Starting phenix.real_space_refine (version: dev) on Sun May 15 01:14:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/05_2022/7d4p_30575_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/05_2022/7d4p_30575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/05_2022/7d4p_30575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/05_2022/7d4p_30575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/05_2022/7d4p_30575_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4p_30575/05_2022/7d4p_30575_updated.pdb" } resolution = 2.7 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= 0.010 sd= 0.196 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: 22472 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5438 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 644, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5438 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 644, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5438 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 644, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 5438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5438 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 644, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {' ZN': 1, 'POV': 1, 'YZY': 1, ' CA': 1, 'Y01': 1, 'GX0': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {' ZN': 1, 'POV': 1, 'YZY': 1, ' CA': 1, 'Y01': 1, 'GX0': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {' ZN': 1, 'POV': 1, 'YZY': 1, ' CA': 1, 'Y01': 1, 'GX0': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {' ZN': 1, 'POV': 1, 'YZY': 1, ' CA': 1, 'Y01': 1, 'GX0': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1155 SG CYS A 176 98.631 69.677 61.888 1.00147.88 S ATOM 1169 SG CYS A 178 99.979 72.459 59.636 1.00161.95 S ATOM 1191 SG CYS A 181 96.242 71.752 59.728 1.00162.23 S ATOM 6593 SG CYS B 176 43.183 98.630 61.882 1.00147.88 S ATOM 6607 SG CYS B 178 40.401 99.978 59.628 1.00161.95 S ATOM 6629 SG CYS B 181 41.108 96.241 59.721 1.00162.23 S ATOM 12031 SG CYS C 176 14.230 43.182 61.876 1.00147.88 S ATOM 12045 SG CYS C 178 12.882 40.400 59.623 1.00161.95 S ATOM 12067 SG CYS C 181 16.619 41.107 59.716 1.00162.23 S ATOM 17469 SG CYS D 176 69.678 14.229 61.883 1.00147.88 S ATOM 17483 SG CYS D 178 72.460 12.881 59.630 1.00161.95 S ATOM 17505 SG CYS D 181 71.753 16.618 59.723 1.00162.23 S Time building chain proxies: 12.58, per 1000 atoms: 0.56 Number of scatterers: 22472 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: 8 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 Cl 4 17.00 S 116 16.00 P 8 15.00 O 3988 8.00 N 3592 7.00 C 14756 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=2.04 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.04 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.04 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.04 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: 9.17 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 181 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 176 " pdb=" ZN B 805 " pdb="ZN ZN B 805 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 181 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 176 " pdb=" ZN C 805 " pdb="ZN ZN C 805 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 181 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 176 " pdb=" ZN D 805 " pdb="ZN ZN D 805 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 181 " pdb="ZN ZN D 805 " - pdb=" SG CYS D 176 " Number of angles added : 12 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 0 sheets defined 69.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.655A 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 92 Processing helix chain 'A' and resid 99 through 106 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 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: 4.233A 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 432 Processing helix chain 'A' and resid 434 through 459 removed outlier: 3.837A pdb=" N MET A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) 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: 4.202A pdb=" N LEU A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR A 498 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 4.982A 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: 3.938A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR A 541 " --> pdb=" O GLN A 537 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 580 removed outlier: 3.666A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 588 Processing helix chain 'A' and resid 595 through 614 Processing helix chain 'A' and resid 616 through 631 Processing helix chain 'A' and resid 635 through 650 removed outlier: 3.608A pdb=" N TYR A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 733 Processing helix chain 'A' and resid 740 through 761 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.655A 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 92 Processing helix chain 'B' and resid 99 through 106 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 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: 4.233A 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 432 Processing helix chain 'B' and resid 434 through 459 removed outlier: 3.837A pdb=" N MET B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) 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: 4.202A pdb=" N LEU B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 498 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 4.982A 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: 