) cc_final: 0.6708 (ptt) REVERT: E 101 ILE cc_start: 0.8518 (mt) cc_final: 0.8185 (mt) REVERT: E 135 GLU cc_start: 0.8029 (pt0) cc_final: 0.7805 (pt0) REVERT: E 146 PHE cc_start: 0.8419 (p90) cc_final: 0.8074 (p90) REVERT: E 149 VAL cc_start: 0.8907 (t) cc_final: 0.8474 (p) REVERT: E 179 SER cc_start: 0.8526 (p) cc_final: 0.8300 (p) REVERT: E 193 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7469 (mt-10) REVERT: E 255 LEU cc_start: 0.8286 (mp) cc_final: 0.7996 (mm) REVERT: E 260 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: E 296 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8205 (mm-40) REVERT: E 305 ASP cc_start: 0.8433 (m-30) cc_final: 0.5859 (m-30) REVERT: E 314 ARG cc_start: 0.8509 (mtt90) cc_final: 0.7322 (mtt-85) REVERT: E 325 ILE cc_start: 0.8668 (mt) cc_final: 0.8421 (mp) REVERT: E 332 ARG cc_start: 0.8624 (mmt180) cc_final: 0.8329 (mpt180) REVERT: E 411 GLU cc_start: 0.7955 (mp0) cc_final: 0.7476 (mp0) REVERT: E 549 GLN cc_start: 0.8302 (tp40) cc_final: 0.8013 (tt0) REVERT: F 40 ILE cc_start: 0.8403 (mt) cc_final: 0.7982 (tp) REVERT: F 77 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7587 (mm-30) REVERT: F 81 ARG cc_start: 0.8668 (ttp80) cc_final: 0.6870 (pmt-80) REVERT: F 89 LYS cc_start: 0.8414 (tppt) cc_final: 0.8019 (tppt) REVERT: F 163 LYS cc_start: 0.8235 (mttt) cc_final: 0.7979 (mttt) REVERT: F 173 LEU cc_start: 0.8521 (tp) cc_final: 0.8195 (tt) REVERT: F 192 SER cc_start: 0.8395 (t) cc_final: 0.7943 (p) REVERT: F 222 HIS cc_start: 0.8906 (p90) cc_final: 0.8330 (p-80) REVERT: F 239 ASP cc_start: 0.8025 (m-30) cc_final: 0.7707 (m-30) REVERT: F 244 TYR cc_start: 0.8564 (m-80) cc_final: 0.8327 (m-80) REVERT: F 249 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8487 (t) REVERT: F 265 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8076 (p) REVERT: F 293 SER cc_start: 0.8330 (t) cc_final: 0.7991 (p) REVERT: F 411 GLU cc_start: 0.7887 (mp0) cc_final: 0.7596 (mp0) REVERT: F 472 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8209 (ttpp) REVERT: F 475 ASP cc_start: 0.7888 (t70) cc_final: 0.7545 (t70) REVERT: F 566 ILE cc_start: 0.9188 (pt) cc_final: 0.8942 (pp) REVERT: G 87 MET cc_start: 0.7364 (ptm) cc_final: 0.7137 (ptm) REVERT: G 89 LYS cc_start: 0.8705 (tttt) cc_final: 0.8364 (ttmm) REVERT: G 177 LEU cc_start: 0.8514 (tm) cc_final: 0.8258 (tm) REVERT: G 187 PRO cc_start: 0.8787 (Cg_endo) cc_final: 0.8475 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8919 (pt) cc_final: 0.8678 (pp) REVERT: G 335 GLU cc_start: 0.7779 (tt0) cc_final: 0.7384 (tt0) REVERT: G 375 ASN cc_start: 0.7951 (m110) cc_final: 0.7653 (m110) REVERT: G 393 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7739 (mt-10) REVERT: G 396 GLU cc_start: 0.8015 (tp30) cc_final: 0.7793 (tp30) REVERT: G 400 TYR cc_start: 0.8345 (t80) cc_final: 0.7871 (t80) REVERT: G 401 ILE cc_start: 0.8562 (mm) cc_final: 0.8286 (mp) REVERT: G 426 ASN cc_start: 0.8525 (t0) cc_final: 0.8267 (t0) REVERT: G 439 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8515 (mmtm) REVERT: G 473 GLU cc_start: 0.7874 (tp30) cc_final: 0.7609 (tp30) REVERT: G 475 ASP cc_start: 0.7686 (t70) cc_final: 0.7178 (t70) REVERT: G 511 ASP cc_start: 0.7903 (t0) cc_final: 0.7695 (t0) REVERT: G 524 TYR cc_start: 0.8769 (p90) cc_final: 0.8530 (p90) REVERT: G 536 LYS cc_start: 0.8140 (ttpp) cc_final: 0.7872 (ttpp) REVERT: G 549 GLN cc_start: 0.8255 (tp40) cc_final: 0.7862 (tp-100) REVERT: I 40 ILE cc_start: 0.8602 (mt) cc_final: 0.8378 (mp) REVERT: I 41 SER cc_start: 0.8454 (t) cc_final: 0.8166 (p) REVERT: I 89 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8257 (ttmt) REVERT: I 96 MET cc_start: 0.7987 (mpp) cc_final: 0.6613 (ppp) REVERT: I 100 ASP cc_start: 0.7460 (m-30) cc_final: 0.7123 (m-30) REVERT: I 163 LYS cc_start: 0.8086 (mttp) cc_final: 0.7836 (mttp) REVERT: I 193 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7585 (mt-10) REVERT: I 233 TYR cc_start: 0.8141 (t80) cc_final: 0.7540 (t80) REVERT: I 303 PHE cc_start: 0.8346 (m-80) cc_final: 0.8021 (m-10) REVERT: I 312 LYS cc_start: 0.8655 (mttt) cc_final: 0.8311 (mttt) REVERT: I 436 ILE cc_start: 0.8647 (mm) cc_final: 0.8412 (mp) REVERT: I 439 LYS cc_start: 0.4705 (mmtt) cc_final: 0.2952 (mmmt) REVERT: I 501 LYS cc_start: 0.8790 (tttt) cc_final: 0.8476 (tttm) REVERT: I 518 MET cc_start: 0.6994 (ptp) cc_final: 0.6568 (ptp) outliers start: 110 outliers final: 60 residues processed: 1142 average time/residue: 0.6079 time to fit residues: 828.6039 Evaluate side-chains 1141 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 1074 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 411 GLU Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 472 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 198 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 50.0000 chunk 148 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 309 optimal weight: 3.9990 chunk 194 optimal weight: 0.6980 chunk 153 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 242 GLN A 403 HIS A 468 GLN A 554 ASN B 48 GLN B 166 ASN B 383 GLN B 404 GLN B 468 GLN B 558 GLN C 47 ASN C 248 ASN C 383 GLN C 459 ASN D 47 ASN D 350 GLN D 383 GLN E 47 ASN E 95 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 ASN F 505 ASN G 282 ASN G 577 GLN I 47 ASN I 72 ASN I 147 ASN I 310 GLN I 404 GLN I 459 ASN I 549 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107598 restraints weight = 47288.842| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.16 r_work: 0.3236 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33486 Z= 0.137 Angle : 0.542 15.979 45804 Z= 0.269 Chirality : 0.042 0.190 4980 Planarity : 0.004 0.052 6021 Dihedral : 5.131 85.069 4441 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.06 % Allowed : 20.67 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 3895 helix: 0.62 (0.46), residues: 93 sheet: -0.17 (0.16), residues: 979 loop : -0.19 (0.11), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 408 TYR 0.027 0.001 TYR A 444 PHE 0.022 0.001 PHE G 303 TRP 0.012 0.001 TRP G 545 HIS 0.008 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00315 (33478) covalent geometry : angle 0.54223 (45788) SS BOND : bond 0.00426 ( 8) SS BOND : angle 1.04991 ( 16) hydrogen bonds : bond 0.03317 ( 386) hydrogen bonds : angle 5.72358 ( 702) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1099 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 87 MET cc_start: 0.7643 (ttm) cc_final: 0.7424 (ttm) REVERT: A 131 ASN cc_start: 0.8359 (m-40) cc_final: 