Starting phenix.real_space_refine (version: dev) on Sun May 15 00:22:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/05_2022/7e4t_30987_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/05_2022/7e4t_30987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/05_2022/7e4t_30987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/05_2022/7e4t_30987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/05_2022/7e4t_30987_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4t_30987/05_2022/7e4t_30987_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.176 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 22276 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 23, 'TRANS': 639, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 23, 'TRANS': 639, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 23, 'TRANS': 639, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 5412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5412 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 23, 'TRANS': 639, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' ZN': 1, 'POV': 1, 'YZY': 1, ' CA': 1, 'Y01': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' ZN': 1, 'POV': 1, 'YZY': 1, ' CA': 1, 'Y01': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' ZN': 1, 'POV': 1, 'YZY': 1, ' CA': 1, 'Y01': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 157 Unusual residues: {' ZN': 1, 'POV': 1, 'YZY': 1, ' CA': 1, 'Y01': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 176 14.234 43.015 61.526 1.00172.12 S ATOM 1162 SG CYS A 178 13.069 40.045 59.271 1.00194.88 S ATOM 1184 SG CYS A 181 16.749 40.871 59.364 1.00197.66 S ATOM 6560 SG CYS B 176 69.847 14.233 61.520 1.00172.12 S ATOM 6574 SG CYS B 178 72.817 13.068 59.264 1.00194.88 S ATOM 6596 SG CYS B 181 71.991 16.748 59.358 1.00197.66 S ATOM 11972 SG CYS C 176 98.629 69.846 61.512 1.00172.12 S ATOM 11986 SG CYS C 178 99.793 72.816 59.256 1.00194.88 S ATOM 12008 SG CYS C 181 96.113 71.990 59.350 1.00197.66 S ATOM 17384 SG CYS D 176 43.016 98.628 61.518 1.00172.12 S ATOM 17398 SG CYS D 178 40.046 99.793 59.263 1.00194.88 S ATOM 17420 SG CYS D 181 40.871 96.112 59.357 1.00197.66 S Time building chain proxies: 12.85, per 1000 atoms: 0.58 Number of scatterers: 22276 At special positions: 0 Unit cell: (113.905, 113.905, 136.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 116 16.00 P 8 15.00 O 3948 8.00 N 3564 7.00 C 14632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 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: 9.74 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 181 " pdb=" ZN C 804 " pdb="ZN ZN C 804 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 804 " - pdb=" SG CYS C 181 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " Number of angles added : 12 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 0 sheets defined 68.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.693A pdb=" N ILE A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 109 through 117 Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.504A pdb=" N SER A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 216 through 233 Processing helix chain 'A' and resid 238 through 257 Processing helix chain 'A' and resid 262 through 269 Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 299 through 302 No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 363 through 385 removed outlier: 3.913A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 428 through 431 No H-bonds generated for 'chain 'A' and resid 428 through 431' Processing helix chain 'A' and resid 436 through 459 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 474 through 499 removed outlier: 4.188A pdb=" N LEU A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 542 Proline residue: A 505 - end of helix removed outlier: 4.102A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TYR A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N TYR A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.695A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 595 through 612 Processing helix chain 'A' and resid 615 through 632 removed outlier: 3.639A pdb=" N GLN A 629 " --> pdb=" O ASN A 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 650 removed outlier: 3.700A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 730 Processing helix chain 'A' and resid 740 through 760 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.693A pdb=" N ILE B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 99 through 105 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 179 through 187 Processing helix chain 'B' and resid 189 through 203 removed outlier: 3.503A pdb=" N SER B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 216 through 233 Processing helix chain 'B' and resid 238 through 257 Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 299 through 302 No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 305 through 315 Processing helix chain 'B' and resid 327 through 339 Processing helix chain 'B' and resid 341 through 350 Processing helix chain 'B' and resid 363 through 385 removed outlier: 3.913A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 428 through 431 