3.938A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N TYR B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 580 removed outlier: 3.666A pdb=" N VAL B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 580 " --> pdb=" O PHE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 588 Processing helix chain 'B' and resid 595 through 614 Processing helix chain 'B' and resid 616 through 631 Processing helix chain 'B' and resid 635 through 650 removed outlier: 3.608A pdb=" N TYR B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 733 Processing helix chain 'B' and resid 740 through 761 Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.655A 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 92 Processing helix chain 'C' and resid 99 through 106 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 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: 4.234A 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 432 Processing helix chain 'C' and resid 434 through 459 removed outlier: 3.837A pdb=" N MET C 438 " --> pdb=" O TRP C 434 " (cutoff:3.500A) 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: 4.203A pdb=" N LEU C 493 " --> pdb=" O SER C 489 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE C 494 " --> pdb=" O SER C 490 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR C 498 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 4.982A 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: 3.938A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR C 541 " --> pdb=" O GLN C 537 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 580 removed outlier: 3.666A pdb=" N VAL C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE C 580 " --> pdb=" O PHE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 588 Processing helix chain 'C' and resid 595 through 614 Processing helix chain 'C' and resid 616 through 631 Processing helix chain 'C' and resid 635 through 650 removed outlier: 3.608A pdb=" N TYR C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 733 Processing helix chain 'C' and resid 740 through 761 Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 45 through 58 removed outlier: 3.655A 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 106 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 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: 4.233A 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 432 Processing helix chain 'D' and resid 434 through 459 removed outlier: 3.836A pdb=" N MET D 438 " --> pdb=" O TRP D 434 " (cutoff:3.500A) 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: 4.203A pdb=" N LEU D 493 " --> pdb=" O SER D 489 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE D 494 " --> pdb=" O SER D 490 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR D 498 " --> pdb=" O ILE D 494 " (cutoff:3.500A) removed outlier: 4.982A 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: 3.938A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TYR D 541 " --> pdb=" O GLN D 537 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 580 removed outlier: 3.666A pdb=" N VAL D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 588 Processing helix chain 'D' and resid 595 through 614 Processing helix chain 'D' and resid 616 through 631 Processing helix chain 'D' and resid 635 through 650 removed outlier: 3.609A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 733 Processing helix chain 'D' and resid 740 through 761 1239 hydrogen bonds defined for protein. 3705 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: 6.65 Time building geometry restraints manager: 9.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3520 1.29 - 1.42: 5964 1.42 - 1.56: 13284 1.56 - 1.69: 16 1.69 - 1.82: 192 Bond restraints: 22976 Sorted by residual: bond pdb=" C12 YZY D 807 " pdb=" C13 YZY D 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY A 807 " pdb=" C13 YZY A 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY C 807 " pdb=" C13 YZY C 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY B 807 " pdb=" C13 YZY B 807 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C29 YZY A 807 " pdb=" C30 YZY A 807 " ideal model delta sigma weight residual 1.497 1.325 0.172 2.00e-02 2.50e+03 7.44e+01 ... (remaining 22971 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.95: 622 106.95 - 113.87: 13268 113.87 - 120.80: 10818 120.80 - 127.73: 6092 127.73 - 134.66: 252 Bond angle restraints: 31052 Sorted by residual: angle pdb=" C27 YZY C 807 " pdb=" C28 YZY C 807 " pdb=" C29 YZY C 807 " ideal model delta sigma weight residual 128.13 108.84 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C27 YZY A 807 " pdb=" C28 YZY A 807 " pdb=" C29 YZY A 807 " ideal model delta sigma weight residual 128.13 108.84 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C27 YZY D 807 " pdb=" C28 YZY D 807 " pdb=" C29 YZY D 807 " ideal model delta sigma weight residual 128.13 108.84 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C27 YZY B 807 " pdb=" C28 YZY B 807 " pdb=" C29 YZY B 807 " ideal model delta sigma weight residual 128.13 108.85 19.28 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C21 YZY C 807 " pdb=" C20 YZY C 807 " pdb=" O4 YZY C 807 " ideal model delta sigma weight residual 111.77 126.94 -15.17 3.00e+00 1.11e-01 2.56e+01 ... (remaining 31047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.83: 13432 32.83 - 65.67: 232 65.67 - 98.50: 40 98.50 - 131.34: 4 131.34 - 164.17: 8 Dihedral angle restraints: 13716 sinusoidal: 5800 harmonic: 7916 Sorted by residual: dihedral pdb=" C5 YZY D 807 " pdb=" C3 YZY D 807 " pdb=" C4 YZY D 807 " pdb=" O2 YZY D 807 " ideal