0.8091 (m-40) REVERT: A 142 GLU cc_start: 0.8027 (pt0) cc_final: 0.7804 (pt0) REVERT: A 144 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7547 (mt-10) REVERT: A 221 SER cc_start: 0.8888 (m) cc_final: 0.8617 (t) REVERT: A 239 ASP cc_start: 0.7893 (t0) cc_final: 0.7581 (t0) REVERT: A 245 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7785 (m) REVERT: A 296 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7708 (mm-40) REVERT: A 302 ASN cc_start: 0.7480 (m110) cc_final: 0.6965 (m110) REVERT: A 460 VAL cc_start: 0.8830 (m) cc_final: 0.8529 (p) REVERT: A 519 SER cc_start: 0.8658 (t) cc_final: 0.8432 (t) REVERT: A 530 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8399 (ttmt) REVERT: B 51 PHE cc_start: 0.8439 (m-80) cc_final: 0.8163 (m-80) REVERT: B 53 PHE cc_start: 0.8561 (m-80) cc_final: 0.8174 (m-80) REVERT: B 77 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 87 MET cc_start: 0.8065 (ptm) cc_final: 0.7774 (ptm) REVERT: B 96 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8064 (ptp) REVERT: B 101 ILE cc_start: 0.8539 (mt) cc_final: 0.8025 (mt) REVERT: B 135 GLU cc_start: 0.8255 (pt0) cc_final: 0.7998 (pt0) REVERT: B 154 SER cc_start: 0.8726 (m) cc_final: 0.8235 (t) REVERT: B 178 ASP cc_start: 0.7581 (t0) cc_final: 0.7369 (t0) REVERT: B 210 TYR cc_start: 0.8848 (p90) cc_final: 0.8637 (p90) REVERT: B 216 ARG cc_start: 0.8242 (ttt90) cc_final: 0.7578 (ttt90) REVERT: B 221 SER cc_start: 0.8711 (p) cc_final: 0.8094 (p) REVERT: B 271 LYS cc_start: 0.8307 (ptmt) cc_final: 0.8000 (ptmt) REVERT: B 408 ARG cc_start: 0.5339 (mtm180) cc_final: 0.4293 (mtm180) REVERT: B 411 GLU cc_start: 0.8409 (tt0) cc_final: 0.7945 (tt0) REVERT: B 479 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8131 (mmtm) REVERT: B 553 ILE cc_start: 0.6438 (mp) cc_final: 0.5923 (tt) REVERT: B 576 SER cc_start: 0.8378 (t) cc_final: 0.7905 (p) REVERT: C 50 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7539 (mt-10) REVERT: C 52 LYS cc_start: 0.8401 (ttpt) cc_final: 0.7997 (ttpt) REVERT: C 77 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7298 (tm-30) REVERT: C 99 ASP cc_start: 0.7302 (t70) cc_final: 0.7076 (t70) REVERT: C 133 MET cc_start: 0.8124 (mmt) cc_final: 0.7865 (mmm) REVERT: C 151 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8080 (mtpp) REVERT: C 155 GLU cc_start: 0.7567 (pp20) cc_final: 0.7157 (pp20) REVERT: C 193 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7287 (mt-10) REVERT: C 204 ILE cc_start: 0.9009 (pt) cc_final: 0.8784 (pp) REVERT: C 209 ARG cc_start: 0.8402 (pmt170) cc_final: 0.8001 (pmt170) REVERT: C 221 SER cc_start: 0.8862 (p) cc_final: 0.8614 (t) REVERT: C 232 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8308 (pp) REVERT: C 260 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7383 (mt-10) REVERT: C 397 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7395 (mtm-85) REVERT: C 404 GLN cc_start: 0.7777 (pp30) cc_final: 0.7414 (pp30) REVERT: C 470 TRP cc_start: 0.8625 (p90) cc_final: 0.8355 (p90) REVERT: C 479 LYS cc_start: 0.8716 (mttm) cc_final: 0.8462 (mttm) REVERT: C 509 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 511 ASP cc_start: 0.7803 (t0) cc_final: 0.7479 (t0) REVERT: C 574 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7173 (mm-30) REVERT: D 51 PHE cc_start: 0.8375 (m-80) cc_final: 0.7871 (m-80) REVERT: D 82 VAL cc_start: 0.8358 (t) cc_final: 0.8080 (m) REVERT: D 98 LEU cc_start: 0.8347 (mm) cc_final: 0.8132 (mp) REVERT: D 101 ILE cc_start: 0.8631 (mt) cc_final: 0.8355 (mp) REVERT: D 167 ASN cc_start: 0.8159 (m-40) cc_final: 0.7824 (m-40) REVERT: D 232 ILE cc_start: 0.8592 (pt) cc_final: 0.8365 (pp) REVERT: D 257 THR cc_start: 0.7621 (t) cc_final: 0.7185 (m) REVERT: D 396 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7625 (tm-30) REVERT: D 511 ASP cc_start: 0.7841 (t0) cc_final: 0.7417 (t0) REVERT: D 513 ASP cc_start: 0.7974 (t0) cc_final: 0.7646 (t0) REVERT: D 532 LYS cc_start: 0.8793 (ttpt) cc_final: 0.8517 (ttpp) REVERT: D 581 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8265 (ttp80) REVERT: D 583 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7793 (mt) REVERT: E 60 GLU cc_start: 0.7667 (tt0) cc_final: 0.7462 (tt0) REVERT: E 77 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7490 (mm-30) REVERT: E 96 MET cc_start: 0.7992 (pmm) cc_final: 0.6711 (ptt) REVERT: E 101 ILE cc_start: 0.8488 (mt) cc_final: 0.8192 (mt) REVERT: E 135 GLU cc_start: 0.8009 (pt0) cc_final: 0.7791 (pt0) REVERT: E 146 PHE cc_start: 0.8437 (p90) cc_final: 0.8143 (p90) REVERT: E 149 VAL cc_start: 0.8905 (t) cc_final: 0.8480 (p) REVERT: E 179 SER cc_start: 0.8504 (p) cc_final: 0.8267 (p) REVERT: E 193 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7451 (mt-10) REVERT: E 260 GLU cc_start: 0.7656 (tt0) cc_final: 0.7238 (tt0) REVERT: E 296 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8174 (mm-40) REVERT: E 305 ASP cc_start: 0.8440 (m-30) cc_final: 0.5879 (m-30) REVERT: E 314 ARG cc_start: 0.8491 (mtt90) cc_final: 0.7373 (mtt-85) REVERT: E 325 ILE cc_start: 0.8656 (mt) cc_final: 0.8436 (mp) REVERT: E 332 ARG cc_start: 0.8632 (mmt180) cc_final: 0.8311 (mpt180) REVERT: E 411 GLU cc_start: 0.7948 (mp0) cc_final: 0.7483 (mp0) REVERT: E 472 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8365 (ttpp) REVERT: E 549 GLN cc_start: 0.8291 (tp40) cc_final: 0.8000 (tt0) REVERT: F 42 THR cc_start: 0.8219 (p) cc_final: 0.7590 (t) REVERT: F 77 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7574 (mm-30) REVERT: F 81 ARG cc_start: 0.8671 (ttp80) cc_final: 0.6847 (pmt-80) REVERT: F 89 LYS cc_start: 0.8405 (tppt) cc_final: 0.8013 (tppt) REVERT: F 163 LYS cc_start: 0.8229 (mttt) cc_final: 0.7969 (mttt) REVERT: F 173 LEU cc_start: 0.8516 (tp) cc_final: 0.8223 (tt) REVERT: F 192 SER cc_start: 0.8368 (t) cc_final: 0.7910 (p) REVERT: F 222 HIS cc_start: 0.8916 (p90) cc_final: 0.8405 (p-80) REVERT: F 244 TYR cc_start: 0.8554 (m-80) cc_final: 0.8306 (m-80) REVERT: F 249 SER cc_start: 0.8880 (OUTLIER) cc_final: 0.8474 (t) REVERT: F 265 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8040 (p) REVERT: F 411 GLU cc_start: 0.7872 (mp0) cc_final: 0.7585 (mp0) REVERT: F 425 THR cc_start: 0.8532 (m) cc_final: 0.8142 (t) REVERT: F 472 LYS cc_start: 0.8512 (ttpp) cc_final: 0.8281 (ttpp) REVERT: F 475 ASP cc_start: 0.7877 (t70) cc_final: 0.7517 (t70) REVERT: F 566 ILE cc_start: 0.9190 (pt) cc_final: 0.8942 (pp) REVERT: G 49 THR cc_start: 0.8548 (m) cc_final: 0.8180 (t) REVERT: G 87 MET cc_start: 