No H-bonds generated for 'chain 'B' and resid 428 through 431' Processing helix chain 'B' and resid 436 through 459 Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 474 through 499 removed outlier: 4.187A pdb=" N LEU B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA B 499 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 542 Proline residue: B 505 - end of helix removed outlier: 4.101A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TYR B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 579 removed outlier: 3.695A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 595 through 612 Processing helix chain 'B' and resid 615 through 632 removed outlier: 3.639A pdb=" N GLN B 629 " --> pdb=" O ASN B 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 650 removed outlier: 3.700A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 730 Processing helix chain 'B' and resid 740 through 760 Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.693A pdb=" N ILE C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 99 through 105 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 145 through 152 Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 179 through 187 Processing helix chain 'C' and resid 189 through 203 removed outlier: 3.504A pdb=" N SER C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 216 through 233 Processing helix chain 'C' and resid 238 through 257 Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 299 through 302 No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 327 through 339 Processing helix chain 'C' and resid 341 through 350 Processing helix chain 'C' and resid 363 through 385 removed outlier: 3.912A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 428 through 431 No H-bonds generated for 'chain 'C' and resid 428 through 431' Processing helix chain 'C' and resid 436 through 459 Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 474 through 499 removed outlier: 4.187A pdb=" N LEU C 493 " --> pdb=" O SER C 489 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE C 494 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR C 498 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA C 499 " --> pdb=" O SER C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 542 Proline residue: C 505 - end of helix removed outlier: 4.101A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 579 removed outlier: 3.695A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 595 through 612 Processing helix chain 'C' and resid 615 through 632 removed outlier: 3.638A pdb=" N GLN C 629 " --> pdb=" O ASN C 625 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 631 " --> pdb=" O SER C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 650 removed outlier: 3.701A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 730 Processing helix chain 'C' and resid 740 through 760 Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 45 through 58 removed outlier: 3.693A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 79 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 109 through 117 Processing helix chain 'D' and resid 145 through 152 Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 179 through 187 Processing helix chain 'D' and resid 189 through 203 removed outlier: 3.504A pdb=" N SER D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 216 through 233 Processing helix chain 'D' and resid 238 through 257 Processing helix chain 'D' and resid 262 through 269 Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 299 through 302 No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 305 through 315 Processing helix chain 'D' and resid 327 through 339 Processing helix chain 'D' and resid 341 through 350 Processing helix chain 'D' and resid 363 through 385 removed outlier: 3.912A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 428 through 431 No H-bonds generated for 'chain 'D' and resid 428 through 431' Processing helix chain 'D' and resid 436 through 459 Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 474 through 499 removed outlier: 4.187A pdb=" N LEU D 493 " --> pdb=" O SER D 489 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE D 494 " --> pdb=" O SER D 490 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR D 498 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA D 499 " --> pdb=" O SER D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 542 Proline residue: D 505 - end of helix removed outlier: 4.102A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 579 removed outlier: 3.695A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 587 No H-bonds generated for 'chain 'D' and resid 585 through 587' Processing helix chain 'D' and resid 595 through 612 Processing helix chain 'D' and resid 615 through 632 removed outlier: 3.639A pdb=" N GLN D 629 " --> pdb=" O ASN D 625 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 650 removed outlier: 3.701A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 730 Processing helix chain 'D' and resid 740 through 760 1184 hydrogen bonds defined for protein. 3552 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: 7.31 Time building geometry restraints manager: 10.