Starting phenix.real_space_refine on Sat Jul 20 23:20:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrr_36603/07_2024/8jrr_36603_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrr_36603/07_2024/8jrr_36603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrr_36603/07_2024/8jrr_36603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrr_36603/07_2024/8jrr_36603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrr_36603/07_2024/8jrr_36603_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrr_36603/07_2024/8jrr_36603_neut.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.002 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 36 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 70 5.16 5 C 7868 2.51 5 N 2108 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 168": "NH1" <-> "NH2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 240": "NH1" <-> "NH2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C GLU 727": "OE1" <-> "OE2" Residue "C GLU 754": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12370 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5087 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 27, 'TRANS': 617} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "B" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1096 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 5087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5087 Classifications: {'peptide': 645} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 27, 'TRANS': 617} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 152 Chain: "D" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1096 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5263 SG CYS B 37 62.978 32.443 94.524 1.00178.25 S ATOM 5537 SG CYS B 70 60.683 35.235 93.633 1.00162.28 S ATOM 5560 SG CYS B 73 63.463 37.412 93.236 1.00146.37 S ATOM 5901 SG CYS B 113 59.383 34.814 78.871 1.00162.87 S ATOM 6163 SG CYS B 143 58.033 35.303 75.513 1.00192.52 S ATOM 11446 SG CYS D 37 74.110 74.657 94.524 1.00178.25 S ATOM 11720 SG CYS D 70 76.405 71.865 93.633 1.00162.28 S ATOM 11743 SG CYS D 73 73.625 69.688 93.236 1.00146.37 S ATOM 12084 SG CYS D 113 77.705 72.286 78.871 1.00162.87 S ATOM 12346 SG CYS D 143 79.055 71.797 75.513 1.00192.52 S Time building chain proxies: 6.86, per 1000 atoms: 0.55 Number of scatterers: 12370 At special positions: 0 Unit cell: (138.159, 108.171, 111.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 70 16.00 O 2320 8.00 N 2108 7.00 C 7868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.65 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 73 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 37 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 73 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 10 sheets defined 50.3% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 146 through 152 removed outlier: 3.609A pdb=" N ILE A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.693A pdb=" N SER A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 removed outlier: 4.246A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 4.254A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 Proline residue: A 265 - end of helix removed outlier: 3.575A pdb=" N GLU A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.974A pdb=" N ARG A 279 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 286 removed outlier: 3.568A pdb=" N LEU A 286 " --> pdb=" O TYR A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 287 through 292 removed outlier: 4.357A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.586A pdb=" N GLU A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix removed outlier: 3.624A pdb=" N LYS A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 330 removed outlier: 5.070A pdb=" N LEU A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 343 removed outlier: 4.059A pdb=" N GLU A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.928A pdb=" N ILE A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 385 removed outlier: 3.795A pdb=" N CYS A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 381 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.760A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 removed outlier: 4.216A pdb=" N VAL A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 506 removed outlier: 5.158A pdb=" N LEU A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY A 492 " --> pdb=" O THR A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 513 removed outlier: 4.351A pdb=" N SER A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 removed outlier: 3.757A pdb=" N ASP A 535 " --> pdb=" O HIS A 531 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 540 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.588A pdb=" N GLU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'A' and resid 611 through 623 removed outlier: 3.980A pdb=" N ILE A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 removed outlier: 4.034A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 655 through 668 removed outlier: 3.895A pdb=" N SER A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 3.888A pdb=" N PHE A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 742 removed outlier: 3.764A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 760 Processing helix chain 'A' and resid 766 through 771 removed outlier: 4.333A pdb=" N LEU A 770 " --> pdb=" O ASP A 766 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 766 through 771' Processing helix chain 'A' and resid 786 through 795 removed outlier: 3.914A pdb=" N TRP A 791 " --> pdb=" O ILE A 787 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU A 792 " --> pdb=" O ARG A 788 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 removed outlier: 3.596A pdb=" N LEU A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU A 863 " --> pdb=" O LYS A 859 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 865 " --> pdb=" O ARG A 861 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 4.501A pdb=" N THR B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.566A pdb=" N TYR B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 51' Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.651A pdb=" N SER B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 96 removed outlier: 4.434A pdb=" N GLU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 96' Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.749A pdb=" N LEU B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.609A pdb=" N ILE C 150 " --> pdb=" O TYR C 146 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.693A pdb=" N SER C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 246 removed outlier: 4.246A pdb=" N THR C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 4.254A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 270 Proline residue: C 265 - end of helix removed outlier: 3.575A pdb=" N GLU C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 removed outlier: 3.974A pdb=" N ARG C 279 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 286 removed outlier: 3.568A pdb=" N LEU C 286 " --> pdb=" O TYR C 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 287 through 292 removed outlier: 4.357A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 315 removed outlier: 3.586A pdb=" N GLU C 303 " --> pdb=" O PRO C 299 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) Proline residue: C 307 - end of helix removed outlier: 3.624A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 330 removed outlier: 5.070A pdb=" N LEU C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 330 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 343 removed outlier: 4.059A pdb=" N GLU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR C 342 " --> pdb=" O ARG C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 354 removed outlier: 3.928A pdb=" N ILE C 347 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 349 " --> pdb=" O GLN C 345 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 354 " --> pdb=" O LYS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 385 removed outlier: 3.795A pdb=" N CYS C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA C 381 " --> pdb=" O MET C 377 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.760A pdb=" N THR C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 removed outlier: 4.216A pdb=" N VAL C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 506 removed outlier: 5.158A pdb=" N LEU C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY C 492 " --> pdb=" O THR C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 513 removed outlier: 4.351A pdb=" N SER C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 546 removed outlier: 3.757A pdb=" N ASP C 535 " --> pdb=" O HIS C 531 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 539 " --> pdb=" O ASP C 535 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 540 " --> pdb=" O ALA C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 582 removed outlier: 3.588A pdb=" N GLU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 610 Processing helix chain 'C' and resid 611 through 623 removed outlier: 3.980A pdb=" N ILE C 615 " --> pdb=" O GLN C 611 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE C 617 " --> pdb=" O THR C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 642 removed outlier: 4.034A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 655 through 668 removed outlier: 3.895A pdb=" N SER C 661 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 723 removed outlier: 3.888A pdb=" N PHE C 713 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 717 " --> pdb=" O PHE C 713 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 742 removed outlier: 3.764A pdb=" N GLY C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 740 " --> pdb=" O GLY C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 760 Processing helix chain 'C' and resid 766 through 771 removed outlier: 4.333A pdb=" N LEU C 770 " --> pdb=" O ASP C 766 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 771 " --> pdb=" O PHE C 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 766 through 771' Processing helix chain 'C' and resid 786 through 795 removed outlier: 3.914A pdb=" N TRP C 791 " --> pdb=" O ILE C 787 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU C 792 " --> pdb=" O ARG C 788 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE C 793 " --> pdb=" O GLU C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 868 removed outlier: 3.596A pdb=" N LEU C 858 " --> pdb=" O SER C 854 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 860 " --> pdb=" O GLU C 856 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG C 861 " --> pdb=" O LYS C 857 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU C 863 " --> pdb=" O LYS C 859 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 865 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR C 868 " --> pdb=" O LYS C 864 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 26 removed outlier: 4.501A pdb=" N THR D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.566A