0.7314 (ptm) cc_final: 0.7108 (ptm) REVERT: G 89 LYS cc_start: 0.8696 (tttt) cc_final: 0.8348 (ttmm) REVERT: G 177 LEU cc_start: 0.8514 (tm) cc_final: 0.8258 (tm) REVERT: G 187 PRO cc_start: 0.8777 (Cg_endo) cc_final: 0.8501 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8916 (pt) cc_final: 0.8679 (pp) REVERT: G 260 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7266 (mt-10) REVERT: G 335 GLU cc_start: 0.7715 (tt0) cc_final: 0.7338 (tt0) REVERT: G 375 ASN cc_start: 0.7942 (m110) cc_final: 0.7648 (m110) REVERT: G 393 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7747 (mt-10) REVERT: G 396 GLU cc_start: 0.7997 (tp30) cc_final: 0.7774 (tp30) REVERT: G 400 TYR cc_start: 0.8356 (t80) cc_final: 0.7880 (t80) REVERT: G 401 ILE cc_start: 0.8559 (mm) cc_final: 0.8283 (mp) REVERT: G 426 ASN cc_start: 0.8525 (t0) cc_final: 0.8268 (t0) REVERT: G 473 GLU cc_start: 0.7871 (tp30) cc_final: 0.7611 (tp30) REVERT: G 475 ASP cc_start: 0.7678 (t70) cc_final: 0.7181 (t70) REVERT: G 511 ASP cc_start: 0.7914 (t0) cc_final: 0.7698 (t0) REVERT: G 524 TYR cc_start: 0.8764 (p90) cc_final: 0.8505 (p90) REVERT: G 536 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7862 (ttpp) REVERT: G 549 GLN cc_start: 0.8264 (tp40) cc_final: 0.8022 (tp-100) REVERT: I 40 ILE cc_start: 0.8584 (mt) cc_final: 0.8376 (mp) REVERT: I 41 SER cc_start: 0.8442 (t) cc_final: 0.8157 (p) REVERT: I 89 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8270 (ttmt) REVERT: I 96 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.6600 (ppp) REVERT: I 100 ASP cc_start: 0.7430 (m-30) cc_final: 0.7091 (m-30) REVERT: I 163 LYS cc_start: 0.8087 (mttp) cc_final: 0.7854 (mttp) REVERT: I 193 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7579 (mt-10) REVERT: I 233 TYR cc_start: 0.8077 (t80) cc_final: 0.7611 (t80) REVERT: I 303 PHE cc_start: 0.8331 (m-80) cc_final: 0.8004 (m-10) REVERT: I 312 LYS cc_start: 0.8638 (mttt) cc_final: 0.8301 (mttt) REVERT: I 436 ILE cc_start: 0.8647 (mm) cc_final: 0.8418 (mp) REVERT: I 439 LYS cc_start: 0.4815 (mmtt) cc_final: 0.3064 (mmmt) REVERT: I 501 LYS cc_start: 0.8751 (tttt) cc_final: 0.8430 (tttm) REVERT: I 518 MET cc_start: 0.7038 (ptp) cc_final: 0.6601 (ptp) outliers start: 106 outliers final: 72 residues processed: 1130 average time/residue: 0.6703 time to fit residues: 902.5363 Evaluate side-chains 1162 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1080 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 411 GLU Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 476 THR Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 387 LYS Chi-restraints excluded: chain I residue 389 THR Chi-restraints excluded: chain I residue 442 ILE Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 92 optimal weight: 0.9990 chunk 310 optimal weight: 10.0000 chunk 302 optimal weight: 7.9990 chunk 247 optimal weight: 0.7980 chunk 59 optimal weight: 0.2980 chunk 158 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 403 HIS A 468 GLN B 48 GLN B 166 ASN B 383 GLN B 404 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN C 550 GLN D 47 ASN D 350 GLN D 383 GLN E 47 ASN E 102 HIS E 137 HIS E 180 ASN E 483 HIS F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 577 GLN I 47 ASN I 72 ASN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN I 166 ASN I 234 HIS I 404 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.123519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107537 restraints weight = 46942.838| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.13 r_work: 0.3226 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33486 Z= 0.190 Angle : 0.567 16.001 45804 Z= 0.282 Chirality : 0.044 0.184 4980 Planarity : 0.005 0.083 6021 Dihedral : 5.179 85.277 4441 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.08 % Allowed : 21.53 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 3895 helix: 0.61 (0.46), residues: 93 sheet: -0.25 (0.16), residues: 987 loop : -0.22 (0.11), residues: 2815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 216 TYR 0.028 0.002 TYR A 444 PHE 0.029 0.002 PHE I 448 TRP 0.018 0.001 TRP C 200 HIS 0.009 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00437 (33478) covalent geometry : angle 0.56690 (45788) SS BOND : bond 0.00483 ( 8) SS BOND : angle 1.14969 ( 16) hydrogen bonds : bond 0.03465 ( 386) hydrogen bonds : angle 5.75487 ( 702) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1099 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7528 (mm-30) REVERT: A 87 MET cc_start: 0.7611 (ttm) cc_final: 0.7358 (ttm) REVERT: A 131 ASN cc_start: 0.8362 (m-40) cc_final: 0.8090 (m-40) REVERT: A 142 GLU cc_start: 0.8021 (pt0) cc_final: 0.7805 (pt0) REVERT: A 144 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 221 SER cc_start: 0.8881 (m) cc_final: 0.8613 (t) REVERT: A 239 ASP cc_start: 0.7941 (t0) cc_final: 0.7595 (t0) REVERT: A 245 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7787 (m) REVERT: A 268 PHE cc_start: 0.8684 (m-80) cc_final: 0.8186 (m-80) REVERT: A 296 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7697 (mm-40) REVERT: A 302 ASN cc_start: 0.7518 (m110) cc_final: 0.7001 (m110) REVERT: A 460 VAL cc_start: 0.8831 (m) cc_final: 0.8526 (p) REVERT: A 519 SER cc_start: 0.8680 (t) cc_final: 0.8455 (t) REVERT: A 530 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8421 (ttmt) REVERT: B 51 PHE cc_start: 0.8457 (m-80) cc_final: 0.8174 (m-80) REVERT: B 53 PHE cc_start: 0.8572 (m-80) cc_final: 0.8195 (m-80) REVERT: B 77 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7079 (tm-30) REVERT: B 78 ASN cc_start: 0.8493 (p0) cc_final: 0.8283 (p0) REVERT: B 87 MET cc_start: 0.8053 (ptm) cc_final: 0.7760 (ptm) REVERT: B 96 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8090 (ptp) REVERT: B 101 ILE cc_start: 0.8544 (mt) cc_final: 0.8142 (mt) REVERT: B 154 SER cc_start: 0.8751 (m) cc_final: 0.8317 (t) REVERT: B 172 SER cc_start: 0.8547 (p) cc_final: 0.8294 (p) REVERT: B 178 ASP cc_start: 0.7586 (t0) cc_final: 0.7375 (t0) REVERT: B 181 ASN cc_start: 0.8342 (m-40) cc_final: 0.7879 (m110) REVERT: B 216 ARG cc_start: 0.8240 (ttt90) cc_final: 0.7823 (ttt90) REVERT: B 221 SER cc_start: 0.8728 (p) cc_final: 0.8138 (p) REVERT: B 271 LYS cc_start: 0.8324 (ptmt) cc_final: 0.8001 (ptmt) REVERT: B 408 ARG cc_start: 0.5381 (mtm180) cc_final: 0.4351 (mtm180) REVERT: B 411 GLU cc_start: 0.8393 (tt0) cc_final: 0.7932 (tt0) REVERT: B 479 LYS cc_start: 0.8653 (mmtm) cc_final: 0.8124 (mmtm) REVERT: B 553 ILE cc_start: 0.6127 (mp) cc_final: 0.5651 (tt) REVERT: B 576 SER cc_start: 0.8393 (t) cc_final: 0.7911 (p) REVERT: C 52 LYS cc_start: 0.8352 (ttpt) cc_final: 0.7932 (ttpt) REVERT: C 77 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7273 (tm-30) REVERT: C 130 VAL cc_start: 0.8199 (t) cc_final: 0.7953 (m) REVERT: C 133 MET cc_start: 0.8160 (mmt) cc_final: 0.7572 (mmm) REVERT: C 155 GLU cc_start: 0.7565 (pp20) cc_final: 0.7166 (pp20) REVERT: C 193 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7307 (mt-10) REVERT: C 204 ILE cc_start: 0.9011 (pt) cc_final: 0.8783 (pp) REVERT: C 209 ARG cc_start: 0.8427 (pmt170) cc_final: 0.8005 (pmt170) REVERT: C 232 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8308 (pp) REVERT: C 260 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7477 (mt-10) REVERT: C 397 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7390 (mtm-85) REVERT: C 404 GLN cc_start: 0.7817 (pp30) cc_final: 0.7466 (pp30) REVERT: C 470 TRP cc_start: 0.8615 (p90) cc_final: 0.8336 (p90) REVERT: C 479 LYS cc_start: 0.8719 (mttm) cc_final: 0.8470 (mttm) REVERT: C 509 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7070 (mm-30) REVERT: C 511 ASP cc_start: 0.7807 (t0) cc_final: 0.7490 (t0) REVERT: C 574 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7196 (mm-30) REVERT: D 51 PHE cc_start: 0.8379 (m-80) cc_final: 0.7908 (m-80) REVERT: D 82 VAL cc_start: 0.8378 (t) cc_final: 0.8092 (m) REVERT: D 98 LEU cc_start: 0.8360 (mm) cc_final: 0.8148 (mp) REVERT: D 101 ILE cc_start: 0.8642 (mt) cc_final: 0.8370 (mp) REVERT: D 167 ASN cc_start: 0.8151 (m-40) cc_final: 0.7808 (m-40) REVERT: D 178 ASP cc_start: 0.7911 (t0) cc_final: 0.7348 (t0) REVERT: D 232 ILE cc_start: 0.8581 (pt) cc_final: 0.8358 (pp) REVERT: D 257 THR cc_start: 0.7652 (t) cc_final: 0.7204 (m) REVERT: D 345 PHE cc_start: 0.8562 (m-80) cc_final: 0.8128 (m-80) REVERT: D 387 LYS cc_start: 0.8316 (tptm) cc_final: 0.8053 (mtpp) REVERT: D 511 ASP cc_start: 0.7873 (t0) cc_final: 0.7450 (t0) REVERT: D 513 ASP cc_start: 0.7977 (t0) cc_final: 0.7643 (t0) REVERT: D 532 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8516 (ttpp) REVERT: D 581 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8254 (ttp80) REVERT: D 583 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7844 (mt) REVERT: E 60 GLU cc_start: 0.7664 (tt0) cc_final: 0.7463 (tt0) REVERT: E 77 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7493 (mm-30) REVERT: E 96 MET cc_start: 0.8008 (pmm) cc_final: 0.6696 (ptt) REVERT: E 101 ILE cc_start: 0.8474 (mt) cc_final: 0.8207 (mt) REVERT: E 135 GLU cc_start: 0.8017 (pt0) cc_final: 0.7802 (pt0) REVERT: E 149 VAL cc_start: 0.8925 (t) cc_final: 0.8506 (p) REVERT: E 179 SER cc_start: 0.8484 (p) cc_final: 0.8276 (p) REVERT: E 193 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7457 (mt-10) REVERT: E 260 GLU cc_start: 0.7668 (tt0) cc_final: 0.7208 (tt0) REVERT: E 296 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8176 (mm-40) REVERT: E 305 ASP cc_start: 0.8447 (m-30) cc_final: 0.6104 (m-30) REVERT: E 314 ARG cc_start: 0.8508 (mtt90) cc_final: 0.7329 (mtt-85) REVERT: E 332 ARG cc_start: 0.8638 (mmt180) cc_final: 0.8320 (mpt180) REVERT: E 342 TYR cc_start: 0.7899 (p90) cc_final: 0.7633 (p90) REVERT: E 411 GLU cc_start: 0.7940 (mp0) cc_final: 0.7522 (mp0) REVERT: E 473 GLU cc_start: 0.7960 (tp30) cc_final: 0.7695 (tp30) REVERT: E 549 GLN cc_start: 0.8281 (tp40) cc_final: 0.8006 (tt0) REVERT: F 77 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7635 (mm-30) REVERT: F 89 LYS cc_start: 0.8458 (tppt) cc_final: 0.8085 (tppt) REVERT: F 163 LYS cc_start: 0.8228 (mttt) cc_final: 0.7964 (mttt) REVERT: F 173 LEU cc_start: 0.8546 (tp) cc_final: 0.8250 (tt) REVERT: F 192 SER cc_start: 0.8387 (t) cc_final: 0.7922 (p) REVERT: F 222 HIS cc_start: 0.9002 (p90) cc_final: 0.8447 (p-80) REVERT: F 244 TYR cc_start: 0.8565 (m-80) cc_final: 0.8304 (m-80) REVERT: F 249 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8463 (t) REVERT: F 265 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.8096 (p) REVERT: F 293 SER cc_start: 0.8299 (t) cc_final: 0.7942 (p) REVERT: F 346 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7478 (mt-10) REVERT: F 411 GLU cc_start: 0.7860 (mp0) cc_final: 0.7588 (mp0) REVERT: F 425 THR cc_start: 0.8544 (m) cc_final: 0.8164 (t) REVERT: F 472 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8301 (ttpp) REVERT: F 566 ILE cc_start: 0.9219 (pt) cc_final: 0.8965 (pp) REVERT: G 49 THR cc_start: 0.8553 (m) cc_final: 0.8184 (t) REVERT: G 87 MET cc_start: 0.7351 (ptm) cc_final: 0.7122 (ptm) REVERT: G 89 LYS cc_start: 0.8718 (tttt) cc_final: 0.8371 (ttmm) REVERT: G 130 VAL cc_start: 0.8466 (m) cc_final: 0.8192 (p) REVERT: G 177 LEU cc_start: 0.8523 (tm) cc_final: 0.8269 (tm) REVERT: G 187 PRO cc_start: 0.8819 (Cg_endo) cc_final: 0.8564 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8930 (pt) cc_final: 0.8705 (pp) REVERT: G 260 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7268 (mt-10) REVERT: G 274 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8114 (ttm110) REVERT: G 335 GLU cc_start: 0.7736 (tt0) cc_final: 0.7383 (tt0) REVERT: G 375 ASN cc_start: 0.7923 (m110) cc_final: 0.7628 (m110) REVERT: G 393 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7714 (mt-10) REVERT: G 396 GLU cc_start: 0.7990 (tp30) cc_final: 0.7770 (tp30) REVERT: G 400 TYR cc_start: 0.8371 (t80) cc_final: 0.7892 (t80) REVERT: G 401 ILE cc_start: 0.8566 (mm) cc_final: 0.8286 (mp) REVERT: G 426 ASN cc_start: 0.8550 (t0) cc_final: 0.8283 (t0) REVERT: G 473 GLU cc_start: 0.7847 (tp30) cc_final: 0.7588 (tp30) REVERT: G 475 ASP cc_start: 0.7667 (t70) cc_final: 0.7238 (t70) REVERT: G 511 ASP cc_start: 0.7929 (t0) cc_final: 0.7723 (t0) REVERT: G 524 TYR cc_start: 0.8741 (p90) cc_final: 0.8453 (p90) REVERT: I 40 ILE cc_start: 0.8590 (mt) cc_final: 0.8384 (mp) REVERT: I 41 SER cc_start: 0.8456 (t) cc_final: 0.8159 (p) REVERT: I 89 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8259 (ttmt) REVERT: I 96 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.6634 (ppp) REVERT: I 100 ASP cc_start: 0.7422 (m-30) cc_final: 0.7111 (m-30) REVERT: I 163 LYS cc_start: 0.8120 (mttp) cc_final: 0.7896 (mttp) REVERT: I 193 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7609 (mt-10) REVERT: I 233 TYR cc_start: 0.8150 (t80) cc_final: 0.7494 (t80) REVERT: I 303 PHE cc_start: 0.8353 (m-80) cc_final: 0.8026 (m-10) REVERT: I 312 LYS cc_start: 0.8649 (mttt) cc_final: 0.8381 (mttt) REVERT: I 387 