Starting phenix.real_space_refine (version: dev) on Wed Feb 22 23:39:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy6_26865/02_2023/7uy6_26865.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy6_26865/02_2023/7uy6_26865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy6_26865/02_2023/7uy6_26865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy6_26865/02_2023/7uy6_26865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy6_26865/02_2023/7uy6_26865.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uy6_26865/02_2023/7uy6_26865.pdb" } resolution = 2.9 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 873": "OE1" <-> "OE2" Residue "A GLU 982": "OE1" <-> "OE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18746 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1367 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8542 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 22, 'TRANS': 989} Chain breaks: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "E" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1195 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 952 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1542 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 1, 'TRANS': 182} Chain: "B" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3293 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 24, 'rna3p_pur': 62, 'rna3p_pyr': 57} Link IDs: {'rna2p': 36, 'rna3p': 119} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10290 SG CYS D 555 76.519 71.540 85.390 1.00102.65 S ATOM 10303 SG CYS D 557 74.797 69.232 87.751 1.00107.36 S ATOM 10423 SG CYS D 572 72.846 70.796 84.821 1.00101.57 S ATOM 10444 SG CYS D 575 73.748 72.898 87.764 1.00108.23 S Time building chain proxies: 11.23, per 1000 atoms: 0.60 Number of scatterers: 18746 At special positions: 0 Unit cell: (151.8, 158.4, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 65 16.00 P 170 15.00 O 3977 8.00 N 3166 7.00 C 11367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.02 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 900 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 572 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 557 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 555 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 575 " Number of angles added : 6 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 49.4% alpha, 21.4% beta 28 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'H' and resid 115 through 130 Processing helix chain 'H' and resid 131 through 139 removed outlier: 3.836A pdb=" N HIS H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'H' and resid 157 through 161 removed outlier: 3.560A pdb=" N LYS H 160 " --> pdb=" O VAL H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 Processing helix chain 'H' and resid 203 through 216 removed outlier: 4.323A pdb=" N GLU H 216 " --> pdb=" O ASP H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 400 removed outlier: 3.620A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 403 No H-bonds generated for 'chain 'H' and resid 401 through 403' Processing helix chain 'H' and resid 469 through 480 removed outlier: 4.093A pdb=" N ARG H 473 " --> pdb=" O SER H 469 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN H 477 " --> pdb=" O ARG H 473 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS H 478 " --> pdb=" O LEU H 474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 480 " --> pdb=" O ILE H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 531 Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.533A pdb=" N GLY A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.503A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 144 through 155 removed outlier: 4.292A pdb=" N TYR A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.634A pdb=" N PHE A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.877A pdb=" N SER A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.508A pdb=" N ARG A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.616A pdb=" N ASN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.809A pdb=" N LYS A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 425 through 426 No H-bonds generated for 'chain 'A' and resid 425 through 426' Processing helix chain 'A' and resid 427 through 431 Processing helix chain 'A' and resid 444 through 467 removed outlier: 3.540A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.920A pdb=" N GLU A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.964A pdb=" N ASN A 556 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 557 " --> pdb=" O GLN A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 557' Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 565 through 579 removed outlier: 3.701A pdb=" N ASP A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.880A pdb=" N ILE A 626 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.735A pdb=" N LYS A 717 " --> pdb=" O GLN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 793 removed outlier: 3.608A pdb=" N LEU A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 804 removed outlier: 4.092A pdb=" N LYS A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.520A pdb=" N GLN A 901 " --> pdb=" O GLN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 911 through 926 Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.687A pdb=" N MET A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 966 through 967 