pdb=" N TYR D 50 " --> pdb=" O ARG D 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 51' Processing helix chain 'D' and resid 70 through 83 removed outlier: 3.651A pdb=" N SER D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 removed outlier: 4.434A pdb=" N GLU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.749A pdb=" N LEU D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 526 removed outlier: 5.513A pdb=" N LEU A 523 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A 558 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU A 525 " --> pdb=" O GLU A 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 590 through 593 removed outlier: 4.044A pdb=" N TRP A 600 " --> pdb=" O THR A 591 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 682 through 684 removed outlier: 3.834A pdb=" N ILE A 682 " --> pdb=" O TYR A 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 694 " --> pdb=" O ILE A 682 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'B' and resid 86 through 91 removed outlier: 7.279A pdb=" N ASN B 134 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B 89 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE B 132 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 135 " --> pdb=" O ARG B 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 523 through 526 removed outlier: 5.513A pdb=" N LEU C 523 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C 558 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU C 525 " --> pdb=" O GLU C 558 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 590 through 593 removed outlier: 4.044A pdb=" N TRP C 600 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 682 through 684 removed outlier: 3.834A pdb=" N ILE C 682 " --> pdb=" O TYR C 694 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR C 694 " --> pdb=" O ILE C 682 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 62 Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 91 removed outlier: 7.279A pdb=" N ASN D 134 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER D 89 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE D 132 " --> pdb=" O SER D 89 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 135 " --> pdb=" O ARG D 138 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 960 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: 3.26 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4008 1.34 - 1.46: 2618 1.46 - 1.58: 5850 1.58 - 1.70: 0 1.70 - 1.82: 104 Bond restraints: 12580 Sorted by residual: bond pdb=" CB PHE C 599 " pdb=" CG PHE C 599 " ideal model delta sigma weight residual 1.502 1.440 0.062 2.30e-02 1.89e+03 7.22e+00 bond pdb=" CB PHE A 599 " pdb=" CG PHE A 599 " ideal model delta sigma weight residual 1.502 1.440 0.062 2.30e-02 1.89e+03 7.22e+00 bond pdb=" CD LYS A 553 " pdb=" CE LYS A 553 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.17e+00 bond pdb=" CD LYS C 553 " pdb=" CE LYS C 553 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.17e+00 bond pdb=" CD2 PHE C 599 " pdb=" CE2 PHE C 599 " ideal model delta sigma weight residual 1.382 1.313 0.069 3.00e-02 1.11e+03 5.32e+00 ... (remaining 12575 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.37: 322 106.37 - 113.34: 6688 113.34 - 120.30: 5214 120.30 - 127.27: 4664 127.27 - 134.23: 92 Bond angle restraints: 16980 Sorted by residual: angle pdb=" N GLY A 433 " pdb=" CA GLY A 433 " pdb=" C GLY A 433 " ideal model delta sigma weight residual 114.25 109.09 5.16 1.30e+00 5.92e-01 1.58e+01 angle pdb=" N GLY C 433 " pdb=" CA GLY C 433 " pdb=" C GLY C 433 " ideal model delta sigma weight residual 114.25 109.09 5.16 1.30e+00 5.92e-01 1.58e+01 angle pdb=" CB LYS C 553 " pdb=" CG LYS C 553 " pdb=" CD LYS C 553 " ideal model delta sigma weight residual 111.30 103.44 7.86 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CB LYS A 553 " pdb=" CG LYS A 553 " pdb=" CD LYS A 553 " ideal model delta sigma weight residual 111.30 103.44 7.86 2.30e+00 1.89e-01 1.17e+01 angle pdb=" C ILE B 135 " pdb=" N ARG B 136 " pdb=" CA ARG B 136 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 ... (remaining 16975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 6520 17.33 - 34.65: 968 34.65 - 51.98: 182 51.98 - 69.30: 38 69.30 - 86.63: 8 Dihedral angle restraints: 7716 sinusoidal: 3124 harmonic: 4592 Sorted by residual: dihedral pdb=" CA ALA C 320 " pdb=" C ALA C 320 " pdb=" N GLN C 321 " pdb=" CA GLN C 321 " ideal model delta harmonic sigma weight residual 180.00 148.23 31.77 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" CA ALA A 320 " pdb=" C ALA A 320 " pdb=" N GLN A 321 " pdb=" CA GLN A 321 " ideal model delta harmonic sigma weight residual 180.00 148.23 31.77 0 5.00e+00 4.00e-02 4.04e+01 dihedral pdb=" CA VAL A 509 " pdb=" C VAL A 509 " pdb=" N LEU A 510 " pdb=" CA LEU A 510 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 7713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1342 0.064 - 0.127: 482 0.127 - 0.190: 80 0.190 - 0.254: 4 0.254 - 0.317: 4 Chirality restraints: 1912 Sorted by residual: chirality pdb=" CB VAL A 234 " pdb=" CA VAL A 234 " pdb=" CG1 VAL A 234 " pdb=" CG2 VAL A 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB VAL C 234 " pdb=" CA VAL C 234 " pdb=" CG1 VAL C 234 " pdb=" CG2 VAL C 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CB ILE A 532 " pdb=" CA ILE A 532 " pdb=" CG1 ILE A 532 " pdb=" CG2 ILE A 532 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1909 not shown) Planarity restraints: 2186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 582 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ILE A 582 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE A 582 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE A 583 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 582 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ILE C 582 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE C 582 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE C 583 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 19 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.67e+00 pdb=" N PRO B 20 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 20 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 20 " -0.036 5.00e-02 4.00e+02 ... (remaining 2183 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2646 2.76 - 3.30: 12628 3.30 - 3.83: 22008 3.83 - 4.37: 26504 4.37 - 4.90: 40111 Nonbonded interactions: 103897 Sorted by model distance: nonbonded pdb=" O GLY A 610 " pdb=" OG1 THR A 613 " model vdw 2.229 2.440 nonbonded pdb=" O GLY C 610 " pdb=" OG1 THR C 613 " model vdw 2.229 2.440 nonbonded pdb=" O SER A 476 " pdb=" OG1 THR A 479 " model vdw 2.249 2.440 nonbonded pdb=" O SER C 476 " pdb=" OG1 THR C 479 " model vdw 2.249 2.440 nonbonded pdb=" O ARG A 240 " pdb=" OG1 THR A 244 " model vdw 2.270 2.440 ... (remaining 103892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.210 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 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 : 0.008 0.082 12580 Z= 0.529 Angle : 1.082 10.174 16980 Z= 0.584 Chirality : 0.063 0.317 1912 Planarity : 0.007 0.065 2186 Dihedral : 16.683 86.629 4720 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 1.66 % Allowed : 16.64 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.20), residues: 1496 helix: -4.04 (0.13), residues: 594 sheet: -1.99 (1.12), residues: 16 loop : -2.03 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 791 HIS 0.011 0.002 HIS A 655 PHE 0.027 0.004 PHE C 633 TYR 0.024 0.003 TYR C 592 ARG 0.009 0.001 ARG A 649 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 453 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ARG cc_start: 0.8387 (mmp80) cc_final: 0.7993 (mmp80) REVERT: A 287 PHE cc_start: 0.7461 (m-80) cc_final: 0.6954 (m-80) REVERT: A 313 MET cc_start: 0.7854 (tpp) cc_final: 0.7621 (tpp) REVERT: A 323 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8225 (mmtm) REVERT: A 328 TRP cc_start: 0.8479 (m-10) cc_final: 0.8012 (m-10) REVERT: A 339 MET cc_start: 0.8832 (ptp) cc_final: 0.8141 (ptp) REVERT: A 340 MET cc_start: 0.7518 (ptm) cc_final: 0.7150 (ptt) REVERT: A 345 GLN cc_start: 0.7717 (mt0) cc_final: 0.7082 (mt0) REVERT: A 354 ASN cc_start: 0.8127 (m-40) cc_final: 0.7868 (p0) REVERT: A 373 LYS cc_start: 0.8605 (tttp) cc_final: 0.8110 (mmmm) REVERT: A 397 ASP cc_start: 0.7125 (m-30) cc_final: 0.6845 (m-30) REVERT: A 403 GLU cc_start: 0.7481 (tp30) cc_final: 0.7213 (tm-30) REVERT: A 454 LEU cc_start: 0.8640 (tp) cc_final: 0.8404 (tt) REVERT: A 472 GLU cc_start: 0.8469 (pt0) cc_final: 0.8205 (pm20) REVERT: A 477 PHE cc_start: 0.8128 (m-80) cc_final: 0.7808 (m-80) REVERT: A 478 MET cc_start: 0.7861 (tpp) cc_final: 0.7486 (tpp) REVERT: A 507 ILE cc_start: 0.7956 (tp) cc_final: 0.7673 (tp) REVERT: A 510 LEU cc_start: 0.8252 (mp) cc_final: 0.7893 (mt) REVERT: A 515 GLN cc_start: 0.7559 (mp10) cc_final: 0.7300 (mp10) REVERT: A 537 LEU cc_start: 0.8320 (tp) cc_final: 0.7957 (tp) REVERT: A 539 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7505 (tpp80) REVERT: A 558 GLU cc_start: 0.8029 (pt0) cc_final: 0.7695 (pm20) REVERT: A 578 VAL cc_start: 0.8078 (t) cc_final: 0.7528 (t) REVERT: A 580 GLU cc_start: 0.7595 (tp30) cc_final: 0.7187 (tp30) REVERT: A 593 ASP cc_start: 0.8209 (t0) cc_final: 0.7873 (t0) REVERT: A 597 LYS cc_start: 0.9044 (mtpp) cc_final: 0.8696 (mtpp) REVERT: A 621 LEU cc_start: 0.8694 (mm) cc_final: 0.8454 (mm) REVERT: A 625 ASN cc_start: 0.6998 (p0) cc_final: 0.6712 (p0) REVERT: A 635 MET cc_start: 0.7679 (mpp) cc_final: 0.7035 (mmp) REVERT: A 639 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7005 (mmm-85) REVERT: A 640 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7947 (mtmt) REVERT: A 649 ARG cc_start: 0.7660 (ppt170) cc_final: 0.7349 (ptt90) REVERT: A 663 LYS cc_start: 0.8385 (ptmm) cc_final: 0.8093 (ptpp) REVERT: A 684 GLN cc_start: 0.7349 (tp40) cc_final: 0.5893 (tm-30) REVERT: A 694 TYR cc_start: 0.6839 (t80) cc_final: 0.6627 (t80) REVERT: A 730 PHE cc_start: 0.7215 (t80) cc_final: 0.6672 (t80) REVERT: A 739 MET cc_start: 0.7858 (ttm) cc_final: 0.7624 (ttm) REVERT: A 754 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 822 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8114 (mmtm) REVERT: B 25 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7754 (mp0) REVERT: B 38 VAL cc_start: 0.7628 (p) cc_final: 0.7228 (m) REVERT: B 58 CYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7112 (t) REVERT: B 59 ILE cc_start: 0.7017 (mm) cc_final: 0.5625 (mm) REVERT: B 107 LEU cc_start: 0.8132 (tp) cc_final: 0.7919 (mm) REVERT: B 121 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6576 (mm-30) REVERT: B 122 LYS cc_start: 0.7817 (mttp) cc_final: 0.7520 (mttp) REVERT: B 124 ARG cc_start: 0.7334 (tpt170) cc_final: 0.6296 (mmm160) REVERT: C 146 TYR cc_start: 0.7902 (p90) cc_final: 0.6944 (p90) REVERT: C 235 ASP cc_start: 0.7024 (m-30) cc_final: 0.6819 (m-30) REVERT: C 241 ARG cc_start: 0.8400 (mmp80) cc_final: 0.7981 (mmp80) REVERT: C 287 PHE cc_start: 0.7626 (m-80) cc_final: 0.7086 (m-80) REVERT: C 323 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8294 (mmtm) REVERT: C 324 LEU cc_start: 0.8693 (mt) cc_final: 0.8318 (mt) REVERT: C 328 TRP cc_start: 0.8504 (m-10) cc_final: 0.8135 (m-10) REVERT: C 335 GLN cc_start: 0.8328 (mm110) cc_final: 0.8072 (mm110) REVERT: C 336 ILE cc_start: 0.8683 (mt) cc_final: 0.8201 (mt) REVERT: C 340 MET cc_start: 0.7315 (ptm) cc_final: 0.7002 (ptt) REVERT: C 345 GLN cc_start: 0.7773 (mt0) cc_final: 0.7166 (mt0) REVERT: C 394 GLU cc_start: 0.7176 (tt0) cc_final: 0.5602 (tt0) REVERT: C 397 ASP cc_start: 0.7808 (m-30) cc_final: 0.7602 (m-30) REVERT: C 450 ILE cc_start: 0.8325 (mt) cc_final: 0.8046 (mt) REVERT: C 478 MET cc_start: 0.7851 (tpp) cc_final: 0.7407 (tpp) REVERT: C 507 ILE cc_start: 0.8079 (tp) cc_final: 0.7831 (tp) REVERT: C 511 TYR cc_start: 0.7259 (m-80) cc_final: 0.7013 (m-80) REVERT: C 531 HIS cc_start: 0.7443 (m90) cc_final: 0.7093 (m90) REVERT: C 537 LEU cc_start: 0.8393 (tp) cc_final: 0.8058 (tp) REVERT: C 539 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7605 (tpp80) REVERT: C 545 MET cc_start: 0.7485 (ptt) cc_final: 0.7281 (ptt) REVERT: C 558 GLU cc_start: 0.8015 (pt0) cc_final: 0.7723 (pm20) REVERT: C 580 GLU cc_start: 0.7685 (tp30) cc_final: 0.7032 (tp30) REVERT: C 597 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8726 (mtpp) REVERT: C 639 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7096 (mmm-85) REVERT: C 648 PHE cc_start: 0.7629 (t80) cc_final: 0.7299 (t80) REVERT: C 649 ARG cc_start: 0.7374 (ppt170) cc_final: 0.6910 (tmm160) REVERT: C 651 LEU cc_start: 0.8484 (tp) cc_final: 0.8275 (tp) REVERT: C 663 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8362 (ptpp) REVERT: C 684 GLN cc_start: 0.7845 (tp40) cc_final: 0.7079 (tm-30) REVERT: C 712 GLU cc_start: 0.8486 (tt0) cc_final: 0.7343 (tp30) REVERT: C 731 LYS cc_start: 0.7706 (tptt) cc_final: 0.7407 (tptt) REVERT: C 734 ARG cc_start: 0.6790 (ttt180) cc_final: 0.6283 (ttt90) REVERT: C 739 MET cc_start: 0.7974 (ttm) cc_final: 0.7646 (ttm) REVERT: C 751 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7139 (tpt170) REVERT: C 801 GLN cc_start: 0.7911 (mt0) cc_final: 0.7702 (mt0) REVERT: C 822 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7971 (tptp) REVERT: D 38 VAL cc_start: 0.7675 (p) cc_final: 0.7293 (m) REVERT: D 55 ARG cc_start: 0.8223 (mpt-90) cc_final: 0.7937 (mmt-90) REVERT: D 58 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7482 (t) REVERT: D 121 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7413 (mm-30) REVERT: D 122 LYS cc_start: 0.7846 (mttp) cc_final: 0.7534 (mttp) REVERT: D 124 ARG cc_start: 0.7254 (tpt170) cc_final: 0.6351 (tpt90) outliers start: 22 outliers final: 10 residues processed: 465 average time/residue: 0.3219 time to fit residues: 196.9331 Evaluate side-chains 405 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 393 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.0040 chunk 62 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 139 optimal weight: 6.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN A 660 GLN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 85 HIS B 98 GLN B 114 GLN C 285 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C 660 GLN C 681 GLN C 738 HIS D 21 GLN D 85 HIS D 98 GLN D 114 GLN ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12580 Z= 0.200 Angle : 0.696 11.660 16980 Z= 0.361 Chirality : 0.045 0.204 1912 Planarity : 0.005 0.061 2186 Dihedral : 6.650 24.259 1688 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.30 % Allowed : 4.99 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.21), residues: 1496 helix: -3.12 (0.16), residues: 644 sheet: -2.44 (0.81), residues: 40 loop : -1.59 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 328 HIS 0.006 0.001 HIS C 531 PHE 0.031 0.002 PHE C 633 TYR 0.024 0.002 TYR C 464 ARG 0.005 0.001 ARG C 861 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 446 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ARG cc_start: 0.8555 (mmp80) cc_final: 0.7736 (mmp80) REVERT: A 245 ARG cc_start: 0.6916 (mtt90) cc_final: 0.6614 (mtt-85) REVERT: A 282 ASN cc_start: 0.8102 (t0) cc_final: 0.7730 (t0) REVERT: A 323 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7831 (mmtm) REVERT: A 324 LEU cc_start: 0.8441 (mt) cc_final: 0.7959 (mt) REVERT: A 328 TRP cc_start: 0.8432 (m-10) cc_final: 0.8149 (m-10) REVERT: A 339 MET cc_start: 0.8875 (ptp) cc_final: 0.8414 (ptp) REVERT: A 345 GLN cc_start: 0.7534 (mt0) cc_final: 0.7259 (mt0) REVERT: A 354 ASN cc_start: 0.8138 (m-40) cc_final: 0.7716 (p0) REVERT: A 383 VAL cc_start: 0.7923 (t) cc_final: 0.7706 (t) REVERT: A 410 GLN cc_start: 0.8796 (pt0) cc_final: 0.8454 (pt0) REVERT: A 472 GLU cc_start: 0.8423 (pt0) cc_final: 0.8180 (pp20) REVERT: A 478 MET cc_start: 0.7848 (tpp) cc_final: 0.6943 (tpp) REVERT: A 482 PHE cc_start: 0.7403 (p90) cc_final: 0.7134 (p90) REVERT: A 507 ILE cc_start: 0.8083 (tp) cc_final: 0.7795 (tp) REVERT: A 510 LEU cc_start: 0.8489 (mp) cc_final: 0.8053 (mm) REVERT: A 514 VAL cc_start: 0.7380 (p) cc_final: 0.6839 (p) REVERT: A 533 ILE cc_start: 0.8679 (mp) cc_final: 0.8282 (tp) REVERT: A 537 LEU cc_start: 0.7879 (tp) cc_final: 0.6982 (tp) REVERT: A 538 VAL cc_start: 0.8293 (p) cc_final: 0.7918 (p) REVERT: A 539 ARG cc_start: 0.8349 (tpp80) cc_final: 0.7782 (tpp80) REVERT: A 542 MET cc_start: 0.7096 (mmp) cc_final: 0.6892 (mmp) REVERT: A 558 GLU cc_start: 0.8032 (pt0) cc_final: 0.7746 (tm-30) REVERT: A 576 GLN cc_start: 0.7291 (tm-30) cc_final: 0.6615 (tm-30) REVERT: A 578 VAL cc_start: 0.7691 (t) cc_final: 0.7436 (t) REVERT: A 593 ASP cc_start: 0.8283 (t0) cc_final: 0.7937 (t0) REVERT: A 597 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8635 (mtmm) REVERT: A 635 MET cc_start: 0.7648 (mpp) cc_final: 0.6758 (mpp) REVERT: A 639 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.6773 (mmm-85) REVERT: A 640 LYS cc_start: 0.7923 (mtmt) cc_final: 0.7469 (mtmt) REVERT: A 641 LEU cc_start: 0.7770 (tt) cc_final: 0.7454 (tt) REVERT: A 648 PHE cc_start: 0.7436 (t80) cc_final: 0.7120 (t80) REVERT: A 651 LEU cc_start: 0.7901 (tp) cc_final: 0.7620 (tp) REVERT: A 663 LYS cc_start: 0.8623 (ptmm) cc_final: 0.8042 (ptpp) REVERT: A 684 GLN cc_start: 0.7232 (tp40) cc_final: 0.6313 (tm-30) REVERT: A 730 PHE cc_start: 0.6664 (t80) cc_final: 0.6175 (t80) REVERT: A 739 MET cc_start: 0.7852 (ttm) cc_final: 0.7484 (ttm) REVERT: A 751 ARG cc_start: 0.7638 (mmm160) cc_final: 0.6921 (mmt-90) REVERT: A 801 GLN cc_start: 0.8147 (mt0) cc_final: 0.7893 (mt0) REVERT: A 807 GLN cc_start: 0.8433 (mt0) cc_final: 0.8107 (mm110) REVERT: A 822 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8035 (mmtm) REVERT: B 25 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7569 (mp0) REVERT: B 79 LYS cc_start: 0.8525 (tptt) cc_final: 0.8033 (tptt) REVERT: B 107 LEU cc_start: 0.8215 (tp) cc_final: 0.7999 (mm) REVERT: B 121 GLU cc_start: 0.7811 (mm-30) cc_final: 0.6901 (tp30) REVERT: B 124 ARG cc_start: 0.7442 (tpt170) cc_final: 0.6460 (mmm160) REVERT: B 131 ARG cc_start: 0.5496 (mtm180) cc_final: 0.5166 (mtm-85) REVERT: B 133 HIS cc_start: 0.7040 (m-70) cc_final: 0.6643 (m-70) REVERT: C 145 ASP cc_start: 0.8528 (m-30) cc_final: 0.8134 (m-30) REVERT: C 146 TYR cc_start: 0.7958 (p90) cc_final: 0.7691 (p90) REVERT: C 237 ASP cc_start: 0.7888 (p0) cc_final: 0.7626 (p0) REVERT: C 240 ARG cc_start: 0.8997 (mtt180) cc_final: 0.8706 (mtt180) REVERT: C 241 ARG cc_start: 0.8505 (mmp80) cc_final: 0.8221 (mmp80) REVERT: C 251 LYS cc_start: 0.7497 (ptpp) cc_final: 0.7246 (ttpp) REVERT: C 287 PHE cc_start: 0.7311 (m-80) cc_final: 0.6740 (m-80) REVERT: C 290 VAL cc_start: 0.7356 (m) cc_final: 0.6893 (t) REVERT: C 323 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7947 (mmtm) REVERT: C 328 TRP cc_start: 0.8408 (m-10) cc_final: 0.8143 (m-10) REVERT: C 339 MET cc_start: 0.8748 (ptp) cc_final: 0.8302 (ptp) REVERT: C 340 MET cc_start: 0.7299 (ptm) cc_final: 0.7077 (ptt) REVERT: C 345 GLN cc_start: 0.7563 (mt0) cc_final: 0.6756 (mt0) REVERT: C 373 LYS cc_start: 0.8674 (tttp) cc_final: 0.8067 (tptp) REVERT: C 398 GLU cc_start: 0.8527 (mp0) cc_final: 0.7605 (mp0) REVERT: C 429 GLU cc_start: 0.7941 (mp0) cc_final: 0.7066 (pm20) REVERT: C 454 LEU cc_start: 0.8531 (tt) cc_final: 0.8139 (tp) REVERT: C 472 GLU cc_start: 0.7973 (pm20) cc_final: 0.7716 (pm20) REVERT: C 473 ASN cc_start: 0.8462 (m-40) cc_final: 0.8239 (m110) REVERT: C 477 PHE cc_start: 0.7984 (m-80) cc_final: 0.7609 (m-80) REVERT: C 478 MET cc_start: 0.7792 (tpp) cc_final: 0.7000 (tpp) REVERT: C 507 ILE cc_start: 0.8002 (tp) cc_final: 0.7719 (tp) REVERT: C 510 LEU cc_start: 0.8553 (mt) cc_final: 0.8232 (mt) REVERT: C 515 GLN cc_start: 0.7726 (mp10) cc_final: 0.7441 (mp10) REVERT: C 533 ILE cc_start: 0.8392 (tp) cc_final: 0.8132 (tp) REVERT: C 537 LEU cc_start: 0.8003 (tp) cc_final: 0.7257 (tp) REVERT: C 539 ARG cc_start: 0.8253 (tpp80) cc_final: 0.7546 (ttt180) REVERT: C 578 VAL cc_start: 0.7997 (t) cc_final: 0.7629 (t) REVERT: C 593 ASP cc_start: 0.8432 (t0) cc_final: 0.8154 (t0) REVERT: C 635 MET cc_start: 0.7693 (mpp) cc_final: 0.6823 (mpp) REVERT: C 639 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.6916 (mmm-85) REVERT: C 640 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7811 (mtmt) REVERT: C 648 PHE cc_start: 0.7425 (t80) cc_final: 0.7080 (t80) REVERT: C 651 LEU cc_start: 0.8090 (tp) cc_final: 0.7789 (tp) REVERT: C 663 LYS cc_start: 0.8925 (ptmm) cc_final: 0.8331 (ptpp) REVERT: C 684 GLN cc_start: 0.7933 (tp40) cc_final: 0.7262 (tm-30) REVERT: C 695 ASP cc_start: 0.7191 (p0) cc_final: 0.6781 (p0) REVERT: C 728 LYS cc_start: 0.7603 (mtmm) cc_final: 0.7380 (mtmm) REVERT: C 739 MET cc_start: 0.7921 (ttm) cc_final: 0.7524 (ttm) REVERT: C 742 ASN cc_start: 0.8559 (p0) cc_final: 0.8335 (p0) REVERT: C 754 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8017 (mt-10) REVERT: C 801 GLN cc_start: 0.7998 (mt0) cc_final: 0.7610 (mt0) REVERT: C 822 LYS cc_start: 0.8214 (mmtm) cc_final: 0.7856 (tptp) REVERT: C 861 ARG cc_start: 0.6775 (ttp-110) cc_final: 0.6261 (mtp85) REVERT: D 38 VAL cc_start: 0.7478 (p) cc_final: 0.7137 (m) REVERT: D 47 ARG cc_start: 0.6247 (tmt-80) cc_final: 0.5925 (tpt170) REVERT: D 79 LYS cc_start: 0.8521 (tptt) cc_final: 0.7968 (tptt) REVERT: D 82 GLU cc_start: 0.7278 (pp20) cc_final: 0.6847 (pp20) REVERT: D 121 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6778 (mm-30) REVERT: D 124 ARG cc_start: 0.7354 (tpt170) cc_final: 0.6407 (mmm160) REVERT: D 133 HIS cc_start: 0.6918 (m-70) cc_final: 0.6530 (m-70) outliers start: 4 outliers final: 2 residues processed: 449 average time/residue: 0.3236 time to fit residues: 193.8486 Evaluate side-chains 396 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 394 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 47 optimal weight: 0.9990 chunk 112 optimal weight: 0.0010 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 497 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 611 GLN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 ASN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12580 Z= 0.189 Angle : 0.673 13.882 16980 Z= 