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8403 (mtpp) REVERT: I 436 ILE cc_start: 0.8668 (mm) cc_final: 0.8441 (mp) REVERT: I 439 LYS cc_start: 0.4704 (mmtt) cc_final: 0.3080 (mmmt) REVERT: I 501 LYS cc_start: 0.8826 (tttt) cc_final: 0.8619 (tttp) REVERT: I 518 MET cc_start: 0.7016 (ptp) cc_final: 0.6571 (ptp) outliers start: 107 outliers final: 72 residues processed: 1134 average time/residue: 0.6714 time to fit residues: 908.6820 Evaluate side-chains 1167 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1084 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 403 HIS Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 472 LYS Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 249 SER Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 274 ARG Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 357 ILE Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 411 GLU Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 293 SER Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 387 LYS Chi-restraints excluded: chain I residue 442 ILE Chi-restraints excluded: chain I residue 472 LYS Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 335 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 411 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 52 optimal weight: 0.0970 chunk 46 optimal weight: 0.6980 chunk 262 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN A 554 ASN B 48 GLN B 383 GLN B 404 GLN B 554 ASN C 47 ASN C 95 ASN C 383 GLN C 550 GLN D 47 ASN D 350 GLN D 383 GLN E 47 ASN E 137 HIS E 180 ASN E 483 HIS E 497 GLN F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 ASN G 47 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 318 GLN G 577 GLN I 72 ASN I 147 ASN I 166 ASN I 310 GLN I 404 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108491 restraints weight = 46941.319| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.14 r_work: 0.3240 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33486 Z= 0.120 Angle : 0.546 15.726 45804 Z= 0.270 Chirality : 0.042 0.194 4980 Planarity : 0.004 0.049 6021 Dihedral : 4.997 84.225 4441 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.83 % Allowed : 22.17 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 3895 helix: 0.66 (0.47), residues: 93 sheet: -0.19 (0.16), residues: 974 loop : -0.17 (0.11), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 408 TYR 0.029 0.001 TYR A 444 PHE 0.027 0.001 PHE I 266 TRP 0.019 0.001 TRP C 200 HIS 0.008 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00277 (33478) covalent geometry : angle 0.54590 (45788) SS BOND : bond 0.00444 ( 8) SS BOND : angle 0.89221 ( 16) hydrogen bonds : bond 0.03201 ( 386) hydrogen bonds : angle 5.71802 ( 702) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1105 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8251 (t0) REVERT: A 77 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 87 MET cc_start: 0.7614 (ttm) cc_final: 0.7358 (ttm) REVERT: A 98 LEU cc_start: 0.8603 (mt) cc_final: 0.8361 (mm) REVERT: A 131 ASN cc_start: 0.8364 (m-40) cc_final: 0.8090 (m-40) REVERT: A 142 GLU cc_start: 0.8033 (pt0) cc_final: 0.7821 (pt0) REVERT: A 144 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 221 SER cc_start: 0.8907 (m) cc_final: 0.8635 (t) REVERT: A 239 ASP cc_start: 0.7763 (t0) cc_final: 0.7522 (t0) REVERT: A 245 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7527 (m) REVERT: A 249 SER cc_start: 0.8070 (p) cc_final: 0.7845 (p) REVERT: A 268 PHE cc_start: 0.8656 (m-80) cc_final: 0.8149 (m-80) REVERT: A 296 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7674 (mm-40) REVERT: A 302 ASN cc_start: 0.7528 (m110) cc_final: 0.7016 (m110) REVERT: A 339 SER cc_start: 0.8644 (m) cc_final: 0.8062 (p) REVERT: A 460 VAL cc_start: 0.8831 (m) cc_final: 0.8524 (p) REVERT: A 519 SER cc_start: 0.8652 (t) cc_final: 0.8432 (t) REVERT: A 520 ARG cc_start: 0.8584 (mtm110) cc_final: 0.8296 (mtm-85) REVERT: A 530 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8445 (ttmt) REVERT: B 51 PHE cc_start: 0.8428 (m-80) cc_final: 0.8155 (m-80) REVERT: B 53 PHE cc_start: 0.8567 (m-80) cc_final: 0.8184 (m-80) REVERT: B 59 VAL cc_start: 0.8668 (t) cc_final: 0.8449 (p) REVERT: B 77 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7011 (tm-30) REVERT: B 87 MET cc_start: 0.8065 (ptm) cc_final: 0.7771 (ptm) REVERT: B 96 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8116 (ptp) REVERT: B 101 ILE cc_start: 0.8429 (mt) cc_final: 0.8023 (mt) REVERT: B 154 SER cc_start: 0.8723 (m) cc_final: 0.8299 (t) REVERT: B 172 SER cc_start: 0.8568 (p) cc_final: 0.8298 (p) REVERT: B 178 ASP cc_start: 0.7546 (t0) cc_final: 0.7334 (t0) REVERT: B 181 ASN cc_start: 0.8332 (m-40) cc_final: 0.7881 (m110) REVERT: B 216 ARG cc_start: 0.8398 (ttt90) cc_final: 0.7988 (ttt90) REVERT: B 221 SER cc_start: 0.8700 (p) cc_final: 0.8089 (p) REVERT: B 271 LYS cc_start: 0.8288 (ptmt) cc_final: 0.7992 (ptmt) REVERT: B 411 GLU cc_start: 0.8401 (tt0) cc_final: 0.7919 (tt0) REVERT: B 479 LYS cc_start: 0.8662 (mmtm) cc_final: 0.8134 (mmtm) REVERT: B 540 ARG cc_start: 0.8862 (ptt-90) cc_final: 0.8651 (ptt-90) REVERT: B 576 SER cc_start: 0.8371 (t) cc_final: 0.7888 (p) REVERT: C 52 LYS cc_start: 0.8320 (ttpt) cc_final: 0.7894 (ttpt) REVERT: C 77 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7286 (tm-30) REVERT: C 133 MET cc_start: 0.8095 (mmt) cc_final: 0.7818 (mmm) REVERT: C 151 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8136 (mtpp) REVERT: C 155 GLU cc_start: 0.7547 (pp20) cc_final: 0.7141 (pp20) REVERT: C 193 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7324 (mt-10) REVERT: C 204 ILE cc_start: 0.8994 (pt) cc_final: 0.8780 (pp) REVERT: C 209 ARG cc_start: 0.8402 (pmt170) cc_final: 0.7999 (pmt170) REVERT: C 232 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8282 (pp) REVERT: C 260 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7451 (mt-10) REVERT: C 397 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7381 (mtm-85) REVERT: C 404 GLN cc_start: 0.7779 (pp30) cc_final: 0.7418 (pp30) REVERT: C 470 TRP cc_start: 0.8592 (p90) cc_final: 0.8286 (p90) REVERT: C 471 ASP cc_start: 0.7997 (t0) cc_final: 0.7422 (t0) REVERT: C 479 LYS cc_start: 0.8719 (mttm) cc_final: 0.8469 (mttm) REVERT: C 509 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7090 (mm-30) REVERT: C 511 ASP cc_start: 0.7789 (t0) cc_final: 0.7440 (t0) REVERT: C 520 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.8269 (mtm110) REVERT: C 574 