No H-bonds generated for 'chain 'A' and resid 966 through 967' Processing helix chain 'A' and resid 968 through 971 removed outlier: 3.641A pdb=" N LYS A 971 " --> pdb=" O ASP A 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 968 through 971' Processing helix chain 'A' and resid 972 through 980 removed outlier: 4.543A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1009 Processing helix chain 'A' and resid 1014 through 1038 Processing helix chain 'A' and resid 1045 through 1075 removed outlier: 3.959A pdb=" N LYS A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A1050 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1094 Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 603 through 615 Processing helix chain 'D' and resid 621 through 634 removed outlier: 4.583A pdb=" N GLN D 625 " --> pdb=" O GLN D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 679 through 697 removed outlier: 4.320A pdb=" N GLU D 683 " --> pdb=" O ASN D 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 110 through 123 removed outlier: 3.540A pdb=" N TYR E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 175 removed outlier: 4.140A pdb=" N SER E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 22 removed outlier: 3.519A pdb=" N MET F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 Processing helix chain 'F' and resid 114 through 119 removed outlier: 3.836A pdb=" N PHE F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.774A pdb=" N LYS G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 removed outlier: 3.623A pdb=" N ILE G 41 " --> pdb=" O LYS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 removed outlier: 4.037A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 94 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 157 removed outlier: 3.606A pdb=" N LYS G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 184 Processing sheet with id=AA1, first strand: chain 'H' and resid 220 through 221 removed outlier: 3.779A pdb=" N LYS H 230 " --> pdb=" O LYS H 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 406 through 411 removed outlier: 4.085A pdb=" N LYS H 382 " --> pdb=" O ILE H 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.747A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ALA A 170 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.747A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ALA A 170 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 115 Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.776A pdb=" N GLY A 531 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 808 through 813 removed outlier: 3.554A pdb=" N LEU A 617 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP A 618 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS A 849 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 850 " --> pdb=" O SER A 869 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 874 through 876 Processing sheet with id=AB1, first strand: chain 'D' and resid 532 through 545 removed outlier: 5.617A pdb=" N LEU D 541 " --> pdb=" O GLN D 592 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN D 592 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER D 543 " --> pdb=" O PHE D 590 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE D 590 " --> pdb=" O SER D 543 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG D 588 " --> pdb=" O GLN D 545 " (cutoff:3.500A) removed outlier: 13.501A pdb=" N THR D 597 " --> pdb=" O ILE D 668 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N TYR D 670 " --> pdb=" O THR D 597 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL D 672 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET D 601 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LYS D 674 " --> pdb=" O MET D 601 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU D 654 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE D 675 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE D 652 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 649 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 533 " --> pdb=" O PHE D 657 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 551 through 554 removed outlier: 3.588A pdb=" N GLN D 582 " --> pdb=" O ARG D 554 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 562 through 564 removed outlier: 3.897A pdb=" N PHE D 571 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 66 through 76 removed outlier: 4.257A pdb=" N MET E 86 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 98 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE E 142 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN E 101 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N TYR E 146 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR E 146 " --> pdb=" O MET E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 87 through 91 removed outlier: 3.809A pdb=" N GLU F 72 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N VAL F 83 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 55 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU F 41 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 26 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 71 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 46 through 51 removed outlier: 7.144A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER G 103 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE G 58 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN G 73 " --> pdb=" O