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3500 1.32 - 1.44: 6112 1.44 - 1.57: 12960 1.57 - 1.69: 16 1.69 - 1.81: 188 Bond restraints: 22776 Sorted by residual: bond pdb=" C12 YZY D 806 " pdb=" C13 YZY D 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY A 806 " pdb=" C13 YZY A 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY C 806 " pdb=" C13 YZY C 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C12 YZY B 806 " pdb=" C13 YZY B 806 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sigma weight residual 1.332 1.504 -0.172 2.00e-02 2.50e+03 7.40e+01 ... (remaining 22771 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.69: 604 106.69 - 113.52: 12666 113.52 - 120.36: 8693 120.36 - 127.19: 8549 127.19 - 134.02: 272 Bond angle restraints: 30784 Sorted by residual: angle pdb=" C27 YZY D 806 " pdb=" C28 YZY D 806 " pdb=" C29 YZY D 806 " ideal model delta sigma weight residual 128.13 107.59 20.54 3.00e+00 1.11e-01 4.69e+01 angle pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sigma weight residual 128.13 107.62 20.51 3.00e+00 1.11e-01 4.68e+01 angle pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sigma weight residual 128.13 107.64 20.49 3.00e+00 1.11e-01 4.67e+01 angle pdb=" C27 YZY B 806 " pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sigma weight residual 128.13 107.65 20.48 3.00e+00 1.11e-01 4.66e+01 angle pdb=" C21 YZY C 806 " pdb=" C20 YZY C 806 " pdb=" O4 YZY C 806 " ideal model delta sigma weight residual 111.77 126.25 -14.48 3.00e+00 1.11e-01 2.33e+01 ... (remaining 30779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 13352 34.84 - 69.68: 212 69.68 - 104.52: 16 104.52 - 139.36: 8 139.36 - 174.21: 12 Dihedral angle restraints: 13600 sinusoidal: 5736 harmonic: 7864 Sorted by residual: dihedral pdb=" C26 YZY B 806 " pdb=" C27 YZY B 806 " pdb=" C28 YZY B 806 " pdb=" C29 YZY B 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.68 -174.21 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY A 806 " pdb=" C27 YZY A 806 " pdb=" C28 YZY A 806 " pdb=" C29 YZY A 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.70 -174.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C26 YZY C 806 " pdb=" C27 YZY C 806 " pdb=" C28 YZY C 806 " pdb=" C29 YZY C 806 " ideal model delta sinusoidal sigma weight residual 119.11 -66.70 -174.19 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2832 0.046 - 0.092: 520 0.092 - 0.138: 76 0.138 - 0.185: 8 0.185 - 0.231: 8 Chirality restraints: 3444 Sorted by residual: chirality pdb=" CBI Y01 A 803 " pdb=" CAU Y01 A 803 " pdb=" CBE Y01 A 803 " pdb=" CBG Y01 A 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBI Y01 B 803 " pdb=" CAU Y01 B 803 " pdb=" CBE Y01 B 803 " pdb=" CBG Y01 B 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBI Y01 C 803 " pdb=" CAU Y01 C 803 " pdb=" CBE Y01 C 803 " pdb=" CBG Y01 C 803 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3441 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN C 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN C 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER C 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN B 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN B 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER B 574 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 573 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" C GLN D 573 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN D 573 " 0.008 2.00e-02 2.50e+03 pdb=" N SER D 574 " 0.007 2.00e-02 2.50e+03 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5607 2.80 - 3.33: 21933 3.33 - 3.85: 37468 3.85 - 4.38: 44487 4.38 - 4.90: 75865 Nonbonded interactions: 185360 Sorted by model distance: nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.278 2.440 nonbonded pdb=" OG1 THR D 140 " pdb=" OD1 ASP D 142 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR C 140 " pdb=" OD1 ASP C 142 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR A 140 " pdb=" OD1 ASP A 142 " model vdw 2.279 2.440 nonbonded pdb=" OD1 ASP C 215 " pdb=" OH TYR C 713 " model vdw 2.328 2.440 ... (remaining 185355 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 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 C 14632 2.51 5 N 3564 2.21 5 O 3948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 6.890 Check model and map are aligned: 0.340 Convert atoms to be neutral: 0.200 Process input model: 64.070 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.204 22776 Z= 0.440 Angle : 0.786 20.541 30784 Z= 0.323 Chirality : 0.036 0.231 3444 Planarity : 0.003 0.029 3784 Dihedral : 13.887 174.205 8468 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 2608 helix: 0.88 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : -0.35 (0.23), residues: 660 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 484 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 500 average time/residue: 1.3279 time to fit residues: 755.3265 Evaluate side-chains 252 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 242 time to evaluate : 2.717 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 1.2187 time to fit residues: 7.7357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 609 ASN ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 