model delta sinusoidal sigma weight residual 177.74 13.57 164.17 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY B 807 " pdb=" C3 YZY B 807 " pdb=" C4 YZY B 807 " pdb=" O2 YZY B 807 " ideal model delta sinusoidal sigma weight residual 177.74 13.61 164.13 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY A 807 " pdb=" C3 YZY A 807 " pdb=" C4 YZY A 807 " pdb=" O2 YZY A 807 " ideal model delta sinusoidal sigma weight residual 177.74 13.61 164.13 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 13713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2866 0.045 - 0.090: 514 0.090 - 0.134: 72 0.134 - 0.179: 8 0.179 - 0.224: 8 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CBI Y01 A 804 " pdb=" CAU Y01 A 804 " pdb=" CBE Y01 A 804 " pdb=" CBG Y01 A 804 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CBI Y01 B 804 " pdb=" CAU Y01 B 804 " pdb=" CBE Y01 B 804 " pdb=" CBG Y01 B 804 " both_signs ideal model delta sigma weight residual False 2.94 2.72 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CBI Y01 C 804 " pdb=" CAU Y01 C 804 " pdb=" CBE Y01 C 804 " pdb=" CBG Y01 C 804 " both_signs ideal model delta sigma weight residual False 2.94 2.72 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3465 not shown) Planarity restraints: 3812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 442 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.60e+00 pdb=" C MET C 442 " 0.037 2.00e-02 2.50e+03 pdb=" O MET C 442 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN C 443 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 441 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C ALA B 441 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA B 441 " 0.014 2.00e-02 2.50e+03 pdb=" N MET B 442 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 441 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C ALA C 441 " 0.037 2.00e-02 2.50e+03 pdb=" O ALA C 441 " -0.014 2.00e-02 2.50e+03 pdb=" N MET C 442 " -0.012 2.00e-02 2.50e+03 ... (remaining 3809 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5198 2.79 - 3.32: 22514 3.32 - 3.85: 38203 3.85 - 4.37: 45106 4.37 - 4.90: 76961 Nonbonded interactions: 187982 Sorted by model distance: nonbonded pdb=" OAH Y01 D 804 " pdb=" OAW Y01 D 804 " model vdw 2.269 3.040 nonbonded pdb=" OAH Y01 A 804 " pdb=" OAW Y01 A 804 " model vdw 2.269 3.040 nonbonded pdb=" OAH Y01 C 804 " pdb=" OAW Y01 C 804 " model vdw 2.269 3.040 nonbonded pdb=" OAH Y01 B 804 " pdb=" OAW Y01 B 804 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR B 140 " pdb=" OD1 ASP B 142 " model vdw 2.290 2.440 ... (remaining 187977 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: 8 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 Cl 4 4.86 5 C 14756 2.51 5 N 3592 2.21 5 O 3988 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.670 Check model and map are aligned: 0.350 Convert atoms to be neutral: 0.190 Process input model: 61.240 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 0.215 22976 Z= 0.438 Angle : 0.798 19.289 31052 Z= 0.333 Chirality : 0.036 0.224 3468 Planarity : 0.004 0.032 3812 Dihedral : 13.567 164.170 8552 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.67 % 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: 2.42 (0.16), residues: 2628 helix: 2.10 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 656 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 495 time to evaluate : 2.741 Fit side-chains outliers start: 16 outliers final: 3 residues processed: 511 average time/residue: 1.3830 time to fit residues: 803.8996 Evaluate side-chains 305 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 302 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 3 average time/residue: 0.2104 time to fit residues: 4.3172 ------------------------------------------------------------------------------- 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: 5.9990 chunk 200 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 573 GLN A 629 GLN A 711 GLN B 573 GLN B 629 GLN B 711 GLN C 551 ASN C 573 GLN C 629 GLN C 711 GLN D 533 ASN D 551 ASN D 573 GLN D 629 GLN D 711 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 22976 Z= 0.246 Angle : 0.513 7.320 31052 Z= 0.250 Chirality : 0.036 0.152 3468 Planarity : 0.004 0.041 3812 Dihedral : 12.900 169.322 3300 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer Outliers : 2.89 % 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: 2.48 (0.16), residues: 2628 helix: 2.15 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : 0.17 (0.24), residues: 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 309 time to evaluate : 2.759 Fit side-chains outliers start: 69 outliers final: 17 residues processed: 347 average time/residue: 1.2440 time to fit residues: 497.9129 Evaluate side-chains 311 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 294 time to evaluate : 2.706 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 3.7315 ------------------------------------------------------------------------------- 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: 6.9990 chunk 74 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 259 optimal weight: 0.0870 chunk 213 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 192 optimal weight: 0.5980 overall best weight: 2.