0.344 Chirality : 0.044 0.169 1912 Planarity : 0.005 0.070 2186 Dihedral : 6.016 24.196 1688 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.21), residues: 1496 helix: -2.71 (0.16), residues: 666 sheet: -0.96 (1.11), residues: 16 loop : -1.53 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 791 HIS 0.005 0.001 HIS A 392 PHE 0.025 0.002 PHE C 633 TYR 0.025 0.001 TYR C 464 ARG 0.013 0.001 ARG C 649 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ARG cc_start: 0.8616 (mmp80) cc_final: 0.8261 (mmp80) REVERT: A 287 PHE cc_start: 0.7331 (m-80) cc_final: 0.6915 (m-80) REVERT: A 323 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7931 (mmtm) REVERT: A 324 LEU cc_start: 0.8507 (mt) cc_final: 0.7574 (mt) REVERT: A 328 TRP cc_start: 0.8401 (m-10) cc_final: 0.8196 (m-10) REVERT: A 334 ASP cc_start: 0.7308 (p0) cc_final: 0.6821 (p0) REVERT: A 335 GLN cc_start: 0.7273 (mp10) cc_final: 0.6760 (mp10) REVERT: A 354 ASN cc_start: 0.8125 (m-40) cc_final: 0.7857 (p0) REVERT: A 398 GLU cc_start: 0.8002 (mp0) cc_final: 0.7756 (mp0) REVERT: A 459 GLU cc_start: 0.7236 (tm-30) cc_final: 0.7032 (tm-30) REVERT: A 464 TYR cc_start: 0.6534 (t80) cc_final: 0.6281 (t80) REVERT: A 472 GLU cc_start: 0.8511 (pt0) cc_final: 0.8124 (pp20) REVERT: A 473 ASN cc_start: 0.8771 (m110) cc_final: 0.8276 (m110) REVERT: A 478 MET cc_start: 0.7673 (tpp) cc_final: 0.7110 (tpp) REVERT: A 525 LEU cc_start: 0.8072 (tp) cc_final: 0.7572 (tp) REVERT: A 539 ARG cc_start: 0.8353 (tpp80) cc_final: 0.7767 (tpp80) REVERT: A 545 MET cc_start: 0.7455 (ptt) cc_final: 0.7144 (ptt) REVERT: A 593 ASP cc_start: 0.8186 (t0) cc_final: 0.7956 (t0) REVERT: A 635 MET cc_start: 0.7708 (mpp) cc_final: 0.6793 (mpp) REVERT: A 639 ARG cc_start: 0.7651 (mmm-85) cc_final: 0.6813 (mmm-85) REVERT: A 640 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7426 (mtmt) REVERT: A 641 LEU cc_start: 0.7683 (tt) cc_final: 0.7390 (tt) REVERT: A 651 LEU cc_start: 0.7869 (tp) cc_final: 0.7597 (tp) REVERT: A 663 LYS cc_start: 0.8398 (ptmm) cc_final: 0.7999 (ptpp) REVERT: A 739 MET cc_start: 0.7925 (ttm) cc_final: 0.7597 (ttm) REVERT: A 742 ASN cc_start: 0.8592 (p0) cc_final: 0.8349 (p0) REVERT: A 801 GLN cc_start: 0.8131 (mt0) cc_final: 0.7886 (mt0) REVERT: A 802 LYS cc_start: 0.7890 (mmtm) cc_final: 0.7627 (mmtm) REVERT: A 807 GLN cc_start: 0.8509 (mt0) cc_final: 0.8188 (mm110) REVERT: A 822 LYS cc_start: 0.8306 (mmtm) cc_final: 0.7956 (mmtm) REVERT: B 25 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7047 (mt-10) REVERT: B 47 ARG cc_start: 0.6176 (tmt-80) cc_final: 0.5916 (tpt170) REVERT: B 58 CYS cc_start: 0.6760 (t) cc_final: 0.6335 (t) REVERT: B 79 LYS cc_start: 0.8582 (tptt) cc_final: 0.8065 (tptt) REVERT: B 82 GLU cc_start: 0.7012 (pp20) cc_final: 0.6579 (pp20) REVERT: B 107 LEU cc_start: 0.8382 (tp) cc_final: 0.8120 (mm) REVERT: B 121 GLU cc_start: 0.7770 (mm-30) cc_final: 0.6684 (tp30) REVERT: B 124 ARG cc_start: 0.7328 (tpt170) cc_final: 0.6497 (mmm160) REVERT: B 126 LEU cc_start: 0.7497 (mp) cc_final: 0.7191 (mp) REVERT: B 133 HIS cc_start: 0.6930 (m-70) cc_final: 0.6728 (m-70) REVERT: C 240 ARG cc_start: 0.9017 (mtt180) cc_final: 0.8675 (mtt180) REVERT: C 241 ARG cc_start: 0.8425 (mmp80) cc_final: 0.7578 (mmp80) REVERT: C 287 PHE cc_start: 0.7335 (m-80) cc_final: 0.6862 (m-80) REVERT: C 323 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8038 (mmtt) REVERT: C 324 LEU cc_start: 0.8490 (mt) cc_final: 0.7567 (mt) REVERT: C 335 GLN cc_start: 0.7169 (mp10) cc_final: 0.6586 (mp10) REVERT: C 340 MET cc_start: 0.7314 (ptm) cc_final: 0.6987 (ptt) REVERT: C 344 GLN cc_start: 0.7842 (tp-100) cc_final: 0.7135 (tp-100) REVERT: C 345 GLN cc_start: 0.7655 (mt0) cc_final: 0.6975 (mt0) REVERT: C 376 LYS cc_start: 0.8392 (tmmt) cc_final: 0.8182 (ttpp) REVERT: C 395 GLU cc_start: 0.7312 (tm-30) cc_final: 0.6997 (tm-30) REVERT: C 454 LEU cc_start: 0.8462 (tt) cc_final: 0.8199 (tp) REVERT: C 458 LEU cc_start: 0.6819 (mt) cc_final: 0.6568 (mt) REVERT: C 464 TYR cc_start: 0.6859 (t80) cc_final: 0.6373 (t80) REVERT: C 468 LYS cc_start: 0.7488 (ttpt) cc_final: 0.6900 (mtpp) REVERT: C 478 MET cc_start: 0.7696 (tpp) cc_final: 0.7234 (tpp) REVERT: C 539 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7425 (ttt180) REVERT: C 543 ILE cc_start: 0.7436 (tp) cc_final: 0.7191 (tp) REVERT: C 597 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8949 (mtpp) REVERT: C 635 MET cc_start: 0.7701 (mpp) cc_final: 0.6872 (mpp) REVERT: C 639 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.6484 (mmm-85) REVERT: C 640 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7873 (mtmt) REVERT: C 651 LEU cc_start: 0.8041 (tp) cc_final: 0.7693 (tp) REVERT: C 663 LYS cc_start: 0.8635 (ptmm) cc_final: 0.8258 (ptmm) REVERT: C 684 GLN cc_start: 0.8022 (tp40) cc_final: 0.7017 (tm-30) REVERT: C 739 MET cc_start: 0.7981 (ttm) cc_final: 0.7738 (ttm) REVERT: C 754 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7960 (mt-10) REVERT: C 801 GLN cc_start: 0.8018 (mt0) cc_final: 0.7692 (mt0) REVERT: C 822 LYS cc_start: 0.8261 (mmtm) cc_final: 0.7865 (tptp) REVERT: D 47 ARG cc_start: 0.6279 (tmt-80) cc_final: 0.5932 (tpt170) REVERT: D 79 LYS cc_start: 0.8504 (tptt) cc_final: 0.7971 (tptt) REVERT: D 82 GLU cc_start: 0.7526 (pp20) cc_final: 0.6972 (pp20) REVERT: D 101 LYS cc_start: 0.6461 (tptp) cc_final: 0.6225 (tptp) REVERT: D 121 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6457 (tp30) REVERT: D 124 ARG cc_start: 0.7216 (tpt170) cc_final: 0.6390 (mmm160) REVERT: D 126 LEU cc_start: 0.7826 (mp) cc_final: 0.7568 (mp) REVERT: D 133 HIS cc_start: 0.6977 (m-70) cc_final: 0.6564 (m-70) outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.3352 time to fit residues: 185.9659 Evaluate side-chains 381 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 381 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 72 optimal weight: 0.0020 chunk 15 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 275 ASN ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 392 HIS A 410 GLN A 707 ASN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS C 275 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 ASN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN D 123 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12580 Z= 0.287 Angle : 0.714 11.110 16980 Z= 0.376 Chirality : 0.046 0.166 1912 Planarity : 0.005 0.050 2186 Dihedral : 6.156 24.739 1688 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 28.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.15 % Allowed : 5.60 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.21), residues: 1496 helix: -2.41 (0.17), residues: 654 sheet: -0.23 (1.29), residues: 16 loop : -1.44 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 139 HIS 0.005 0.001 HIS B 85 PHE 0.028 0.002 PHE B 52 TYR 0.019 0.001 TYR C 464 ARG 0.007 0.001 ARG C 751 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 431 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8182 (p0) cc_final: 0.7975 (p0) REVERT: A 240 ARG cc_start: 0.9111 (mtt180) cc_final: 0.8702 (mtt180) REVERT: A 266 ASN cc_start: 0.7382 (t0) cc_final: 0.6913 (m110) REVERT: A 282 ASN cc_start: 0.8501 (t0) cc_final: 0.8269 (t0) REVERT: A 287 PHE cc_start: 0.7477 (m-80) cc_final: 0.6999 (m-80) REVERT: A 309 PHE cc_start: 0.8095 (t80) cc_final: 0.7799 (t80) REVERT: A 323 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7853 (mmtm) REVERT: A 324 LEU cc_start: 0.8466 (mt) cc_final: 0.7491 (mt) REVERT: A 328 TRP cc_start: 0.8407 (m-10) cc_final: 0.8168 (m-10) REVERT: A 335 GLN cc_start: 0.7391 (mp10) cc_final: 0.6773 (mp10) REVERT: A 336 ILE cc_start: 0.8883 (mt) cc_final: 0.8491 (mt) REVERT: A 339 MET cc_start: 0.8841 (ppp) cc_final: 0.8604 (ppp) REVERT: A 340 MET cc_start: 0.8507 (ptp) cc_final: 0.8160 (ptt) REVERT: A 354 ASN cc_start: 0.8199 (m-40) cc_final: 0.7856 (p0) REVERT: A 373 LYS cc_start: 0.8581 (mttm) cc_final: 0.8234 (mttm) REVERT: A 389 ASP cc_start: 0.6846 (p0) cc_final: 0.6170 (p0) REVERT: A 397 ASP cc_start: 0.7369 (m-30) cc_final: 0.7109 (m-30) REVERT: A 398 GLU cc_start: 0.7611 (mp0) cc_final: 0.7398 (mp0) REVERT: A 460 MET cc_start: 0.6200 (mpp) cc_final: 0.5418 (mpp) REVERT: A 472 GLU cc_start: 0.8405 (pt0) cc_final: 0.8116 (pp20) REVERT: A 473 ASN cc_start: 0.8806 (m110) cc_final: 0.8383 (m110) REVERT: A 478 MET cc_start: 0.7914 (tpp) cc_final: 0.7373 (tpp) REVERT: A 490 ASN cc_start: 0.7716 (p0) cc_final: 0.7321 (p0) REVERT: A 491 LEU cc_start: 0.8437 (tp) cc_final: 0.8206 (tp) REVERT: A 494 TYR cc_start: 0.6913 (t80) cc_final: 0.6670 (t80) REVERT: A 507 ILE cc_start: 0.8290 (tp) cc_final: 0.8058 (tp) REVERT: A 514 VAL cc_start: 0.7464 (p) cc_final: 0.6949 (m) REVERT: A 539 ARG cc_start: 0.8442 (tpp80) cc_final: 0.7698 (ttt180) REVERT: A 553 LYS cc_start: 0.7468 (ttpt) cc_final: 0.7104 (ttpt) REVERT: A 558 GLU cc_start: 0.8305 (pt0) cc_final: 0.8020 (pm20) REVERT: A 589 MET cc_start: 0.5316 (mtt) cc_final: 0.4929 (mtt) REVERT: A 597 LYS cc_start: 0.9278 (mtpp) cc_final: 0.9078 (mtpp) REVERT: A 629 LEU cc_start: 0.8284 (mt) cc_final: 0.7840 (mm) REVERT: A 635 MET cc_start: 0.7890 (mpp) cc_final: 0.6922 (mpp) REVERT: A 639 ARG cc_start: 0.7721 (mmm-85) cc_final: 0.6992 (mmm-85) REVERT: A 640 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7841 (mtmt) REVERT: A 651 LEU cc_start: 0.8004 (tp) cc_final: 0.7741 (tp) REVERT: A 663 LYS cc_start: 0.8524 (ptmm) cc_final: 0.8074 (ptpp) REVERT: A 694 TYR cc_start: 0.7341 (t80) cc_final: 0.6834 (t80) REVERT: A 711 LYS cc_start: 0.8752 (mptt) cc_final: 0.8439 (mppt) REVERT: A 739 MET cc_start: 0.7999 (ttm) cc_final: 0.7762 (ttm) REVERT: A 742 ASN cc_start: 0.8750 (p0) cc_final: 0.8143 (p0) REVERT: A 801 GLN cc_start: 0.8109 (mt0) cc_final: 0.7802 (mt0) REVERT: A 805 PHE cc_start: 0.7479 (t80) cc_final: 0.7232 (t80) REVERT: A 807 GLN cc_start: 0.8579 (mt0) cc_final: 0.8231 (mm110) REVERT: A 822 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7932 (mmtm) REVERT: B 47 ARG cc_start: 0.6394 (tmt-80) cc_final: 0.6031 (tpt170) REVERT: B 79 LYS cc_start: 0.8677 (tptt) cc_final: 0.7955 (tptt) REVERT: B 82 GLU cc_start: 0.7244 (pp20) cc_final: 0.6763 (pp20) REVERT: B 107 LEU cc_start: 0.8455 (tp) cc_final: 0.8219 (mm) REVERT: B 121 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7184 (tp30) REVERT: B 124 ARG cc_start: 0.7365 (tpt170) cc_final: 0.6474 (mmm160) REVERT: C 138 GLU cc_start: 0.8156 (tp30) cc_final: 0.7838 (tp30) REVERT: C 240 ARG cc_start: 0.9117 (mtt180) cc_final: 0.8070 (tpp-160) REVERT: C 241 ARG cc_start: 0.8407 (mmp80) cc_final: 0.7819 (mmp80) REVERT: C 287 PHE cc_start: 0.7565 (m-80) cc_final: 0.7186 (m-80) REVERT: C 321 GLN cc_start: 0.8380 (mt0) cc_final: 0.8085 (mm-40) REVERT: C 324 LEU cc_start: 0.8422 (mt) cc_final: 0.8112 (mt) REVERT: C 335 GLN cc_start: 0.7455 (mp10) cc_final: 0.6848 (mp10) REVERT: C 340 MET cc_start: 0.7794 (ptm) cc_final: 0.7379 (ptt) REVERT: C 344 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7543 (tp-100) REVERT: C 345 GLN cc_start: 0.7902 (mt0) cc_final: 0.7547 (mt0) REVERT: C 354 ASN cc_start: 0.8379 (m-40) cc_final: 0.8045 (p0) REVERT: C 395 