609 ASN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN C 609 ASN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 609 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.041 22776 Z= 0.432 Angle : 0.633 7.340 30784 Z= 0.310 Chirality : 0.041 0.145 3444 Planarity : 0.004 0.046 3784 Dihedral : 14.322 175.238 3240 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.29 (0.16), residues: 2608 helix: 1.21 (0.11), residues: 1944 sheet: None (None), residues: 0 loop : 0.01 (0.23), residues: 664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 267 time to evaluate : 2.967 Fit side-chains outliers start: 107 outliers final: 59 residues processed: 327 average time/residue: 1.2320 time to fit residues: 468.1450 Evaluate side-chains 292 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 44 residues processed: 15 average time/residue: 0.5619 time to fit residues: 14.8817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 4.9990 chunk 259 optimal weight: 0.1980 chunk 213 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 192 optimal weight: 0.9980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 135 GLN C 135 GLN C 192 HIS D 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 22776 Z= 0.209 Angle : 0.464 7.078 30784 Z= 0.234 Chirality : 0.036 0.191 3444 Planarity : 0.003 0.034 3784 Dihedral : 13.998 178.814 3240 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 4.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.87 (0.16), residues: 2608 helix: 1.66 (0.11), residues: 1940 sheet: None (None), residues: 0 loop : 0.16 (0.23), residues: 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 265 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 51 residues processed: 331 average time/residue: 1.0893 time to fit residues: 422.2372 Evaluate side-chains 291 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 2.675 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 40 residues processed: 11 average time/residue: 0.6974 time to fit residues: 13.3658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 241 optimal weight: 0.5980 chunk 255 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 135 GLN C 135 GLN C 192 HIS D 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 22776 Z= 0.179 Angle : 0.444 6.919 30784 Z= 0.224 Chirality : 0.035 0.141 3444 Planarity : 0.003 0.035 3784 Dihedral : 13.620 176.520 3240 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer Outliers : 4.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.20 (0.16), residues: 2608 helix: 1.89 (0.11), residues: 1940 sheet: None (None), residues: 0 loop : 0.29 (0.23), residues: 668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 255 time to evaluate : 2.715 Fit side-chains revert: symmetry clash outliers start: 100 outliers final: 61 residues processed: 318 average time/residue: 1.1242 time to fit residues: 417.8500 Evaluate side-chains 292 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 231 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 48 residues processed: 17 average time/residue: 0.3454 time to fit residues: 12.6654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 22776 Z= 0.376 Angle : 0.552 11.462 30784 Z= 0.276 Chirality : 0.039 0.143 3444 Planarity : 0.004 0.033 3784 Dihedral : 13.217 162.725 3240 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.76 (0.16), residues: 2608 helix: 1.60 (0.12), residues: 1920 sheet: None (None), residues: 0 loop : 0.10 (0.22), residues: 688 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 254 time to evaluate : 2.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 64 residues processed: 323 average time/residue: 1.1841 time to fit residues: 444.3312 Evaluate side-chains 297 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 233 time to evaluate : 2.651 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 42 residues processed: 22 average time/residue: 0.4554 time to fit residues: 17.5640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 212 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 135 GLN C 135 GLN C 192 HIS D 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 22776 Z= 0.168 Angle : 0.441 9.772 30784 Z= 0.223 Chirality : 0.035 0.141 3444 Planarity : 0.003 0.033 3784 Dihedral : 12.625 155.473 3240 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer Outliers : 4.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.14 (0.16), residues: 2608 helix: 1.87 (0.12), residues: 1932 sheet: None (None), residues: 0 loop : 0.22 (0.23), residues: 676 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 265 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 67 residues processed: 331 average time/residue: 1.1133 time to fit residues: 432.7625 Evaluate side-chains 314 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 247 time to evaluate : 2.661 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 51 residues processed: 20 average time/residue: 0.5482 time to fit residues: 18.1269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 0.3980 chunk 186 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 22776 Z= 0.165 Angle : 0.441 6.869 30784 Z= 0.225 Chirality : 0.035 0.142 3444 Planarity : 0.003 0.034 3784 Dihedral : 12.223 153.819 3240 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 4.