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7086 (mm-30) REVERT: D 51 PHE cc_start: 0.8365 (m-80) cc_final: 0.7857 (m-80) REVERT: D 82 VAL cc_start: 0.8358 (t) cc_final: 0.8096 (m) REVERT: D 101 ILE cc_start: 0.8619 (mt) cc_final: 0.8336 (mp) REVERT: D 167 ASN cc_start: 0.8159 (m-40) cc_final: 0.7802 (m-40) REVERT: D 232 ILE cc_start: 0.8582 (pt) cc_final: 0.8359 (pp) REVERT: D 257 THR cc_start: 0.7527 (t) cc_final: 0.7074 (m) REVERT: D 345 PHE cc_start: 0.8565 (m-80) cc_final: 0.8064 (m-80) REVERT: D 387 LYS cc_start: 0.8284 (tptm) cc_final: 0.8027 (mtpp) REVERT: D 502 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8510 (t) REVERT: D 511 ASP cc_start: 0.7803 (t0) cc_final: 0.7366 (t0) REVERT: D 513 ASP cc_start: 0.7954 (t0) cc_final: 0.7623 (t0) REVERT: D 532 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8516 (ttpp) REVERT: D 583 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7884 (mt) REVERT: E 60 GLU cc_start: 0.7669 (tt0) cc_final: 0.7469 (tt0) REVERT: E 77 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7460 (mm-30) REVERT: E 96 MET cc_start: 0.7991 (pmm) cc_final: 0.6702 (ptt) REVERT: E 101 ILE cc_start: 0.8458 (mt) cc_final: 0.8193 (mt) REVERT: E 135 GLU cc_start: 0.7955 (pt0) cc_final: 0.7728 (pt0) REVERT: E 149 VAL cc_start: 0.8935 (t) cc_final: 0.8507 (p) REVERT: E 179 SER cc_start: 0.8494 (p) cc_final: 0.8238 (p) REVERT: E 193 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7468 (mt-10) REVERT: E 255 LEU cc_start: 0.8283 (mp) cc_final: 0.7982 (mm) REVERT: E 285 LEU cc_start: 0.8257 (mp) cc_final: 0.8031 (mm) REVERT: E 296 GLN cc_start: 0.8401 (mm-40) cc_final: 0.8143 (mm-40) REVERT: E 305 ASP cc_start: 0.8434 (m-30) cc_final: 0.6048 (m-30) REVERT: E 314 ARG cc_start: 0.8541 (mtt90) cc_final: 0.7348 (mtt-85) REVERT: E 411 GLU cc_start: 0.7906 (mp0) cc_final: 0.7487 (mp0) REVERT: E 472 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8333 (ttpp) REVERT: E 473 GLU cc_start: 0.7980 (tp30) cc_final: 0.7678 (tp30) REVERT: E 524 TYR cc_start: 0.8757 (p90) cc_final: 0.8493 (p90) REVERT: E 548 ILE cc_start: 0.8471 (pp) cc_final: 0.8238 (pt) REVERT: F 42 THR cc_start: 0.8176 (p) cc_final: 0.7551 (t) REVERT: F 77 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7623 (mm-30) REVERT: F 89 LYS cc_start: 0.8415 (tppt) cc_final: 0.8047 (tppt) REVERT: F 163 LYS cc_start: 0.8237 (mttt) cc_final: 0.7977 (mttt) REVERT: F 173 LEU cc_start: 0.8527 (tp) cc_final: 0.8212 (tt) REVERT: F 192 SER cc_start: 0.8369 (t) cc_final: 0.7915 (p) REVERT: F 244 TYR cc_start: 0.8559 (m-80) cc_final: 0.8337 (m-80) REVERT: F 249 SER cc_start: 0.8897 (t) cc_final: 0.8467 (t) REVERT: F 346 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7474 (mt-10) REVERT: F 411 GLU cc_start: 0.7849 (mp0) cc_final: 0.7587 (mp0) REVERT: F 425 THR cc_start: 0.8531 (m) cc_final: 0.8144 (t) REVERT: F 472 LYS cc_start: 0.8557 (ttpp) cc_final: 0.8318 (ttpp) REVERT: F 475 ASP cc_start: 0.7758 (t70) cc_final: 0.7379 (t70) REVERT: F 558 GLN cc_start: 0.7490 (tt0) cc_final: 0.7246 (tt0) REVERT: G 49 THR cc_start: 0.8542 (m) cc_final: 0.8156 (t) REVERT: G 89 LYS cc_start: 0.8707 (tttt) cc_final: 0.8374 (ttmm) REVERT: G 130 VAL cc_start: 0.8457 (m) cc_final: 0.8180 (p) REVERT: G 177 LEU cc_start: 0.8526 (tm) cc_final: 0.8255 (tm) REVERT: G 187 PRO cc_start: 0.8688 (Cg_endo) cc_final: 0.8461 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8929 (pt) cc_final: 0.8694 (pp) REVERT: G 274 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8132 (ttm110) REVERT: G 302 ASN cc_start: 0.7954 (m110) cc_final: 0.7739 (m-40) REVERT: G 335 GLU cc_start: 0.7733 (tt0) cc_final: 0.7380 (tt0) REVERT: G 375 ASN cc_start: 0.7925 (m110) cc_final: 0.7638 (m110) REVERT: G 393 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7703 (mt-10) REVERT: G 396 GLU cc_start: 0.7982 (tp30) cc_final: 0.7761 (tp30) REVERT: G 401 ILE cc_start: 0.8562 (mm) cc_final: 0.8273 (mp) REVERT: G 426 ASN cc_start: 0.8518 (t0) cc_final: 0.8301 (t0) REVERT: G 439 LYS cc_start: 0.8799 (mmtp) cc_final: 0.8579 (mttp) REVERT: G 473 GLU cc_start: 0.7872 (tp30) cc_final: 0.7627 (tp30) REVERT: G 475 ASP cc_start: 0.7615 (t70) cc_final: 0.7175 (t70) REVERT: G 511 ASP cc_start: 0.7860 (t0) cc_final: 0.7645 (t0) REVERT: G 524 TYR cc_start: 0.8742 (p90) cc_final: 0.8503 (p90) REVERT: I 41 SER cc_start: 0.8420 (t) cc_final: 0.8164 (p) REVERT: I 89 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8265 (ttmt) REVERT: I 96 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.6611 (ptt) REVERT: I 100 ASP cc_start: 0.7410 (m-30) cc_final: 0.7090 (m-30) REVERT: I 163 LYS cc_start: 0.8128 (mttp) cc_final: 0.7900 (mttp) REVERT: I 193 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7606 (mt-10) REVERT: I 233 TYR cc_start: 0.7986 (t80) cc_final: 0.7685 (t80) REVERT: I 242 GLN cc_start: 0.8185 (mt0) cc_final: 0.7706 (mt0) REVERT: I 303 PHE cc_start: 0.8308 (m-80) cc_final: 0.7983 (m-10) REVERT: I 312 LYS cc_start: 0.8644 (mttt) cc_final: 0.8428 (mttt) REVERT: I 436 ILE cc_start: 0.8656 (mm) cc_final: 0.8412 (mp) REVERT: I 439 LYS cc_start: 0.4745 (mmtt) cc_final: 0.3099 (mmmt) REVERT: I 501 LYS cc_start: 0.8808 (tttt) cc_final: 0.8487 (tttm) REVERT: I 518 MET cc_start: 0.7034 (ptp) cc_final: 0.6575 (ptp) outliers start: 98 outliers final: 62 residues processed: 1138 average time/residue: 0.6796 time to fit residues: 921.7079 Evaluate side-chains 1153 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 1080 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 403 HIS Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain F residue 87 MET Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 201 LYS Chi-restraints excluded: chain G residue 274 ARG Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 411 GLU Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 442 ILE Chi-restraints excluded: chain I residue 569 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 153 optimal weight: 8.9990 chunk 344 optimal weight: 8.9990 chunk 351 optimal weight: 4.9990 chunk 280 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 342 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 393 optimal weight: 0.3980 chunk 264 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 HIS A 468 GLN A 558 GLN B 48 GLN B 383 GLN B 404 GLN B 558 GLN B 565 ASN C 47 ASN C 95 ASN C 248 ASN C 383 GLN D 47 ASN D 167 ASN D 383 GLN E 47 ASN E 137 HIS E 180 ASN E 483 HIS F 180 ASN F 505 ASN F 549 GLN F 554 ASN G 310 GLN G 577 GLN I 72 ASN ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 