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7082 (tm-30) REVERT: C 398 GLU cc_start: 0.8098 (mp0) cc_final: 0.7642 (mp0) REVERT: C 458 LEU cc_start: 0.7159 (mt) cc_final: 0.6869 (pp) REVERT: C 460 MET cc_start: 0.6450 (mpp) cc_final: 0.5879 (mpp) REVERT: C 472 GLU cc_start: 0.8139 (pm20) cc_final: 0.7857 (pm20) REVERT: C 478 MET cc_start: 0.8087 (tpp) cc_final: 0.7759 (tpp) REVERT: C 482 PHE cc_start: 0.7441 (p90) cc_final: 0.6857 (p90) REVERT: C 491 LEU cc_start: 0.8523 (tp) cc_final: 0.8319 (tp) REVERT: C 511 TYR cc_start: 0.7583 (m-10) cc_final: 0.7238 (m-80) REVERT: C 515 GLN cc_start: 0.7554 (mp10) cc_final: 0.7247 (mp10) REVERT: C 539 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7404 (ttt180) REVERT: C 593 ASP cc_start: 0.8167 (t0) cc_final: 0.7957 (t0) REVERT: C 597 LYS cc_start: 0.9281 (mtpp) cc_final: 0.8917 (mmmt) REVERT: C 607 GLU cc_start: 0.8190 (pm20) cc_final: 0.7902 (pm20) REVERT: C 635 MET cc_start: 0.7855 (mpp) cc_final: 0.6945 (mpp) REVERT: C 639 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7243 (mmm-85) REVERT: C 648 PHE cc_start: 0.7360 (t80) cc_final: 0.7157 (t80) REVERT: C 651 LEU cc_start: 0.8147 (tp) cc_final: 0.7754 (tp) REVERT: C 663 LYS cc_start: 0.8807 (ptmm) cc_final: 0.8395 (ptpp) REVERT: C 684 GLN cc_start: 0.7975 (tp40) cc_final: 0.6881 (tm-30) REVERT: C 728 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7435 (mtpt) REVERT: C 731 LYS cc_start: 0.8262 (tptt) cc_final: 0.7792 (tppt) REVERT: C 739 MET cc_start: 0.7987 (ttm) cc_final: 0.7738 (ttm) REVERT: C 742 ASN cc_start: 0.8882 (p0) cc_final: 0.8615 (p0) REVERT: C 754 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8103 (mt-10) REVERT: C 801 GLN cc_start: 0.7961 (mt0) cc_final: 0.7593 (mt0) REVERT: C 807 GLN cc_start: 0.8114 (mm110) cc_final: 0.7782 (mm110) REVERT: D 47 ARG cc_start: 0.6577 (tmt-80) cc_final: 0.6283 (tpt170) REVERT: D 79 LYS cc_start: 0.8639 (tptt) cc_final: 0.7922 (tptt) REVERT: D 82 GLU cc_start: 0.7223 (pp20) cc_final: 0.6780 (pp20) REVERT: D 101 LYS cc_start: 0.6438 (tptp) cc_final: 0.6218 (tptp) REVERT: D 124 ARG cc_start: 0.7442 (tpt170) cc_final: 0.6542 (tpt90) REVERT: D 133 HIS cc_start: 0.7358 (m-70) cc_final: 0.6956 (m-70) outliers start: 2 outliers final: 2 residues processed: 432 average time/residue: 0.3079 time to fit residues: 177.8322 Evaluate side-chains 397 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 395 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 707 ASN ** A 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12580 Z= 0.202 Angle : 0.670 11.549 16980 Z= 0.337 Chirality : 0.044 0.178 1912 Planarity : 0.005 0.049 2186 Dihedral : 5.617 23.906 1688 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.21), residues: 1496 helix: -2.03 (0.18), residues: 680 sheet: 0.53 (1.32), residues: 16 loop : -1.29 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 328 HIS 0.004 0.001 HIS B 85 PHE 0.031 0.002 PHE C 466 TYR 0.013 0.001 TYR B 91 ARG 0.010 0.001 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.9063 (mtt180) cc_final: 0.8679 (mtt180) REVERT: A 266 ASN cc_start: 0.7057 (t0) cc_final: 0.6715 (m110) REVERT: A 282 ASN cc_start: 0.8483 (t0) cc_final: 0.8262 (t0) REVERT: A 287 PHE cc_start: 0.7583 (m-80) cc_final: 0.6944 (m-80) REVERT: A 324 LEU cc_start: 0.8349 (mt) cc_final: 0.7313 (mt) REVERT: A 328 TRP cc_start: 0.8343 (m-10) cc_final: 0.8056 (m-10) REVERT: A 335 GLN cc_start: 0.7465 (mp10) cc_final: 0.6720 (mp10) REVERT: A 336 ILE cc_start: 0.8903 (mt) cc_final: 0.8464 (mt) REVERT: A 339 MET cc_start: 0.8730 (ppp) cc_final: 0.8477 (ppp) REVERT: A 340 MET cc_start: 0.8485 (ptp) cc_final: 0.8089 (ptt) REVERT: A 373 LYS cc_start: 0.8418 (mttm) cc_final: 0.8071 (mttm) REVERT: A 398 GLU cc_start: 0.7489 (mp0) cc_final: 0.7254 (mp0) REVERT: A 464 TYR cc_start: 0.6780 (t80) cc_final: 0.6217 (t80) REVERT: A 473 ASN cc_start: 0.8754 (m110) cc_final: 0.8425 (m110) REVERT: A 478 MET cc_start: 0.7667 (tpp) cc_final: 0.7306 (tpp) REVERT: A 490 ASN cc_start: 0.7855 (p0) cc_final: 0.7520 (p0) REVERT: A 491 LEU cc_start: 0.8452 (tp) cc_final: 0.8152 (tp) REVERT: A 494 TYR cc_start: 0.6966 (t80) cc_final: 0.6723 (t80) REVERT: A 539 ARG cc_start: 0.8356 (tpp80) cc_final: 0.7536 (ttt180) REVERT: A 558 GLU cc_start: 0.8188 (pt0) cc_final: 0.7871 (pm20) REVERT: A 589 MET cc_start: 0.4936 (mtt) cc_final: 0.4592 (mtt) REVERT: A 629 LEU cc_start: 0.8221 (mt) cc_final: 0.7841 (mm) REVERT: A 635 MET cc_start: 0.7753 (mpp) cc_final: 0.6812 (mpp) REVERT: A 639 ARG cc_start: 0.7669 (mmm-85) cc_final: 0.6868 (mmm-85) REVERT: A 648 PHE cc_start: 0.7500 (t80) cc_final: 0.7161 (t80) REVERT: A 651 LEU cc_start: 0.8009 (tp) cc_final: 0.7736 (tp) REVERT: A 663 LYS cc_start: 0.8518 (ptmm) cc_final: 0.7846 (mtmm) REVERT: A 694 TYR cc_start: 0.6563 (t80) cc_final: 0.5781 (t80) REVERT: A 720 TYR cc_start: 0.7531 (t80) cc_final: 0.6875 (t80) REVERT: A 739 MET cc_start: 0.7922 (ttm) cc_final: 0.7687 (ttm) REVERT: A 751 ARG cc_start: 0.7441 (mmm160) cc_final: 0.6959 (tpp-160) REVERT: A 801 GLN cc_start: 0.8144 (mt0) cc_final: 0.7784 (mt0) REVERT: A 805 PHE cc_start: 0.7382 (t80) cc_final: 0.7160 (t80) REVERT: A 822 LYS cc_start: 0.8301 (mmtm) cc_final: 0.7944 (mmtm) REVERT: B 47 ARG cc_start: 0.6316 (tmt-80) cc_final: 0.5940 (tpt170) REVERT: B 79 LYS cc_start: 0.8517 (tptt) cc_final: 0.7835 (tptt) REVERT: B 82 GLU cc_start: 0.7159 (pp20) cc_final: 0.6692 (pp20) REVERT: B 101 LYS cc_start: 0.6149 (tptp) cc_final: 0.5933 (tptp) REVERT: B 107 LEU cc_start: 0.8571 (tp) cc_final: 0.8298 (mm) REVERT: B 121 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7224 (tp30) REVERT: B 124 ARG cc_start: 0.7465 (tpt170) cc_final: 0.6405 (mmm160) REVERT: C 235 ASP cc_start: 0.8070 (p0) cc_final: 0.7717 (m-30) REVERT: C 240 ARG cc_start: 0.9091 (mtt180) cc_final: 0.8741 (mtt180) REVERT: C 241 ARG cc_start: 0.8292 (mmp80) cc_final: 0.7589 (mmp80) REVERT: C 309 PHE cc_start: 0.7917 (t80) cc_final: 0.7600 (t80) REVERT: C 313 MET cc_start: 0.7756 (mmm) cc_final: 0.7399 (tpp) REVERT: C 324 LEU cc_start: 0.8397 (mt) cc_final: 0.8093 (mt) REVERT: C 335 GLN cc_start: 0.7519 (mp10) cc_final: 0.6910 (mp10) REVERT: C 340 MET cc_start: 0.7796 (ptm) cc_final: 0.7462 (ptt) REVERT: C 344 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7471 (tp-100) REVERT: C 345 GLN cc_start: 0.7763 (mt0) cc_final: 0.7411 (mt0) REVERT: C 354 ASN cc_start: 0.8383 (m-40) cc_final: 0.8074 (p0) REVERT: C 395 GLU cc_start: 0.7304 (tm-30) cc_final: 0.7047 (tm-30) REVERT: C 398 GLU cc_start: 0.7713 (mp0) cc_final: 0.7245 (mp0) REVERT: C 406 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6965 (tm-30) REVERT: C 407 LEU cc_start: 0.8463 (mt) cc_final: 0.8259 (mt) REVERT: C 412 LEU cc_start: 0.8767 (tt) cc_final: 0.8500 (tt) REVERT: C 440 ARG cc_start: 0.6703 (mtp85) cc_final: 0.5661 (ttt180) REVERT: C 458 LEU cc_start: 0.7135 (mt) cc_final: 0.6863 (pp) REVERT: C 460 MET cc_start: 0.6353 (mpp) cc_final: 0.6143 (mpp) REVERT: C 478 MET cc_start: 0.7868 (tpp) cc_final: 0.7289 (tpp) REVERT: C 482 PHE cc_start: 0.7391 (p90) cc_final: 0.6896 (p90) REVERT: C 539 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7365 (ttt180) REVERT: C 578 VAL cc_start: 0.7844 (t) cc_final: 0.7517 (p) REVERT: C 597 LYS cc_start: 0.9284 (mtpp) cc_final: 0.8950 (mmmt) REVERT: C 607 GLU cc_start: 0.8029 (pm20) cc_final: 0.7749 (pm20) REVERT: C 633 PHE cc_start: 0.8082 (m-80) cc_final: 0.7876 (m-80) REVERT: C 635 MET cc_start: 0.7622 (mpp) cc_final: 0.6884 (mpp) REVERT: C 639 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.6815 (mmm-85) REVERT: C 651 LEU cc_start: 0.8178 (tp) cc_final: 0.7802 (tp) REVERT: C 684 GLN cc_start: 0.7682 (tp40) cc_final: 0.7174 (tm-30) REVERT: C 711 LYS cc_start: 0.8927 (ptpp) cc_final: 0.8684 (ptpt) REVERT: C 728 LYS cc_start: 0.7718 (mtpt) cc_final: 0.7450 (mtpt) REVERT: C 731 LYS cc_start: 0.8146 (tptt) cc_final: 0.7884 (tptt) REVERT: C 739 MET cc_start: 0.7935 (ttm) cc_final: 0.7723 (ttm) REVERT: C 801 GLN cc_start: 0.8035 (mt0) cc_final: 0.7568 (mt0) REVERT: C 805 PHE cc_start: 0.7543 (t80) cc_final: 0.7276 (t80) REVERT: C 807 GLN cc_start: 0.8064 (mm110) cc_final: 0.7721 (mm110) REVERT: C 861 ARG cc_start: 0.7194 (mtp180) cc_final: 0.6833 (mtp85) REVERT: D 47 ARG cc_start: 0.6441 (tmt-80) cc_final: 0.6127 (tpt170) REVERT: D 79 LYS cc_start: 0.8557 (tptt) cc_final: 0.7789 (tptt) REVERT: D 82 GLU cc_start: 0.7591 (pp20) cc_final: 0.7044 (pp20) REVERT: D 101 LYS cc_start: 0.6300 (tptp) cc_final: 0.5998 (tptm) REVERT: D 121 GLU cc_start: 0.7427 (tp30) cc_final: 0.7102 (tp30) REVERT: D 124 ARG cc_start: 0.7453 (tpt170) cc_final: 0.6985 (mmm160) REVERT: D 133 HIS cc_start: 0.7241 (m-70) cc_final: 0.6817 (m-70) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.3268 time to fit residues: 178.7747 Evaluate side-chains 379 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 149 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 78 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN A 715 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 382 ASN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12580 Z= 0.169 Angle : 0.642 11.964 16980 Z= 0.317 Chirality : 0.043 0.190 1912 Planarity : 0.004 0.053 2186 Dihedral : 5.157 23.945 1688 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.08 % Allowed : 2.19 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.22), residues: 1496 helix: -1.75 (0.18), residues: 684 sheet: 1.27 (1.43), residues: 16 loop : -1.16 (0.24), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 328 HIS 0.003 0.001 HIS A 632 PHE 0.035 0.002 PHE C 648 TYR 0.020 0.001 TYR C 464 ARG 0.008 0.000 ARG C 649 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 423 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8058 (p0) cc_final: 0.7747 (p0) REVERT: A 240 ARG cc_start: 0.9015 (mtt180) cc_final: 0.8603 (mtt180) REVERT: A 241 ARG cc_start: 0.8740 (mmp80) cc_final: 0.7879 (mmp80) REVERT: A 266 ASN cc_start: 0.7078 (t0) cc_final: 0.6770 (m110) REVERT: A 282 ASN cc_start: 0.8486 (t0) cc_final: 0.8207 (t0) REVERT: A 287 PHE cc_start: 0.7654 (m-80) cc_final: 0.7328 (m-80) REVERT: A 309 PHE cc_start: 0.8103 (t80) cc_final: 0.7768 (t80) REVERT: A 321 GLN cc_start: 0.8408 (mp10) cc_final: 0.8102 (mp-120) REVERT: A 323 LYS cc_start: 0.8134 (mppt) cc_final: 0.7889 (mmtm) REVERT: A 324 LEU cc_start: 0.8294 (mt) cc_final: 0.7251 (mt) REVERT: A 328 TRP cc_start: 0.8307 (m-10) cc_final: 0.7987 (m-10) REVERT: A 334 ASP cc_start: 0.7357 (p0) cc_final: 0.6938 (p0) REVERT: A 335 GLN cc_start: 0.7515 (mp10) cc_final: 0.6849 (mp10) REVERT: A 336 ILE cc_start: 0.8861 (mt) cc_final: 0.7899 (mt) REVERT: A 339 MET cc_start: 0.8674 (ppp) cc_final: 0.8393 (ppp) REVERT: A 373 LYS cc_start: 0.8368 (mttm) cc_final: 0.7959 (mttm) REVERT: A 389 ASP cc_start: 0.6284 (p0) cc_final: 0.5883 (p0) REVERT: A 398 GLU cc_start: 0.7332 (mp0) cc_final: 0.7088 (mp0) REVERT: A 439 CYS cc_start: 0.7183 (m) cc_final: 0.6845 (m) REVERT: A 478 MET cc_start: 0.7548 (tpp) cc_final: 0.7045 (tpp) REVERT: A 490 ASN cc_start: 0.7868 (p0) cc_final: 0.7623 (p0) REVERT: A 539 ARG cc_start: 0.8337 (tpp80) cc_final: 