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 551 ASN A 629 GLN B 551 ASN B 629 GLN C 551 ASN C 629 GLN D 533 ASN D 551 ASN D 629 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 22976 Z= 0.354 Angle : 0.545 6.198 31052 Z= 0.271 Chirality : 0.038 0.156 3468 Planarity : 0.004 0.047 3812 Dihedral : 12.877 176.922 3300 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 3.40 % 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: 1.99 (0.16), residues: 2628 helix: 1.83 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : -0.11 (0.23), residues: 668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 322 time to evaluate : 2.677 Fit side-chains outliers start: 81 outliers final: 37 residues processed: 356 average time/residue: 1.1866 time to fit residues: 490.9794 Evaluate side-chains 329 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 292 time to evaluate : 2.642 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 21 residues processed: 16 average time/residue: 0.2758 time to fit residues: 10.9523 ------------------------------------------------------------------------------- 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: 5.9990 chunk 180 optimal weight: 4.9990 chunk 124 optimal weight: 0.0170 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 241 optimal weight: 0.8980 chunk 255 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 228 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN B 551 ASN B 629 GLN C 629 GLN D 533 ASN D 629 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 22976 Z= 0.142 Angle : 0.441 6.822 31052 Z= 0.217 Chirality : 0.034 0.154 3468 Planarity : 0.003 0.038 3812 Dihedral : 11.893 159.091 3300 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 2.14 % 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: 2.40 (0.16), residues: 2628 helix: 2.15 (0.12), residues: 1972 sheet: None (None), residues: 0 loop : -0.11 (0.23), residues: 656 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 284 time to evaluate : 2.805 Fit side-chains outliers start: 51 outliers final: 25 residues processed: 318 average time/residue: 1.1399 time to fit residues: 422.3987 Evaluate side-chains 298 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 273 time to evaluate : 2.607 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 3.4719 ------------------------------------------------------------------------------- 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: 7.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 229 optimal weight: 0.3980 chunk 64 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 533 ASN A 629 GLN B 326 HIS B 533 ASN B 629 GLN C 326 HIS C 533 ASN C 629 GLN D 326 HIS D 533 ASN D 629 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.038 22976 Z= 0.439 Angle : 0.596 7.124 31052 Z= 0.290 Chirality : 0.040 0.158 3468 Planarity : 0.004 0.037 3812 Dihedral : 12.259 158.326 3300 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer Outliers : 3.36 % 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: 1.75 (0.16), residues: 2628 helix: 1.70 (0.11), residues: 1960 sheet: None (None), residues: 0 loop : -0.36 (0.23), residues: 668 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 306 time to evaluate : 2.822 Fit side-chains outliers start: 80 outliers final: 37 residues processed: 359 average time/residue: 1.3006 time to fit residues: 541.4156 Evaluate side-chains 330 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 293 time to evaluate : 2.644 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 25 residues processed: 12 average time/residue: 0.3059 time to fit residues: 9.6453 ------------------------------------------------------------------------------- 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: 1.9990 chunk 229 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 533 ASN A 629 GLN B 326 HIS B 533 ASN B 629 GLN C 326 HIS C 533 ASN C 629 GLN D 326 HIS D 533 ASN D 629 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 22976 Z= 0.200 Angle : 0.472 7.809 31052 Z= 0.231 Chirality : 0.035 0.155 3468 Planarity : 0.003 0.034 3812 Dihedral : 11.408 157.789 3300 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 2.22 % 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: 2.13 (0.16), residues: 2628 helix: 2.00 (0.12), residues: 1964 sheet: None (None), residues: 0 loop : -0.31 (0.23), residues: 664 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 294 time to evaluate : 2.625 Fit side-chains outliers start: 53 outliers final: 28 residues processed: 328 average time/residue: 1.2361 time to fit residues: 469.0487 Evaluate side-chains 312 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 2.633 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.2466 time to fit residues: 5.0336 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 0.0980 chunk 145 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 chunk 159 optimal weight: 0.4980 chunk 155 optimal weight: 1.9990 chunk 117 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 326 HIS A 533 ASN A 629 GLN B 326 HIS B 533 ASN B 629 GLN C 326 HIS C 533 ASN C 629 GLN D 326 HIS D 629 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 22976 Z= 0.138 Angle : 0.441 8.446 31052 Z= 0.216 Chirality : 0.034 0.158 3468 Planarity : 0.003 0.035 3812 Dihedral : 10.397 153.984 3300 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer Outliers : 2.22 % 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: 2.47 (0.16), residues: 2628 helix: 2.23 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.17 (0.23), residues: 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 290 time to evaluate : 2.659 Fit side-chains outliers start: 53 outliers final: 28 residues processed: 316 average time/residue: 1.1674 time to fit residues: 429.0956 Evaluate side-chains 304 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 276 time to evaluate : 2.542 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.2399 time to fit residues: 5.1948 ------------------------------------------------------------------------------- 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: 1.