GLN G 63 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS G 65 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 71 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 46 through 51 removed outlier: 7.144A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER G 103 " --> pdb=" O ASP G 134 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP G 134 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL G 105 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS G 132 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 107 " --> pdb=" O MET G 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN G 109 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 21.376A pdb=" N LYS G 80 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 16.095A pdb=" N ILE G 123 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N ILE G 82 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU G 125 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) 754 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 7.94 Time building geometry restraints manager: 8.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4358 1.33 - 1.45: 4756 1.45 - 1.57: 9896 1.57 - 1.69: 338 1.69 - 1.81: 97 Bond restraints: 19445 Sorted by residual: bond pdb=" C THR A 814 " pdb=" O THR A 814 " ideal model delta sigma weight residual 1.243 1.226 0.017 9.50e-03 1.11e+04 3.38e+00 bond pdb=" CG1 ILE A 376 " pdb=" CD1 ILE A 376 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 bond pdb=" CA THR A 814 " pdb=" CB THR A 814 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.53e-02 4.27e+03 1.28e+00 bond pdb=" CA ILE A1104 " pdb=" CB ILE A1104 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.05e+00 bond pdb=" CB PRO E 28 " pdb=" CG PRO E 28 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.18e-01 ... (remaining 19440 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.91: 1195 106.91 - 113.68: 10773 113.68 - 120.45: 7503 120.45 - 127.22: 7136 127.22 - 133.99: 395 Bond angle restraints: 27002 Sorted by residual: angle pdb=" CA THR A 814 " pdb=" C THR A 814 " pdb=" N ASP A 815 " ideal model delta sigma weight residual 119.98 116.56 3.42 8.50e-01 1.38e+00 1.62e+01 angle pdb=" N ASP A 816 " pdb=" CA ASP A 816 " pdb=" C ASP A 816 " ideal model delta sigma weight residual 109.24 114.57 -5.33 1.63e+00 3.76e-01 1.07e+01 angle pdb=" N LEU A 813 " pdb=" CA LEU A 813 " pdb=" C LEU A 813 " ideal model delta sigma weight residual 108.52 103.45 5.07 1.63e+00 3.76e-01 9.66e+00 angle pdb=" C THR A 814 " pdb=" CA THR A 814 " pdb=" CB THR A 814 " ideal model delta sigma weight residual 117.23 113.42 3.81 1.36e+00 5.41e-01 7.83e+00 angle pdb=" C TRP A 876 " pdb=" N ILE A 877 " pdb=" CA ILE A 877 " ideal model delta sigma weight residual 121.97 126.43 -4.46 1.80e+00 3.09e-01 6.14e+00 ... (remaining 26997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 11087 35.72 - 71.44: 287 71.44 - 107.16: 30 107.16 - 142.88: 0 142.88 - 178.60: 8 Dihedral angle restraints: 11412 sinusoidal: 5904 harmonic: 5508 Sorted by residual: dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 200.00 21.40 178.60 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C B 43 " pdb=" C1' C B 43 " pdb=" N1 C B 43 " pdb=" C2 C B 43 " ideal model delta sinusoidal sigma weight residual 200.00 39.35 160.65 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' U B 158 " pdb=" C1' U B 158 " pdb=" N1 U B 158 " pdb=" C2 U B 158 " ideal model delta sinusoidal sigma weight residual -128.00 50.10 -178.10 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2484 0.041 - 0.082: 475 0.082 - 0.123: 142 0.123 - 0.164: 9 0.164 - 0.205: 3 Chirality restraints: 3113 Sorted by residual: chirality pdb=" CG LEU A 920 " pdb=" CB LEU A 920 " pdb=" CD1 LEU A 920 " pdb=" CD2 LEU A 920 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU A 813 " pdb=" N LEU A 813 " pdb=" C LEU A 813 " pdb=" CB LEU A 813 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA THR A 814 " pdb=" N THR A 814 " pdb=" C THR A 814 " pdb=" CB THR A 814 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3110 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1104 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A1105 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A1105 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1105 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 588 " -0.092 9.50e-02 1.11e+02 4.14e-02 1.18e+00 pdb=" NE ARG D 588 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG D 588 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG D 588 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 588 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 924 " -0.008 2.00e-02 2.50e+03 7.74e-03 1.05e+00 pdb=" CG PHE A 924 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE A 924 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 924 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 924 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 924 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 924 " -0.002 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2114 2.75 - 3.29: 17264 3.29 - 3.83: 30683 3.83 - 4.36: 36344 4.36 - 4.90: 60190 Nonbonded interactions: 146595 Sorted by model distance: nonbonded pdb=" OH TYR A1061 " pdb=" O2' G B 61 " model vdw 2.215 2.440 nonbonded pdb=" O GLN A 228 " pdb=" NH1 ARG A 473 " model vdw 2.245 2.520 nonbonded pdb=" O2' U B 41 " pdb=" OP1 C B 43 " model vdw 2.264 2.440 nonbonded