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.23 (0.16), residues: 2608 helix: 1.90 (0.12), residues: 1940 sheet: None (None), residues: 0 loop : 0.34 (0.24), residues: 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 260 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 75 residues processed: 330 average time/residue: 1.0797 time to fit residues: 420.8429 Evaluate side-chains 327 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 252 time to evaluate : 2.660 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 59 residues processed: 20 average time/residue: 0.5701 time to fit residues: 18.5604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 231 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 22776 Z= 0.449 Angle : 0.572 7.163 30784 Z= 0.287 Chirality : 0.041 0.148 3444 Planarity : 0.004 0.040 3784 Dihedral : 12.619 158.075 3240 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 4.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.61 (0.16), residues: 2608 helix: 1.47 (0.11), residues: 1920 sheet: None (None), residues: 0 loop : 0.12 (0.23), residues: 688 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 245 time to evaluate : 2.831 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 outliers start: 113 outliers final: 70 residues processed: 320 average time/residue: 1.1578 time to fit residues: 433.6703 Evaluate side-chains 314 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 244 time to evaluate : 2.743 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 55 residues processed: 19 average time/residue: 0.5734 time to fit residues: 18.1664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 9.9990 chunk 222 optimal weight: 0.8980 chunk 237 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 214 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 236 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 625 ASN B 135 GLN C 135 GLN D 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 22776 Z= 0.173 Angle : 0.447 6.900 30784 Z= 0.226 Chirality : 0.035 0.141 3444 Planarity : 0.003 0.033 3784 Dihedral : 11.957 155.814 3240 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 3.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.02 (0.16), residues: 2608 helix: 1.76 (0.12), residues: 1936 sheet: None (None), residues: 0 loop : 0.28 (0.23), residues: 672 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 259 time to evaluate : 2.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 64 residues processed: 324 average time/residue: 1.1446 time to fit residues: 433.2797 Evaluate side-chains 313 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 249 time to evaluate : 2.844 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 55 residues processed: 13 average time/residue: 0.2664 time to fit residues: 9.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 174 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 22776 Z= 0.189 Angle : 0.461 6.900 30784 Z= 0.233 Chirality : 0.035 0.142 3444 Planarity : 0.003 0.034 3784 Dihedral : 11.623 155.202 3240 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.16 (0.16), residues: 2608 helix: 1.84 (0.12), residues: 1936 sheet: None (None), residues: 0 loop : 0.37 (0.24), residues: 672 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 251 time to evaluate : 2.823 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 outliers start: 77 outliers final: 63 residues processed: 316 average time/residue: 1.1367 time to fit residues: 419.5313 Evaluate side-chains 308 residues out of total 2372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 245 time to evaluate : 2.610 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 55 residues processed: 8 average time/residue: 0.9995 time to fit residues: 12.9429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 193 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 184 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.155969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120366 restraints weight = 24383.256| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.55 r_work: 0.3356 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 1.41 restraints_weight: 0.2500 r_work: 0.3320 rms_B_bonded: 1.55 restraints_weight: 0.1250 r_work: 0.3296 rms_B_bonded: 1.79 restraints_weight: 0.0625 r_work: 0.3268 rms_B_bonded: 2.15 restraints_weight: 0.0312 r_work: 0.3232 rms_B_bonded: 2.64 restraints_weight: 0.0156 r_work: 0.3186 rms_B_bonded: 3.33 restraints_weight: 0.0078 r_work: 0.3127 rms_B_bonded: 4.30 restraints_weight: 0.0039 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 22776 Z= 0.142 Angle : 0.437 7.375 30784 Z= 0.219 Chirality : 0.035 0.143 3444 Planarity : 0.003 0.034 3784 Dihedral : 10.657 152.953 3240 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.36 (0.16), residues: 2608 helix: 2.00 (0.12), residues: 1932 sheet: None (None), residues: 0 loop : 0.38 (0.24), residues: 676 =============================================================================== Job complete usr+sys time: 6953.31 seconds wall clock time: 125 minutes 0.55 seconds (7500.55 seconds total)