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 200 optimal weight: 8.9990 chunk 231 optimal weight: 0.7980 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 326 HIS A 629 GLN B 326 HIS ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN C 326 HIS C 629 GLN D 326 HIS ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 22976 Z= 0.190 Angle : 0.473 8.415 31052 Z= 0.230 Chirality : 0.035 0.158 3468 Planarity : 0.003 0.035 3812 Dihedral : 10.376 152.045 3300 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer Outliers : 1.68 % 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: 2.43 (0.16), residues: 2628 helix: 2.20 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.17 (0.23), residues: 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 281 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 310 average time/residue: 1.2055 time to fit residues: 435.0002 Evaluate side-chains 309 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 280 time to evaluate : 2.599 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.2590 time to fit residues: 5.3822 ------------------------------------------------------------------------------- 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: 0.7980 chunk 222 optimal weight: 0.4980 chunk 237 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN B 326 HIS B 629 GLN C 326 HIS ** C 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN D 326 HIS D 629 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 22976 Z= 0.182 Angle : 0.472 8.576 31052 Z= 0.230 Chirality : 0.034 0.156 3468 Planarity : 0.003 0.035 3812 Dihedral : 10.325 150.143 3300 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 1.43 % 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: 2.45 (0.16), residues: 2628 helix: 2.22 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.16 (0.23), residues: 660 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 281 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 29 residues processed: 308 average time/residue: 1.2181 time to fit residues: 436.3130 Evaluate side-chains 310 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 281 time to evaluate : 2.415 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.2371 time to fit residues: 5.0612 ------------------------------------------------------------------------------- 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: 2.9990 chunk 153 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 chunk 263 optimal weight: 9.9990 chunk 242 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 22976 Z= 0.152 Angle : 0.463 9.238 31052 Z= 0.225 Chirality : 0.034 0.156 3468 Planarity : 0.003 0.035 3812 Dihedral : 9.987 146.807 3300 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer Outliers : 1.34 % 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: 2.56 (0.16), residues: 2628 helix: 2.30 (0.12), residues: 1968 sheet: None (None), residues: 0 loop : -0.13 (0.23), residues: 660 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5256 Ramachandran restraints generated. 2628 Oldfield, 0 Emsley, 2628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 283 time to evaluate : 2.649 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 308 average time/residue: 1.1692 time to fit residues: 423.7513 Evaluate side-chains 297 residues out of total 2388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 2.808 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 3.7126 ------------------------------------------------------------------------------- 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: 10.0000 chunk 193 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 58 optimal weight: 0.0870 chunk 209 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 215 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN C 629 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.160671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116111 restraints weight = 23723.000| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.17 r_work: 0.3375 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.3348 rms_B_bonded: 2.00 restraints_weight: 0.1250 r_work: 0.3333 rms_B_bonded: 2.08 restraints_weight: 0.0625 r_work: 0.3318 rms_B_bonded: 2.20 restraints_weight: 0.0312 r_work: 0.3302 rms_B_bonded: 2.36 restraints_weight: 0.0156 r_work: 0.3286 rms_B_bonded: 2.54 restraints_weight: 0.0078 r_work: 0.3268 rms_B_bonded: 2.76 restraints_weight: 0.0039 r_work: 0.3249 rms_B_bonded: 3.01 restraints_weight: 0.0020 r_work: 0.3229 rms_B_bonded: 3.30 restraints_weight: 0.0010 r_work: 0.3207 rms_B_bonded: 3.63 restraints_weight: 0.0005 r_work: 0.3184 rms_B_bonded: 4.00 restraints_weight: 0.0002 r_work: 0.3158 rms_B_bonded: 4.42 restraints_weight: 0.0001 r_work: 0.3131 rms_B_bonded: 4.90 restraints_weight: 0.0001 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 22976 Z= 0.127 Angle : 0.448 9.758 31052 Z= 0.217 Chirality : 0.033 0.163 3468 Planarity : 0.003 0.035 3812 Dihedral : 9.522 141.931 3300 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 0.92 % 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: 2.72 (0.16), residues: 2628 helix: 2.41 (0.12), residues: 1972 sheet: None (None), residues: 0 loop : -0.10 (0.23), residues: 656 =============================================================================== Job complete usr+sys time: 7313.66 seconds wall clock time: 131 minutes 13.30 seconds (7873.30 seconds total)