pdb=" OE1 GLN A1008 " pdb=" OH TYR A1025 " model vdw 2.272 2.440 nonbonded pdb=" OE1 GLN A 417 " pdb=" OH TYR A 422 " model vdw 2.283 2.440 ... (remaining 146590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 170 5.49 5 S 65 5.16 5 C 11367 2.51 5 N 3166 2.21 5 O 3977 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: 5.070 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: 0.010 Extract box with map and model: 16.740 Check model and map are aligned: 0.290 Process input model: 57.190 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.002 0.052 19445 Z= 0.140 Angle : 0.443 6.325 27002 Z= 0.243 Chirality : 0.036 0.205 3113 Planarity : 0.003 0.041 2835 Dihedral : 15.878 178.601 7832 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1823 helix: 2.06 (0.19), residues: 790 sheet: 0.07 (0.31), residues: 287 loop : -0.24 (0.23), residues: 746 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.013 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 1.4529 time to fit residues: 430.5483 Evaluate side-chains 191 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 2.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 0.9990 chunk 149 optimal weight: 0.3980 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 484 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN A 55 GLN A 102 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 GLN A 865 HIS D 619 HIS D 693 HIS E 169 GLN F 7 GLN F 31 ASN F 110 GLN G 6 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 19445 Z= 0.167 Angle : 0.493 6.361 27002 Z= 0.268 Chirality : 0.038 0.152 3113 Planarity : 0.003 0.027 2835 Dihedral : 14.887 178.266 3989 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1823 helix: 2.19 (0.19), residues: 800 sheet: 0.21 (0.32), residues: 279 loop : -0.31 (0.23), residues: 744 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 218 average time/residue: 1.3335 time to fit residues: 327.5185 Evaluate side-chains 205 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 193 time to evaluate : 2.137 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 8 average time/residue: 0.7215 time to fit residues: 9.9419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 193 optimal weight: 10.0000 chunk 159 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 467 GLN H 484 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 294 GLN A 865 HIS D 619 HIS ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 19445 Z= 0.176 Angle : 0.484 6.863 27002 Z= 0.262 Chirality : 0.038 0.207 3113 Planarity : 0.003 0.027 2835 Dihedral : 14.940 177.943 3989 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1823 helix: 2.21 (0.19), residues: 803 sheet: 0.24 (0.31), residues: 275 loop : -0.31 (0.23), residues: 745 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 2.047 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 12 residues processed: 221 average time/residue: 1.3709 time to fit residues: 340.4814 Evaluate side-chains 204 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.6934 time to fit residues: 8.2132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 177 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 467 GLN ** H 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 484 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 619 HIS D 693 HIS F 110 GLN G 6 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.060 19445 Z= 0.159 Angle : 0.473 8.594 27002 Z= 0.256 Chirality : 0.037 0.155 3113 Planarity : 0.003 0.027 2835 Dihedral : 14.940 178.195 3989 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1823 helix: 2.26 (0.19), residues: 802 sheet: 0.15 (0.31), residues: 280 loop : -0.32 (0.23), residues: 741 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 228 average time/residue: 1.3178 time to fit residues: 339.9947 Evaluate side-chains 216 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.3548 time to fit residues: 6.0555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 108 optimal weight: 0.7980 chunk 2 optimal weight: 30.0000 chunk 141 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 482 HIS A 865 HIS D 619 HIS F 110 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.057 19445 Z= 0.151 Angle : 0.459 7.358 27002 Z= 0.249 Chirality : 0.036 0.149 3113 Planarity : 0.003 0.026 2835 Dihedral : 14.938 178.505 3989 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1823 helix: 2.33 (0.19), residues: 802 sheet: 0.17 (0.31), residues: 284 loop : -0.33 (0.23), residues: 737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 203 time to evaluate : 1.891 Fit side-chains outliers start: 48 outliers final: 18 residues processed: 231 average time/residue: 1.2796 time to fit residues: 334.7111 Evaluate side-chains 213 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.2000 time to fit residues: 4.6047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 171 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 190 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 484 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 619 HIS D 693 HIS E 40 ASN F 110 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 19445 Z= 0.166 Angle : 0.477 7.748 27002 Z= 0.259 Chirality : 0.037 0.150 3113 Planarity : 0.003 0.038 2835 Dihedral : 14.958 178.182 3989 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1823 helix: 2.29 (0.19), residues: 801 sheet: 0.17 (0.31), residues: 280 loop : -0.37 (0.23), residues: 742 