0.7741 (tpp80) REVERT: A 558 GLU cc_start: 0.8132 (pt0) cc_final: 0.7848 (pm20) REVERT: A 589 MET cc_start: 0.4916 (mtt) cc_final: 0.4465 (mtt) REVERT: A 597 LYS cc_start: 0.9248 (mtpp) cc_final: 0.8980 (mtpp) REVERT: A 635 MET cc_start: 0.7661 (mpp) cc_final: 0.6892 (mpp) REVERT: A 640 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7714 (mtmt) REVERT: A 648 PHE cc_start: 0.7594 (t80) cc_final: 0.7373 (t80) REVERT: A 651 LEU cc_start: 0.7968 (tp) cc_final: 0.7694 (tp) REVERT: A 663 LYS cc_start: 0.8377 (ptmm) cc_final: 0.7938 (mtmm) REVERT: A 694 TYR cc_start: 0.6481 (t80) cc_final: 0.5536 (t80) REVERT: A 720 TYR cc_start: 0.7164 (t80) cc_final: 0.6719 (t80) REVERT: A 739 MET cc_start: 0.7696 (ttm) cc_final: 0.7466 (ttm) REVERT: A 751 ARG cc_start: 0.7161 (mmm160) cc_final: 0.6391 (tpp-160) REVERT: A 801 GLN cc_start: 0.8044 (mt0) cc_final: 0.7664 (mt0) REVERT: A 807 GLN cc_start: 0.8417 (mt0) cc_final: 0.8190 (mm110) REVERT: A 861 ARG cc_start: 0.7601 (ptp-170) cc_final: 0.6949 (mtp85) REVERT: B 47 ARG cc_start: 0.6251 (tmt-80) cc_final: 0.5826 (tpt170) REVERT: B 107 LEU cc_start: 0.8608 (tp) cc_final: 0.8228 (mm) REVERT: B 121 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7104 (tp30) REVERT: B 124 ARG cc_start: 0.7585 (tpt170) cc_final: 0.6543 (mmm160) REVERT: C 235 ASP cc_start: 0.7821 (p0) cc_final: 0.7551 (m-30) REVERT: C 241 ARG cc_start: 0.8310 (mmp80) cc_final: 0.7611 (mmp80) REVERT: C 242 VAL cc_start: 0.8579 (t) cc_final: 0.8321 (t) REVERT: C 309 PHE cc_start: 0.7887 (t80) cc_final: 0.7550 (t80) REVERT: C 313 MET cc_start: 0.7672 (mmm) cc_final: 0.7071 (tpp) REVERT: C 324 LEU cc_start: 0.8353 (mt) cc_final: 0.8074 (mt) REVERT: C 340 MET cc_start: 0.7689 (ptm) cc_final: 0.7379 (ptt) REVERT: C 344 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7331 (tp-100) REVERT: C 345 GLN cc_start: 0.7804 (mt0) cc_final: 0.7431 (mt0) REVERT: C 395 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6964 (tm-30) REVERT: C 398 GLU cc_start: 0.7622 (mp0) cc_final: 0.6909 (mp0) REVERT: C 406 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7007 (tm-30) REVERT: C 407 LEU cc_start: 0.8559 (mt) cc_final: 0.8190 (mt) REVERT: C 478 MET cc_start: 0.7559 (tpp) cc_final: 0.7139 (tpp) REVERT: C 539 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7369 (ttt180) REVERT: C 542 MET cc_start: 0.7102 (mpp) cc_final: 0.6845 (mpp) REVERT: C 580 GLU cc_start: 0.7961 (tp30) cc_final: 0.7606 (tp30) REVERT: C 597 LYS cc_start: 0.9293 (mtpp) cc_final: 0.8943 (mmmt) REVERT: C 607 GLU cc_start: 0.8024 (pm20) cc_final: 0.7693 (pm20) REVERT: C 629 LEU cc_start: 0.7996 (mt) cc_final: 0.7532 (mt) REVERT: C 635 MET cc_start: 0.7602 (mpp) cc_final: 0.6797 (mpp) REVERT: C 639 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.6538 (mmm-85) REVERT: C 649 ARG cc_start: 0.6946 (ptt-90) cc_final: 0.6509 (ptt90) REVERT: C 651 LEU cc_start: 0.8111 (tp) cc_final: 0.7792 (tp) REVERT: C 684 GLN cc_start: 0.8004 (tp40) cc_final: 0.6872 (tm-30) REVERT: C 711 LYS cc_start: 0.8894 (ptpp) cc_final: 0.8686 (ptpt) REVERT: C 728 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7405 (mtpt) REVERT: C 731 LYS cc_start: 0.8053 (tptt) cc_final: 0.7608 (tptt) REVERT: C 739 MET cc_start: 0.7773 (ttm) cc_final: 0.7556 (ttm) REVERT: C 801 GLN cc_start: 0.7964 (mt0) cc_final: 0.7490 (mt0) REVERT: C 807 GLN cc_start: 0.8043 (mm110) cc_final: 0.7697 (mm110) REVERT: C 861 ARG cc_start: 0.7221 (mtp180) cc_final: 0.6826 (mtp85) REVERT: D 47 ARG cc_start: 0.6354 (tmt-80) cc_final: 0.6046 (tpt170) REVERT: D 52 PHE cc_start: 0.6999 (t80) cc_final: 0.6730 (t80) REVERT: D 58 CYS cc_start: 0.6704 (t) cc_final: 0.5927 (t) REVERT: D 79 LYS cc_start: 0.8511 (tptt) cc_final: 0.7735 (tptt) REVERT: D 82 GLU cc_start: 0.7517 (pp20) cc_final: 0.6937 (pp20) REVERT: D 101 LYS cc_start: 0.6253 (tptp) cc_final: 0.5880 (tptm) REVERT: D 121 GLU cc_start: 0.7607 (tp30) cc_final: 0.7373 (tp30) REVERT: D 124 ARG cc_start: 0.7720 (tpt170) cc_final: 0.6936 (tpt90) REVERT: D 133 HIS cc_start: 0.7139 (m-70) cc_final: 0.6756 (m-70) outliers start: 1 outliers final: 0 residues processed: 423 average time/residue: 0.3259 time to fit residues: 183.0448 Evaluate side-chains 392 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 0.0060 chunk 91 optimal weight: 2.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 715 ASN ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12580 Z= 0.169 Angle : 0.663 11.657 16980 Z= 0.325 Chirality : 0.044 0.204 1912 Planarity : 0.004 0.056 2186 Dihedral : 5.078 27.111 1688 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.22), residues: 1496 helix: -1.77 (0.18), residues: 732 sheet: -1.38 (0.93), residues: 40 loop : -1.20 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 791 HIS 0.007 0.001 HIS B 85 PHE 0.043 0.002 PHE A 633 TYR 0.021 0.001 TYR B 91 ARG 0.009 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8046 (p0) cc_final: 0.7748 (p0) REVERT: A 240 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8571 (mtt180) REVERT: A 266 ASN cc_start: 0.7145 (t0) cc_final: 0.6844 (m110) REVERT: A 282 ASN cc_start: 0.8511 (t0) cc_final: 0.8221 (t0) REVERT: A 287 PHE cc_start: 0.7710 (m-80) cc_final: 0.7298 (m-80) REVERT: A 309 PHE cc_start: 0.8087 (t80) cc_final: 0.7764 (t80) REVERT: A 323 LYS cc_start: 0.8156 (mppt) cc_final: 0.7910 (mmtm) REVERT: A 328 TRP cc_start: 0.8310 (m-10) cc_final: 0.7903 (m-10) REVERT: A 334 ASP cc_start: 0.7498 (p0) cc_final: 0.7069 (p0) REVERT: A 335 GLN cc_start: 0.7633 (mp10) cc_final: 0.7058 (mp10) REVERT: A 336 ILE cc_start: 0.8820 (mt) cc_final: 0.7760 (mm) REVERT: A 337 ARG cc_start: 0.8002 (mmp80) cc_final: 0.7281 (mmm160) REVERT: A 339 MET cc_start: 0.8563 (ppp) cc_final: 0.8201 (ppp) REVERT: A 340 MET cc_start: 0.8462 (ptp) cc_final: 0.7238 (ptp) REVERT: A 343 PHE cc_start: 0.6659 (p90) cc_final: 0.5882 (p90) REVERT: A 373 LYS cc_start: 0.8213 (mttm) cc_final: 0.7838 (mttm) REVERT: A 389 ASP cc_start: 0.6330 (p0) cc_final: 0.6014 (p0) REVERT: A 398 GLU cc_start: 0.7328 (mp0) cc_final: 0.7078 (mp0) REVERT: A 470 GLU cc_start: 0.7295 (tt0) cc_final: 0.6814 (pm20) REVERT: A 542 MET cc_start: 0.7137 (mmt) cc_final: 0.6891 (mmt) REVERT: A 580 GLU cc_start: 0.7884 (tp30) cc_final: 0.7580 (tp30) REVERT: A 589 MET cc_start: 0.4708 (mtt) cc_final: 0.4376 (mtt) REVERT: A 597 LYS cc_start: 0.9278 (mtpp) cc_final: 0.9072 (mtpp) REVERT: A 635 MET cc_start: 0.7629 (mpp) cc_final: 0.6831 (mpp) REVERT: A 639 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7629 (mmm-85) REVERT: A 640 LYS cc_start: 0.8019 (mtmt) cc_final: 0.7794 (mtmt) REVERT: A 651 LEU cc_start: 0.7750 (tp) cc_final: 0.7491 (tp) REVERT: A 663 LYS cc_start: 0.8417 (ptmm) cc_final: 0.7962 (mtmm) REVERT: A 694 TYR cc_start: 0.6454 (t80) cc_final: 0.5539 (t80) REVERT: A 720 TYR cc_start: 0.7186 (t80) cc_final: 0.6718 (t80) REVERT: A 739 MET cc_start: 0.7759 (ttm) cc_final: 0.7509 (ttm) REVERT: A 751 ARG cc_start: 0.7206 (mmm160) cc_final: 0.6256 (tpp-160) REVERT: A 801 GLN cc_start: 0.7950 (mt0) cc_final: 0.7581 (mt0) REVERT: A 822 LYS cc_start: 0.7853 (tptp) cc_final: 0.7544 (tptp) REVERT: A 861 ARG cc_start: 0.7669 (ptp-170) cc_final: 0.7285 (mtt180) REVERT: B 47 ARG cc_start: 0.6262 (tmt-80) cc_final: 0.5810 (tpt170) REVERT: B 107 LEU cc_start: 0.8592 (tp) cc_final: 0.8232 (mm) REVERT: B 121 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7113 (tp30) REVERT: B 124 ARG cc_start: 0.7737 (tpt170) cc_final: 0.6823 (mmm160) REVERT: B 129 LYS cc_start: 0.5617 (mttm) cc_final: 0.5405 (mttm) REVERT: C 241 ARG cc_start: 0.8310 (mmp80) cc_final: 0.7275 (mmp80) REVERT: C 242 VAL cc_start: 0.8611 (t) cc_final: 0.8377 (t) REVERT: C 287 PHE cc_start: 0.7565 (m-10) cc_final: 0.7087 (m-10) REVERT: C 340 MET cc_start: 0.7638 (ptm) cc_final: 0.7329 (ptt) REVERT: C 344 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7248 (tp-100) REVERT: C 345 GLN cc_start: 0.7757 (mt0) cc_final: 0.7395 (mt0) REVERT: C 395 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6895 (tm-30) REVERT: C 398 GLU cc_start: 0.7637 (mp0) cc_final: 0.7261 (mp0) REVERT: C 406 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6937 (tm-30) REVERT: C 407 LEU cc_start: 0.8598 (mt) cc_final: 0.8244 (mt) REVERT: C 411 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8100 (tp30) REVERT: C 441 LYS cc_start: 0.7708 (mptt) cc_final: 0.7485 (mmtm) REVERT: C 478 MET cc_start: 0.7582 (tpp) cc_final: 0.7170 (tpp) REVERT: C 507 ILE cc_start: 0.8354 (tp) cc_final: 0.8087 (tp) REVERT: C 539 ARG cc_start: 0.7962 (tpp80) cc_final: 0.7276 (tpp80) REVERT: C 542 MET cc_start: 0.7095 (mpp) cc_final: 0.6851 (mpp) REVERT: C 554 GLN cc_start: 0.7893 (tt0) cc_final: 0.7630 (tt0) REVERT: C 580 GLU cc_start: 0.8018 (tp30) cc_final: 0.7655 (tp30) REVERT: C 597 LYS cc_start: 0.9306 (mtpp) cc_final: 0.8855 (mmmm) REVERT: C 607 GLU cc_start: 0.8020 (pm20) cc_final: 0.7681 (pm20) REVERT: C 635 MET cc_start: 0.7575 (mpp) cc_final: 0.6852 (mpp) REVERT: C 639 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.6810 (mmm-85) REVERT: C 651 LEU cc_start: 0.8109 (tp) cc_final: 0.7789 (tp) REVERT: C 684 GLN cc_start: 0.8047 (tp40) cc_final: 0.6682 (tm-30) REVERT: C 728 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7420 (mtpt) REVERT: C 731 LYS cc_start: 0.7992 (tptt) cc_final: 0.7512 (tptt) REVERT: C 739 MET cc_start: 0.7743 (ttm) cc_final: 0.7498 (ttm) REVERT: C 801 GLN cc_start: 0.7947 (mt0) cc_final: 0.7507 (mt0) REVERT: C 807 GLN cc_start: 0.7991 (mm110) cc_final: 0.7659 (mm110) REVERT: C 822 LYS cc_start: 0.8470 (mmmm) cc_final: 0.8205 (mppt) REVERT: C 861 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6689 (mtp85) REVERT: D 25 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7211 (mt-10) REVERT: D 47 ARG cc_start: 0.6440 (tmt-80) cc_final: 0.6151 (tpt170) REVERT: D 52 PHE cc_start: 0.7047 (t80) cc_final: 0.6770 (t80) REVERT: D 58 CYS cc_start: 0.6615 (t) cc_final: 0.5719 (t) REVERT: D 59 ILE cc_start: 0.6789 (mm) cc_final: 0.5562 (mm) REVERT: D 101 LYS cc_start: 0.6217 (tptp) cc_final: 0.5861 (tptm) REVERT: D 124 ARG cc_start: 0.7884 (tpt170) cc_final: 0.7094 (tpt90) REVERT: D 133 HIS cc_start: 0.7128 (m-70) cc_final: 0.6838 (m-70) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.3183 time to fit residues: 173.9166 Evaluate side-chains 378 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.0270 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 0.0670 chunk 135 optimal weight: 0.0970 overall best weight: 0.