404 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 560 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105685 restraints weight = 47474.956| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.13 r_work: 0.3196 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 33486 Z= 0.325 Angle : 0.641 16.355 45804 Z= 0.321 Chirality : 0.048 0.245 4980 Planarity : 0.005 0.095 6021 Dihedral : 5.394 84.995 4440 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.83 % Allowed : 22.48 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.13), residues: 3895 helix: 0.03 (0.42), residues: 117 sheet: -0.40 (0.16), residues: 994 loop : -0.33 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 408 TYR 0.036 0.002 TYR I 524 PHE 0.031 0.002 PHE I 266 TRP 0.036 0.002 TRP D 58 HIS 0.010 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00740 (33478) covalent geometry : angle 0.64030 (45788) SS BOND : bond 0.00618 ( 8) SS BOND : angle 1.10213 ( 16) hydrogen bonds : bond 0.03921 ( 386) hydrogen bonds : angle 5.90703 ( 702) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7790 Ramachandran restraints generated. 3895 Oldfield, 0 Emsley, 3895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1102 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8347 (t0) REVERT: A 77 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 87 MET cc_start: 0.7502 (ttm) cc_final: 0.7240 (ttm) REVERT: A 131 ASN cc_start: 0.8368 (m-40) cc_final: 0.8022 (m-40) REVERT: A 142 GLU cc_start: 0.8019 (pt0) cc_final: 0.7817 (pt0) REVERT: A 144 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7573 (mt-10) REVERT: A 221 SER cc_start: 0.8867 (m) cc_final: 0.8497 (t) REVERT: A 232 ILE cc_start: 0.8592 (pp) cc_final: 0.8345 (pt) REVERT: A 239 ASP cc_start: 0.8006 (t0) cc_final: 0.7742 (t0) REVERT: A 245 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7810 (m) REVERT: A 296 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7661 (mm-40) REVERT: A 302 ASN cc_start: 0.7535 (m110) cc_final: 0.6998 (m110) REVERT: A 339 SER cc_start: 0.8700 (m) cc_final: 0.8150 (p) REVERT: A 400 TYR cc_start: 0.8585 (t80) cc_final: 0.8044 (t80) REVERT: A 460 VAL cc_start: 0.8826 (m) cc_final: 0.8526 (p) REVERT: A 519 SER cc_start: 0.8673 (t) cc_final: 0.8463 (t) REVERT: A 530 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8391 (ttmt) REVERT: A 549 GLN cc_start: 0.8427 (tt0) cc_final: 0.7966 (tt0) REVERT: B 51 PHE cc_start: 0.8482 (m-80) cc_final: 0.8235 (m-80) REVERT: B 77 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 87 MET cc_start: 0.8075 (ptm) cc_final: 0.7785 (ptm) REVERT: B 96 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8109 (ptp) REVERT: B 101 ILE cc_start: 0.8478 (mt) cc_final: 0.8166 (mt) REVERT: B 154 SER cc_start: 0.8745 (m) cc_final: 0.8338 (t) REVERT: B 172 SER cc_start: 0.8572 (p) cc_final: 0.8332 (p) REVERT: B 178 ASP cc_start: 0.7568 (t0) cc_final: 0.7358 (t0) REVERT: B 181 ASN cc_start: 0.8352 (m-40) cc_final: 0.7900 (m110) REVERT: B 216 ARG cc_start: 0.8383 (ttt90) cc_final: 0.7940 (ttt90) REVERT: B 271 LYS cc_start: 0.8333 (ptmt) cc_final: 0.8034 (ptmt) REVERT: B 408 ARG cc_start: 0.5628 (mtt180) cc_final: 0.3551 (mtm110) REVERT: B 411 GLU cc_start: 0.8422 (tt0) cc_final: 0.7919 (tt0) REVERT: B 439 LYS cc_start: 0.8558 (mmtm) cc_final: 0.8224 (mmtt) REVERT: B 479 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8148 (mmtm) REVERT: C 52 LYS cc_start: 0.8359 (ttpt) cc_final: 0.7940 (ttpt) REVERT: C 77 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7333 (tm-30) REVERT: C 133 MET cc_start: 0.8222 (mmt) cc_final: 0.7932 (mmm) REVERT: C 155 GLU cc_start: 0.7608 (pp20) cc_final: 0.7231 (pp20) REVERT: C 193 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7279 (mt-10) REVERT: C 204 ILE cc_start: 0.9023 (pt) cc_final: 0.8786 (pp) REVERT: C 221 SER cc_start: 0.8902 (p) cc_final: 0.8647 (t) REVERT: C 260 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 397 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7456 (mtm-85) REVERT: C 404 GLN cc_start: 0.7820 (pp30) cc_final: 0.7473 (pp30) REVERT: C 470 TRP cc_start: 0.8637 (p90) cc_final: 0.8347 (p90) REVERT: C 479 LYS cc_start: 0.8743 (mttm) cc_final: 0.8498 (mttm) REVERT: C 509 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7170 (mm-30) REVERT: C 511 ASP cc_start: 0.7806 (t0) cc_final: 0.7495 (t0) REVERT: C 540 ARG cc_start: 0.8310 (ptt90) cc_final: 0.8064 (ptt90) REVERT: C 574 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7095 (mm-30) REVERT: D 82 VAL cc_start: 0.8422 (t) cc_final: 0.8112 (m) REVERT: D 101 ILE cc_start: 0.8670 (mt) cc_final: 0.8409 (mp) REVERT: D 167 ASN cc_start: 0.8152 (m110) cc_final: 0.7811 (m-40) REVERT: D 178 ASP cc_start: 0.8019 (t0) cc_final: 0.7445 (t0) REVERT: D 232 ILE cc_start: 0.8589 (pt) cc_final: 0.8364 (pp) REVERT: D 511 ASP cc_start: 0.7889 (t0) cc_final: 0.7463 (t0) REVERT: D 513 ASP cc_start: 0.7944 (t0) cc_final: 0.7625 (t0) REVERT: D 532 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8514 (ttpp) REVERT: D 583 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7909 (mt) REVERT: E 60 GLU cc_start: 0.7726 (tt0) cc_final: 0.7525 (tt0) REVERT: E 77 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7488 (mm-30) REVERT: E 90 THR cc_start: 0.8566 (m) cc_final: 0.8283 (t) REVERT: E 96 MET cc_start: 0.8017 (pmm) cc_final: 0.6597 (ptt) REVERT: E 101 ILE cc_start: 0.8521 (mt) cc_final: 0.8211 (mt) REVERT: E 133 MET cc_start: 0.8379 (mpp) cc_final: 0.7874 (mpp) REVERT: E 135 GLU cc_start: 0.8023 (pt0) cc_final: 0.7806 (pt0) REVERT: E 149 VAL cc_start: 0.8897 (t) cc_final: 0.8462 (p) REVERT: E 193 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7470 (mt-10) REVERT: E 255 LEU cc_start: 0.8383 (mp) cc_final: 0.8030 (mm) REVERT: E 260 GLU cc_start: 0.7597 (tt0) cc_final: 0.7205 (tm-30) REVERT: E 261 PHE cc_start: 0.8563 (t80) cc_final: 0.8292 (t80) REVERT: E 296 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8168 (mm-40) REVERT: E 305 ASP cc_start: 0.8456 (m-30) cc_final: 0.5913 (m-30) REVERT: E 312 LYS cc_start: 0.5505 (tptp) cc_final: 0.4655 (mtpt) REVERT: E 314 ARG cc_start: 0.8528 (mtt90) cc_final: 0.7332 (mtt-85) REVERT: E 411 GLU cc_start: 0.7968 (mp0) cc_final: 0.7553 (mp0) REVERT: E 473 GLU cc_start: 0.7989 (tp30) cc_final: 0.7731 (tp30) REVERT: E 549 GLN cc_start: 0.8289 (tp40) cc_final: 0.8025 (tt0) REVERT: F 77 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7639 (mm-30) REVERT: F 89 LYS cc_start: 0.8468 (tppt) cc_final: 0.8119 (tppt) REVERT: F 163 LYS cc_start: 0.8257 (mttt) cc_final: 0.7999 (mttt) REVERT: F 173 LEU cc_start: 0.8672 (tp) cc_final: 0.8395 (tt) REVERT: F 222 HIS cc_start: 0.9002 (p90) cc_final: 0.8400 (p-80) REVERT: F 244 TYR cc_start: 0.8567 (m-80) cc_final: 0.8307 (m-80) REVERT: F 249 SER cc_start: 0.8959 (t) cc_final: 0.8560 (t) REVERT: F 265 THR cc_start: 0.8536 (OUTLIER) cc_final: 0.8232 (p) REVERT: F 293 SER cc_start: 0.8349 (t) cc_final: 0.8013 (p) REVERT: F 319 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7461 (mtm) REVERT: F 346 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7518 (mt-10) REVERT: F 411 GLU cc_start: 0.7863 (mp0) cc_final: 0.7587 (mp0) REVERT: F 425 THR cc_start: 0.8591 (m) cc_final: 0.8257 (t) REVERT: F 439 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8263 (mmtp) REVERT: F 472 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8382 (ttpp) REVERT: F 475 ASP cc_start: 0.7728 (t70) cc_final: 0.7328 (t70) REVERT: F 558 GLN cc_start: 0.7498 (tt0) cc_final: 0.7262 (tt0) REVERT: G 49 THR cc_start: 0.8543 (m) cc_final: 0.8171 (t) REVERT: G 81 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8137 (ttp80) REVERT: G 89 LYS cc_start: 0.8723 (tttt) cc_final: 0.8447 (ttmm) REVERT: G 130 VAL cc_start: 0.8506 (m) cc_final: 0.8235 (p) REVERT: G 177 LEU cc_start: 0.8519 (tm) cc_final: 0.8268 (tm) REVERT: G 187 PRO cc_start: 0.8874 (Cg_endo) cc_final: 0.8565 (Cg_exo) REVERT: G 204 ILE cc_start: 0.8952 (pt) cc_final: 0.8736 (pp) REVERT: G 274 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8161 (ttm110) REVERT: G 335 GLU cc_start: 0.7782 (tt0) cc_final: 0.7401 (tt0) REVERT: G 375 ASN cc_start: 0.7905 (m110) cc_final: 0.7625 (m110) REVERT: G 393 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7688 (mt-10) REVERT: G 396 GLU cc_start: 0.7997 (tp30) cc_final: 0.7786 (tp30) REVERT: G 401 ILE cc_start: 0.8556 (mm) cc_final: 0.8279 (mp) REVERT: G 426 ASN cc_start: 0.8642 (t0) cc_final: 0.8400 (t0) REVERT: G 473 GLU cc_start: 0.7841 (tp30) cc_final: 0.7599 (tp30) REVERT: G 475 ASP cc_start: 0.7716 (t70) cc_final: 0.7328 (t70) REVERT: G 509 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7303 (mm-30) REVERT: G 511 ASP cc_start: 0.8011 (t0) cc_final: 0.7768 (t0) REVERT: G 524 TYR cc_start: 0.8746 (p90) cc_final: 0.8493 (p90) REVERT: I 41 SER cc_start: 0.8503 (t) cc_final: 0.8159 (p) REVERT: I 89 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8312 (ttmt) REVERT: I 96 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.6667 (ptt) REVERT: I 100 ASP cc_start: 0.7290 (m-30) cc_final: 0.6972 (m-30) REVERT: I 163 LYS cc_start: 0.8149 (mttp) cc_final: 0.7928 (mttp) REVERT: I 193 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7612 (mt-10) REVERT: I 249 SER cc_start: 0.8562 (t) cc_final: 0.8203 (p) REVERT: I 303 PHE cc_start: 0.8387 (m-80) cc_final: 0.8068 (m-10) REVERT: I 312 LYS cc_start: 0.8719 (mttt) cc_final: 0.8501 (mttt) REVERT: I 387 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8494 (mtpp) REVERT: I 436 ILE cc_start: 0.8696 (mm) cc_final: 0.8477 (mp) REVERT: I 439 LYS cc_start: 0.4802 (mmtt) cc_final: 0.3182 (mmmt) REVERT: I 501 LYS cc_start: 0.8826 (tttt) cc_final: 0.8625 (tttp) REVERT: I 518 MET cc_start: 0.7105 (ptp) cc_final: 0.6656 (ptp) outliers start: 98 outliers final: 60 residues processed: 1135 average time/residue: 0.6506 time to fit residues: 883.5725 Evaluate side-chains 1160 residues out of total 3469 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1089 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 475 ASP Chi-restraints excluded: chain A residue 530 LYS Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 397 ARG Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 583 LEU Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 293 SER Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 444 TYR Chi-restraints excluded: chain E residue 472 LYS Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 319 MET Chi-restraints excluded: chain F residue 326 THR Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 424 VAL Chi-restraints excluded: chain F residue 494 CYS Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 274 ARG Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 411 GLU Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 494 CYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 73 MET Chi-restraints excluded: chain I residue 96 MET Chi-restraints excluded: chain I residue 260 GLU Chi-restraints excluded: chain I residue 317 THR Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 387 LYS Chi-restraints excluded: chain I residue 442 ILE Chi-restraints excluded: chain I residue 553 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 342 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 378 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 144 optimal weight: 0.1980 chunk 47 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN A 558 GLN B 48 GLN B 383 GLN B 404 GLN B 554 ASN C 95 ASN C 383 GLN C 550 GLN D 47 ASN D 383 GLN E 47 ASN E 137 HIS E 180 ASN E 483 HIS F 180 ASN ** F 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN F 505 ASN ** G 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN G 550 GLN G 577 GLN I 147 ASN I 166 ASN I 404 GLN I 459 ASN I 549 GLN ** I 558 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.124733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108847 restraints weight = 47181.470| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.14 r_work: 0.3246 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33486 Z= 0.108 Angle : 0.557 15.418 45804 Z= 0.275 Chirality : 0.042 0.230 4980 Planarity : 0.004 0.077 6021 Dihedral : 5.030 83.744 4440 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.99 % Allowed : 23.64 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.13), residues: 3895 helix: 0.56 (0.46), residues: 87 sheet: -0.21 (0.17), residues: 925 loop : -0.20 (0.11), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 520 TYR 0.026 0.001 TYR I 524 PHE 0.024 0.001 PHE I 266 TRP 0.023 0.001 TRP C 200 HIS 0.008 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00249 (33478) covalent geometry : angle 0.55719 (45788) SS BOND : bond 0.00449 ( 8) SS BOND : angle 0.77666 ( 16) hydrogen bonds : bond 0.03165 ( 386) hydrogen bonds : angle 5.84325 ( 702) =============================================================================== Job complete usr+sys time: 15919.67 seconds wall clock time: 270 minutes 43.45 seconds (16243.45 seconds total)