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 197 time to evaluate : 2.199 Fit side-chains outliers start: 49 outliers final: 27 residues processed: 221 average time/residue: 1.3091 time to fit residues: 328.5532 Evaluate side-chains 219 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 192 time to evaluate : 2.067 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 16 residues processed: 12 average time/residue: 0.4236 time to fit residues: 9.8805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 160 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 512 ASN A 55 GLN A 301 GLN A 865 HIS F 110 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 19445 Z= 0.191 Angle : 0.491 7.978 27002 Z= 0.267 Chirality : 0.038 0.225 3113 Planarity : 0.003 0.031 2835 Dihedral : 15.014 177.967 3989 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1823 helix: 2.22 (0.19), residues: 795 sheet: 0.13 (0.30), residues: 282 loop : -0.39 (0.23), residues: 746 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.162 Fit side-chains outliers start: 40 outliers final: 23 residues processed: 222 average time/residue: 1.2872 time to fit residues: 324.2406 Evaluate side-chains 213 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 1.989 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.5084 time to fit residues: 7.8299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.0170 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 172 optimal weight: 6.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 619 HIS D 693 HIS F 110 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 19445 Z= 0.175 Angle : 0.487 8.246 27002 Z= 0.265 Chirality : 0.037 0.164 3113 Planarity : 0.003 0.030 2835 Dihedral : 15.009 178.155 3989 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1823 helix: 2.24 (0.19), residues: 794 sheet: 0.08 (0.30), residues: 280 loop : -0.38 (0.23), residues: 749 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 195 time to evaluate : 2.095 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 22 residues processed: 219 average time/residue: 1.2624 time to fit residues: 313.9706 Evaluate side-chains 214 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 192 time to evaluate : 2.110 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 14 residues processed: 8 average time/residue: 0.4999 time to fit residues: 8.1339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 20.0000 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 54 optimal weight: 0.0070 chunk 159 optimal weight: 20.0000 chunk 167 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS F 110 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 19445 Z= 0.202 Angle : 0.506 8.302 27002 Z= 0.273 Chirality : 0.038 0.153 3113 Planarity : 0.003 0.033 2835 Dihedral : 15.060 177.901 3989 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.31 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1823 helix: 2.17 (0.19), residues: 794 sheet: 0.10 (0.31), residues: 275 loop : -0.42 (0.22), residues: 754 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 2.054 Fit side-chains outliers start: 35 outliers final: 23 residues processed: 209 average time/residue: 1.3240 time to fit residues: 316.5418 Evaluate side-chains 208 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 1.895 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 7 average time/residue: 0.2520 time to fit residues: 5.7313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 356 GLN A 840 ASN A 865 HIS D 693 HIS F 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 19445 Z= 0.256 Angle : 0.543 8.367 27002 Z= 0.294 Chirality : 0.039 0.163 3113 Planarity : 0.003 0.042 2835 Dihedral : 15.179 177.787 3989 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.09 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.20), residues: 1823 helix: 2.07 (0.19), residues: 789 sheet: 0.04 (0.31), residues: 277 loop : -0.46 (0.22), residues: 757 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 2.057 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 23 residues processed: 209 average time/residue: 1.2948 time to fit residues: 307.0879 Evaluate side-chains 211 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 2.136 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 7 average time/residue: 0.3883 time to fit residues: 6.6474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 47 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 156 optimal weight: 0.0370 chunk 65 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 472 GLN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 619 HIS F 110 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.168277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.114220 restraints weight = 24013.538| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.03 r_work: 0.3084 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 19445 Z= 0.157 Angle : 0.492 8.599 27002 Z= 0.266 Chirality : 0.037 0.171 3113 Planarity : 0.003 0.031 2835 Dihedral : 15.081 178.405 3989 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.19 % Favored : 97.75 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1823 helix: 2.11 (0.19), residues: 805 sheet: 0.22 (0.31), residues: 278 loop : -0.43 (0.23), residues: 740 =============================================================================== Job complete usr+sys time: 6206.43 seconds wall clock time: 110 minutes 54.95 seconds (6654.95 seconds total)