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12580 Z= 0.158 Angle : 0.670 12.811 16980 Z= 0.323 Chirality : 0.044 0.234 1912 Planarity : 0.004 0.059 2186 Dihedral : 4.929 23.733 1688 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.21), residues: 1496 helix: -1.64 (0.18), residues: 744 sheet: 1.53 (1.37), residues: 16 loop : -1.30 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 791 HIS 0.003 0.001 HIS B 85 PHE 0.035 0.002 PHE A 633 TYR 0.025 0.001 TYR A 638 ARG 0.009 0.000 ARG A 639 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8047 (p0) cc_final: 0.7667 (p0) REVERT: A 240 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8588 (mtt180) REVERT: A 241 ARG cc_start: 0.8729 (mmp80) cc_final: 0.7994 (mmp80) REVERT: A 266 ASN cc_start: 0.7117 (t0) cc_final: 0.6837 (m110) REVERT: A 272 THR cc_start: 0.7394 (t) cc_final: 0.6964 (p) REVERT: A 287 PHE cc_start: 0.7630 (m-80) cc_final: 0.7217 (m-80) REVERT: A 309 PHE cc_start: 0.8125 (t80) cc_final: 0.7817 (t80) REVERT: A 323 LYS cc_start: 0.8082 (mppt) cc_final: 0.7413 (tttt) REVERT: A 334 ASP cc_start: 0.7556 (p0) cc_final: 0.7149 (p0) REVERT: A 335 GLN cc_start: 0.7638 (mp10) cc_final: 0.7120 (mp10) REVERT: A 336 ILE cc_start: 0.8706 (mt) cc_final: 0.7598 (mm) REVERT: A 337 ARG cc_start: 0.7887 (mmp80) cc_final: 0.7189 (mmm160) REVERT: A 339 MET cc_start: 0.8527 (ppp) cc_final: 0.8135 (ppp) REVERT: A 340 MET cc_start: 0.8295 (ptp) cc_final: 0.6973 (ptp) REVERT: A 343 PHE cc_start: 0.6587 (p90) cc_final: 0.5782 (p90) REVERT: A 373 LYS cc_start: 0.8154 (mttm) cc_final: 0.7814 (mttm) REVERT: A 389 ASP cc_start: 0.6309 (p0) cc_final: 0.5796 (p0) REVERT: A 398 GLU cc_start: 0.7241 (mp0) cc_final: 0.6869 (mp0) REVERT: A 441 LYS cc_start: 0.8573 (ptpt) cc_final: 0.8335 (ptpt) REVERT: A 525 LEU cc_start: 0.8141 (tp) cc_final: 0.7758 (tp) REVERT: A 542 MET cc_start: 0.7074 (mmt) cc_final: 0.6869 (mmt) REVERT: A 543 ILE cc_start: 0.7942 (pt) cc_final: 0.7736 (tp) REVERT: A 576 GLN cc_start: 0.7259 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 597 LYS cc_start: 0.9293 (mtpp) cc_final: 0.9059 (mtpp) REVERT: A 635 MET cc_start: 0.7526 (mpp) cc_final: 0.5980 (mmp) REVERT: A 640 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7787 (mtmt) REVERT: A 648 PHE cc_start: 0.7430 (t80) cc_final: 0.7205 (t80) REVERT: A 649 ARG cc_start: 0.6770 (pmt-80) cc_final: 0.6186 (ttp80) REVERT: A 651 LEU cc_start: 0.7698 (tp) cc_final: 0.7367 (tp) REVERT: A 663 LYS cc_start: 0.8459 (ptmm) cc_final: 0.8051 (mtmm) REVERT: A 694 TYR cc_start: 0.6374 (t80) cc_final: 0.5414 (t80) REVERT: A 720 TYR cc_start: 0.7065 (t80) cc_final: 0.6613 (t80) REVERT: A 739 MET cc_start: 0.7617 (ttm) cc_final: 0.7325 (ttm) REVERT: A 742 ASN cc_start: 0.8645 (p0) cc_final: 0.8229 (p0) REVERT: A 751 ARG cc_start: 0.7494 (mmm160) cc_final: 0.7101 (tpp-160) REVERT: A 756 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6585 (mt-10) REVERT: A 801 GLN cc_start: 0.8000 (mt0) cc_final: 0.7594 (mt0) REVERT: A 807 GLN cc_start: 0.7669 (mm110) cc_final: 0.7196 (mm110) REVERT: A 822 LYS cc_start: 0.7800 (tptp) cc_final: 0.7499 (tptp) REVERT: A 861 ARG cc_start: 0.7614 (ptp-170) cc_final: 0.7070 (ptm160) REVERT: B 47 ARG cc_start: 0.6141 (tmt-80) cc_final: 0.5743 (tmt-80) REVERT: B 52 PHE cc_start: 0.7038 (t80) cc_final: 0.6816 (t80) REVERT: B 58 CYS cc_start: 0.6759 (t) cc_final: 0.6403 (t) REVERT: B 59 ILE cc_start: 0.7068 (mm) cc_final: 0.6842 (mm) REVERT: B 107 LEU cc_start: 0.8556 (tp) cc_final: 0.7984 (mm) REVERT: B 121 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7296 (tp30) REVERT: C 241 ARG cc_start: 0.8311 (mmp80) cc_final: 0.7818 (mmp80) REVERT: C 242 VAL cc_start: 0.8660 (t) cc_final: 0.8455 (t) REVERT: C 309 PHE cc_start: 0.7826 (t80) cc_final: 0.7618 (t80) REVERT: C 334 ASP cc_start: 0.7160 (p0) cc_final: 0.6496 (p0) REVERT: C 335 GLN cc_start: 0.7522 (mp10) cc_final: 0.7175 (mp10) REVERT: C 340 MET cc_start: 0.7645 (ptm) cc_final: 0.7363 (ptt) REVERT: C 344 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7681 (tp-100) REVERT: C 345 GLN cc_start: 0.7610 (mt0) cc_final: 0.7132 (mt0) REVERT: C 389 ASP cc_start: 0.7467 (p0) cc_final: 0.6727 (p0) REVERT: C 395 GLU cc_start: 0.7344 (tm-30) cc_final: 0.6912 (tm-30) REVERT: C 398 GLU cc_start: 0.7545 (mp0) cc_final: 0.7210 (mp0) REVERT: C 406 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6692 (tm-30) REVERT: C 407 LEU cc_start: 0.8598 (mt) cc_final: 0.8175 (mt) REVERT: C 478 MET cc_start: 0.7464 (tpp) cc_final: 0.6971 (tpp) REVERT: C 531 HIS cc_start: 0.7389 (m90) cc_final: 0.6343 (m90) REVERT: C 539 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7218 (ttt180) REVERT: C 540 LEU cc_start: 0.8601 (tt) cc_final: 0.8264 (tt) REVERT: C 542 MET cc_start: 0.7106 (mpp) cc_final: 0.6848 (mpp) REVERT: C 554 GLN cc_start: 0.7817 (tt0) cc_final: 0.7601 (tt0) REVERT: C 580 GLU cc_start: 0.7860 (tp30) cc_final: 0.7552 (tp30) REVERT: C 597 LYS cc_start: 0.9304 (mtpp) cc_final: 0.9031 (mmmt) REVERT: C 607 GLU cc_start: 0.7933 (pm20) cc_final: 0.7564 (pm20) REVERT: C 627 CYS cc_start: 0.6299 (p) cc_final: 0.6063 (p) REVERT: C 629 LEU cc_start: 0.7850 (mp) cc_final: 0.7024 (mt) REVERT: C 633 PHE cc_start: 0.7565 (m-80) cc_final: 0.7223 (m-80) REVERT: C 635 MET cc_start: 0.7571 (mpp) cc_final: 0.6859 (mpp) REVERT: C 639 ARG cc_start: 0.7665 (mmm-85) cc_final: 0.6504 (mmm-85) REVERT: C 649 ARG cc_start: 0.6735 (ptt-90) cc_final: 0.6440 (ptt90) REVERT: C 651 LEU cc_start: 0.8193 (tp) cc_final: 0.7871 (tp) REVERT: C 684 GLN cc_start: 0.8078 (tp40) cc_final: 0.6724 (tm-30) REVERT: C 720 TYR cc_start: 0.7127 (t80) cc_final: 0.6806 (t80) REVERT: C 731 LYS cc_start: 0.7910 (tptt) cc_final: 0.7469 (tptt) REVERT: C 739 MET cc_start: 0.7723 (ttm) cc_final: 0.7467 (ttm) REVERT: C 756 GLU cc_start: 0.6697 (mt-10) cc_final: 0.5198 (mt-10) REVERT: C 801 GLN cc_start: 0.8000 (mt0) cc_final: 0.7501 (mt0) REVERT: C 807 GLN cc_start: 0.7877 (mm110) cc_final: 0.7533 (mm110) REVERT: C 822 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8092 (mmtt) REVERT: C 861 ARG cc_start: 0.7070 (mtp180) cc_final: 0.6575 (mtp85) REVERT: D 25 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7339 (mt-10) REVERT: D 47 ARG cc_start: 0.6465 (tmt-80) cc_final: 0.6205 (tpt170) REVERT: D 52 PHE cc_start: 0.7084 (t80) cc_final: 0.6821 (t80) REVERT: D 58 CYS cc_start: 0.6671 (t) cc_final: 0.5949 (t) REVERT: D 121 GLU cc_start: 0.7433 (tp30) cc_final: 0.7098 (tp30) REVERT: D 124 ARG cc_start: 0.7959 (tpt170) cc_final: 0.7369 (mmm160) REVERT: D 133 HIS cc_start: 0.7068 (m-70) cc_final: 0.6788 (m-70) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.3189 time to fit residues: 173.4143 Evaluate side-chains 373 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.2980 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 137 optimal weight: 0.0570 chunk 90 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 HIS A 660 GLN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12580 Z= 0.168 Angle : 0.679 12.790 16980 Z= 0.329 Chirality : 0.044 0.237 1912 Planarity : 0.004 0.058 2186 Dihedral : 4.839 26.408 1688 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.21), residues: 1496 helix: -1.57 (0.18), residues: 742 sheet: -1.37 (0.90), residues: 40 loop : -1.21 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 791 HIS 0.002 0.000 HIS B 85 PHE 0.030 0.002 PHE A 633 TYR 0.014 0.001 TYR A 638 ARG 0.007 0.001 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8650 (mp0) cc_final: 0.8309 (mp0) REVERT: A 237 ASP cc_start: 0.7855 (p0) cc_final: 0.7263 (p0) REVERT: A 240 ARG cc_start: 0.8815 (mtt180) cc_final: 0.8536 (mtt180) REVERT: A 241 ARG cc_start: 0.8476 (mmp80) cc_final: 0.7922 (mmp80) REVERT: A 266 ASN cc_start: 0.7215 (t0) cc_final: 0.6918 (m110) REVERT: A 272 THR cc_start: 0.7369 (t) cc_final: 0.6968 (p) REVERT: A 284 LEU cc_start: 0.7453 (pp) cc_final: 0.7248 (pp) REVERT: A 287 PHE cc_start: 0.7640 (m-80) cc_final: 0.7297 (m-80) REVERT: A 309 PHE cc_start: 0.8161 (t80) cc_final: 0.7553 (t80) REVERT: A 323 LYS cc_start: 0.7977 (mppt) cc_final: 0.7433 (mmtt) REVERT: A 334 ASP cc_start: 0.7521 (p0) cc_final: 0.7136 (p0) REVERT: A 335 GLN cc_start: 0.7651 (mp10) cc_final: 0.7117 (mp10) REVERT: A 336 ILE cc_start: 0.8717 (mt) cc_final: 0.7622 (mm) REVERT: A 337 ARG cc_start: 0.7881 (mmp80) cc_final: 0.7194 (mmm160) REVERT: A 339 MET cc_start: 0.8586 (ppp) cc_final: 0.8180 (ppp) REVERT: A 340 MET cc_start: 0.8282 (ptp) cc_final: 0.6903 (ptp) REVERT: A 343 PHE cc_start: 0.6576 (p90) cc_final: 0.5758 (p90) REVERT: A 373 LYS cc_start: 0.8191 (mttm) cc_final: 0.7826 (mttm) REVERT: A 389 ASP cc_start: 0.6286 (p0) cc_final: 0.5710 (p0) REVERT: A 398 GLU cc_start: 0.7216 (mp0) cc_final: 0.6996 (mp0) REVERT: A 412 LEU cc_start: 0.8380 (tt) cc_final: 0.8052 (tt) REVERT: A 470 GLU cc_start: 0.7249 (tt0) cc_final: 0.6687 (pm20) REVERT: A 477 PHE cc_start: 0.7780 (m-80) cc_final: 0.7336 (m-80) REVERT: A 494 TYR cc_start: 0.6859 (t80) cc_final: 0.6563 (t80) REVERT: A 525 LEU cc_start: 0.8094 (tp) cc_final: 0.7704 (tp) REVERT: A 542 MET cc_start: 0.7081 (mmt) cc_final: 0.6850 (mmt) REVERT: A 576 GLN cc_start: 0.7326 (tm-30) cc_final: 0.7053 (tm-30) REVERT: A 611 GLN cc_start: 0.7818 (mp10) cc_final: 0.7613 (mp10) REVERT: A 615 ILE cc_start: 0.8400 (tp) cc_final: 0.8196 (tp) REVERT: A 635 MET cc_start: 0.7481 (mpp) cc_final: 0.6070 (mmp) REVERT: A 639 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7559 (mmm-85) REVERT: A 640 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7734 (mtmt) REVERT: A 648 PHE cc_start: 0.7540 (t80) cc_final: 0.7278 (t80) REVERT: A 649 ARG cc_start: 0.6624 (pmt-80) cc_final: 0.6356 (tmm160) REVERT: A 651 LEU cc_start: 0.7714 (tp) cc_final: 0.7362 (tp) REVERT: A 663 LYS cc_start: 0.8624 (ptmm) cc_final: 0.7992 (mtmm) REVERT: A 694 TYR cc_start: 0.6369 (t80) cc_final: 0.5444 (t80) REVERT: A 720 TYR cc_start: 0.7214 (t80) cc_final: 0.6758 (t80) REVERT: A 739 MET cc_start: 0.7615 (ttm) cc_final: 0.7306 (ttm) REVERT: A 742 ASN cc_start: 0.8599 (p0) cc_final: 0.8251 (p0) REVERT: A 751 ARG cc_start: 0.7531 (mmm160) cc_final: 0.7199 (tpp-160) REVERT: A 756 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6716 (mt-10) REVERT: A 801 GLN cc_start: 0.7998 (mt0) cc_final: 0.7675 (mt0) REVERT: A 807 GLN cc_start: 0.7713 (mm110) cc_final: 0.7311 (mm110) REVERT: A 822 LYS cc_start: 0.7803 (tptp) cc_final: 0.7479 (tptp) REVERT: A 861 ARG cc_start: 0.7590 (ptp-170) cc_final: 0.7220 (mtt180) REVERT: B 47 ARG cc_start: 0.6170 (tmt-80) cc_final: 0.5774 (tmt-80) REVERT: B 52 PHE cc_start: 0.7023 (t80) cc_final: 0.6795 (t80) REVERT: B 58 CYS cc_start: 0.6766 (t) cc_final: 0.6300 (t) REVERT: B 59 ILE cc_start: 0.7089 (mm) cc_final: 0.6596 (mm) REVERT: B 74 LEU cc_start: 0.7998 (tp) cc_final: 0.7791 (tp) REVERT: B 79 LYS cc_start: 0.8414 (tptt) cc_final: 0.7485 (tptp) REVERT: B 107 LEU cc_start: 0.8534 (tp) cc_final: 0.7949 (mm) REVERT: B 121 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7014 (tp30) REVERT: B 124 ARG cc_start: 0.7928 (tpt170) cc_final: 0.6911 (mmm160) REVERT: C 138 GLU cc_start: 0.7994 (tp30) cc_final: 0.7386 (tp30) REVERT: C 237 ASP cc_start: 0.7867 (p0) cc_final: 0.7023 (p0) REVERT: C 240 ARG cc_start: 0.8743 (mtt180) cc_final: 0.8220 (mtt180) REVERT: C 241 ARG cc_start: 0.8274 (mmp80) cc_final: 0.7798 (mmp80) REVERT: C 242 VAL cc_start: 0.8670 (t) cc_final: 0.8450 (t) REVERT: C 284 LEU cc_start: 0.7543 (pp) cc_final: 0.7278 (pp) REVERT: C 309 PHE cc_start: 0.7952 (t80) cc_final: 0.7608 (t80) REVERT: C 323 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7884 (mmmt) REVERT: C 334 ASP cc_start: 0.7159 (p0) cc_final: 0.6499 (p0) REVERT: C 335 GLN cc_start: 0.7514 (mp10) cc_final: 0.7152 (mp10) REVERT: C 344 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7663 (tp-100) REVERT: C 345 GLN cc_start: 0.7614 (mt0) cc_final: 0.7117 (mt0) REVERT: C 389 ASP cc_start: 0.7448 (p0) cc_final: 0.6538 (p0) REVERT: C 392 HIS cc_start: 0.6776 (p90) cc_final: 0.6520 (p90) REVERT: C 395 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6797 (tm-30) REVERT: C 398 GLU cc_start: 0.7494 (mp0) cc_final: 0.7231 (mp0) REVERT: C 406 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6831 (tm-30) REVERT: C 407 LEU cc_start: 0.8609 (mt) cc_final: 0.8250 (mt) REVERT: C 440 ARG cc_start: 0.6262 (mtp85) cc_final: 0.6036 (ttm110) REVERT: C 441 LYS cc_start: 0.7699 (mptt) cc_final: 0.6926 (mptt) REVERT: C 478 MET cc_start: 0.7510 (tpp) cc_final: 0.7097 (tpp) REVERT: C 539 ARG cc_start: 0.7886 (tpp80) cc_final: 0.7252 (ttt180) REVERT: C 554 GLN cc_start: 0.7879 (tt0) cc_final: 0.7625 (tt0) REVERT: C 580 GLU cc_start: 0.7889 (tp30) cc_final: 0.7532 (tp30) REVERT: C 589 MET cc_start: 0.4072 (ttm) cc_final: 0.3553 (ttm) REVERT: C 597 LYS cc_start: 0.9290 (mtpp) cc_final: 0.9010 (mmmt) REVERT: C 607 GLU cc_start: 0.7939 (pm20) cc_final: 0.7595 (pm20) REVERT: C 627 CYS cc_start: 0.6365 (p) cc_final: 0.6102 (p) REVERT: C 629 LEU cc_start: 0.7935 (mp) cc_final: 0.7146 (mt) REVERT: C 633 PHE cc_start: 0.7740 (m-80) cc_final: 0.7362 (m-80) REVERT: C 635 MET cc_start: 0.7613 (mpp) cc_final: 0.6951 (mpp) REVERT: C 638 TYR cc_start: 0.7327 (m-10) cc_final: 0.7122 (m-10) REVERT: C 639 ARG cc_start: 0.7630 (mmm-85) cc_final: 0.6388 (mmm-85) REVERT: C 649 ARG cc_start: 0.6709 (ptt-90) cc_final: 0.5959 (ptt90) REVERT: C 651 LEU cc_start: 0.8216 (tp) cc_final: 0.7875 (tp) REVERT: C 659 TYR cc_start: 0.7859 (t80) cc_final: 0.7552 (t80) REVERT: C 720 TYR cc_start: 0.7275 (t80) cc_final: 0.6959 (t80) REVERT: C 728 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7471 (mtpt) REVERT: C 731 LYS cc_start: 0.7884 (tptt) cc_final: 0.7494 (tptt) REVERT: C 739 MET cc_start: 0.7647 (ttm) cc_final: 0.7425 (ttm) REVERT: C 801 GLN cc_start: 0.7955 (mt0) cc_final: 0.7445 (mt0) REVERT: C 807 GLN cc_start: 0.7855 (mm110) cc_final: 0.7545 (mm110) REVERT: C 822 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8048 (mmtt) REVERT: C 861 ARG cc_start: 0.7048 (mtp180) cc_final: 0.6522 (mtp85) REVERT: D 25 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7342 (mt-10) REVERT: D 47 ARG cc_start: 0.6441 (tmt-80) cc_final: 0.6184 (tpt170) REVERT: D 52 PHE cc_start: 0.7068 (t80) cc_final: 0.6851 (t80) REVERT: D 58 CYS cc_start: 0.6616 (t) cc_final: 0.6083 (t) REVERT: D 59 ILE cc_start: 0.6833 (mm) cc_final: 0.6625 (mm) REVERT: D 124 ARG cc_start: 0.7966 (tpt170) cc_final: 0.7403 (tpt90) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.3177 time to fit residues: 172.4403 Evaluate side-chains 373 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 0.0000 chunk 97 optimal weight: 6.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.6807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12580 Z= 0.166 Angle : 0.700 19.655 16980 Z= 0.333 Chirality : 0.044 0.236 1912 Planarity : 0.004 0.058 2186 Dihedral : 4.813 25.023 1688 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.21), residues: 1496 helix: -1.52 (0.18), residues: 768 sheet: -1.42 (0.89), residues: 40 loop : -1.24 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 791 HIS 0.002 0.000 HIS B 85 PHE 0.028 0.002 PHE A 633 TYR 0.013 0.001 TYR A 638 ARG 0.010 0.001 ARG A 245 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.8635 (mp0) cc_final: 0.8276 (mp0) REVERT: A 237 ASP cc_start: 0.7866 (p0) cc_final: 0.7216 (p0) REVERT: A 240 ARG cc_start: 0.8817 (mtt180) cc_final: 0.8486 (mtt180) REVERT: A 241 ARG cc_start: 0.8379 (mmp80) cc_final: 0.7913 (mmp80) REVERT: A 266 ASN cc_start: 0.7219 (t0) cc_final: 0.6848 (m-40) REVERT: A 272 THR cc_start: 0.7262 (t) cc_final: 0.6762 (p) REVERT: A 284 LEU cc_start: 0.7490 (pp) cc_final: 0.7251 (pp) REVERT: A 287 PHE cc_start: 0.7600 (m-80) cc_final: 0.7368 (m-80) REVERT: A 309 PHE cc_start: 0.8054 (t80) cc_final: 0.7842 (t80) REVERT: A 311 LYS cc_start: 0.8459 (tptm) cc_final: 0.8045 (tptm) REVERT: A 321 GLN cc_start: 0.8287 (mp-120) cc_final: 0.7888 (mp10) REVERT: A 323 LYS cc_start: 0.8036 (mppt) cc_final: 0.7638 (mmtt) REVERT: A 324 LEU cc_start: 0.8334 (mt) cc_final: 0.8018 (mt) REVERT: A 334 ASP cc_start: 0.7498 (p0) cc_final: 0.7138 (p0) REVERT: A 335 GLN cc_start: 0.7652 (mp10) cc_final: 0.7073 (mp10) REVERT: A 336 ILE cc_start: 0.8766 (mt) cc_final: 0.7602 (mm) REVERT: A 337 ARG cc_start: 0.7897 (mmp80) cc_final: 0.7208 (mmm160) REVERT: A 339 MET cc_start: 0.8583 (ppp) cc_final: 0.8192 (ppp) REVERT: A 340 MET cc_start: 0.8240 (ptp) cc_final: 0.6884 (ptp) REVERT: A 343 PHE cc_start: 0.6603 (p90) cc_final: 0.5760 (p90) REVERT: A 373 LYS cc_start: 0.8129 (mttm) cc_final: 0.7798 (mttm) REVERT: A 389 ASP cc_start: 0.6259 (p0) cc_final: 0.5654 (p0) REVERT: A 398 GLU cc_start: 0.7164 (mp0) cc_final: 0.6788 (mp0) REVERT: A 412 LEU cc_start: 0.8515 (tt) cc_final: 0.8002 (tt) REVERT: A 447 GLU cc_start: 0.7993 (pm20) cc_final: 0.7686 (pm20) REVERT: A 494 TYR cc_start: 0.6956 (t80) cc_final: 0.6628 (t80) REVERT: A 525 LEU cc_start: 0.8068 (tp) cc_final: 0.7733 (tp) REVERT: A 542 MET cc_start: 0.7078 (mmt) cc_final: 0.6869 (mmt) REVERT: A 594 GLU cc_start: 0.7101 (mp0) cc_final: 0.6717 (mp0) REVERT: A 635 MET cc_start: 0.7808 (mpp) cc_final: 0.6937 (mpp) REVERT: A 640 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7634 (mtmt) REVERT: A 641 LEU cc_start: 0.7869 (tt) cc_final: 0.7660 (tt) REVERT: A 649 ARG cc_start: 0.6821 (pmt-80) cc_final: 0.6337 (tmm160) REVERT: A 651 LEU cc_start: 0.7730 (tp) cc_final: 0.7360 (tp) REVERT: A 663 LYS cc_start: 0.8449 (ptmm) cc_final: 0.8004 (mtmm) REVERT: A 684 GLN cc_start: 0.7104 (tp40) cc_final: 0.6537 (tp40) REVERT: A 694 TYR cc_start: 0.6352 (t80) cc_final: 0.5304 (t80) REVERT: A 720 TYR cc_start: 0.7210 (t80) cc_final: 0.6780 (t80) REVERT: A 730 PHE cc_start: 0.6647 (t80) cc_final: 0.6247 (t80) REVERT: A 739 MET cc_start: 0.7585 (ttm) cc_final: 0.7322 (ttm) REVERT: A 751 ARG cc_start: 0.7596 (mmm160) cc_final: 0.7110 (tpp-160) REVERT: A 756 GLU cc_start: 0.7014 (mt-10) cc_final: 0.5518 (mt-10) REVERT: A 801 GLN cc_start: 0.7959 (mt0) cc_final: 0.7707 (mt0) REVERT: A 807 GLN cc_start: 0.7834 (mm110) cc_final: 0.7456 (mm110) REVERT: A 822 LYS cc_start: 0.7706 (tptp) cc_final: 0.7426 (tptp) REVERT: A 861 ARG cc_start: 0.7598 (ptp-170) cc_final: 0.7232 (mtt180) REVERT: B 18 LYS cc_start: 0.8240 (mttt) cc_final: 0.7995 (mttt) REVERT: B 47 ARG cc_start: 0.6171 (tmt-80) cc_final: 0.5801 (tmt-80) REVERT: B 58 CYS cc_start: 0.6703 (t) cc_final: 0.6366 (t) REVERT: B 59 ILE cc_start: 0.7086 (mm) cc_final: 0.6819 (mm) REVERT: B 79 LYS cc_start: 0.8416 (tptt) cc_final: 0.7542 (tptp) REVERT: B 107 LEU cc_start: 0.8495 (tp) cc_final: 0.8159 (mm) REVERT: B 121 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7046 (tp30) REVERT: B 124 ARG cc_start: 0.7885 (tpt170) cc_final: 0.7080 (mmm160) REVERT: C 138 GLU cc_start: 0.8041 (tp30) cc_final: 0.7425 (tp30) REVERT: C 240 ARG cc_start: 0.8735 (mtt180) cc_final: 0.8361 (mtt180) REVERT: C 241 ARG cc_start: 0.8256 (mmp80) cc_final: 0.8024 (mmp80) REVERT: C 284 LEU cc_start: 0.7534 (pp) cc_final: 0.7247 (pp) REVERT: C 303 GLU cc_start: 0.7595 (mp0) cc_final: 0.7394 (mp0) REVERT: C 309 PHE cc_start: 0.7940 (t80) cc_final: 0.7739 (t80) REVERT: C 323 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7878 (tttt) REVERT: C 334 ASP cc_start: 0.7093 (p0) cc_final: 0.6379 (p0) REVERT: C 335 GLN cc_start: 0.7673 (mp10) cc_final: 0.7121 (mp10) REVERT: C 344 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7217 (tp40) REVERT: C 345 GLN cc_start: 0.7681 (mt0) cc_final: 0.7214 (mt0) REVERT: C 395 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6846 (tm-30) REVERT: C 398 GLU cc_start: 0.7407 (mp0) cc_final: 0.7193 (mp0) REVERT: C 406 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6818 (tm-30) REVERT: C 407 LEU cc_start: 0.8686 (mt) cc_final: 0.8154 (mt) REVERT: C 410 GLN cc_start: 0.8590 (pt0) cc_final: 0.8207 (pt0) REVERT: C 411 GLU cc_start: 0.8205 (tt0) cc_final: 0.7739 (tm-30) REVERT: C 441 LYS cc_start: 0.7744 (mptt) cc_final: 0.7319 (mmtm) REVERT: C 478 MET cc_start: 0.7503 (tpp) cc_final: 0.7067 (tpp) REVERT: C 539 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7685 (tpp80) REVERT: C 554 GLN cc_start: 0.7915 (tt0) cc_final: 0.7655 (tt0) REVERT: C 580 GLU cc_start: 0.7913 (tp30) cc_final: 0.7531 (tp30) REVERT: C 589 MET cc_start: 0.3830 (ttm) cc_final: 0.3326 (ttm) REVERT: C 597 LYS cc_start: 0.9275 (mtpp) cc_final: 0.8852 (mmmm) REVERT: C 607 GLU cc_start: 0.7986 (pm20) cc_final: 0.7607 (pm20) REVERT: C 627 CYS cc_start: 0.6334 (p) cc_final: 0.6116 (p) REVERT: C 629 LEU cc_start: 0.7938 (mp) cc_final: 0.7367 (mt) REVERT: C 635 MET cc_start: 0.7791 (mpp) cc_final: 0.7043 (mpp) REVERT: C 639 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.6382 (mmm-85) REVERT: C 649 ARG cc_start: 0.6866 (ptt-90) cc_final: 0.6380 (ptt90) REVERT: C 651 LEU cc_start: 0.8253 (tp) cc_final: 0.7970 (tp) REVERT: C 720 TYR cc_start: 0.7305 (t80) cc_final: 0.6969 (t80) REVERT: C 731 LYS cc_start: 0.7865 (tptt) cc_final: 0.7505 (tptt) REVERT: C 739 MET cc_start: 0.7777 (ttm) cc_final: 0.7499 (ttm) REVERT: C 801 GLN cc_start: 0.7923 (mt0) cc_final: 0.7468 (mt0) REVERT: C 807 GLN cc_start: 0.7983 (mm110) cc_final: 0.7610 (mm110) REVERT: C 822 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8106 (mmtt) REVERT: D 25 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7314 (mt-10) REVERT: D 47 ARG cc_start: 0.6461 (tmt-80) cc_final: 0.6188 (tpt170) REVERT: D 52 PHE cc_start: 0.7057 (t80) cc_final: 0.6854 (t80) REVERT: D 58 CYS cc_start: 0.6730 (t) cc_final: 0.5984 (t) REVERT: D 59 ILE cc_start: 0.6898 (mm) cc_final: 0.6362 (mm) REVERT: D 144 MET cc_start: 0.3586 (ttt) cc_final: 0.3293 (ttt) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.3200 time to fit residues: 170.8706 Evaluate side-chains 379 residues out of total 1442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 125 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.158216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.129829 restraints weight = 26590.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.134719 restraints weight = 17792.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.138399 restraints weight = 12830.584| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.6966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12580 Z= 0.172 Angle : 0.693 20.536 16980 Z= 0.330 Chirality : 0.045 0.226 1912 Planarity : 0.004 0.053 2186 Dihedral : 4.790 29.483 1688 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.22), residues: 1496 helix: -1.40 (0.19), residues: 768 sheet: -1.70 (0.84), residues: 40 loop : -1.15 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 791 HIS 0.002 0.001 HIS A 632 PHE 0.021 0.002 PHE A 583 TYR 0.012 0.001 TYR A 638 ARG 0.009 0.001 ARG A 245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3594.88 seconds wall clock time: 64 minutes 17.79 seconds (3857.79 seconds total)