Starting phenix.real_space_refine (version: dev) on Wed Dec 14 03:08:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lma_23437/12_2022/7lma_23437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lma_23437/12_2022/7lma_23437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lma_23437/12_2022/7lma_23437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lma_23437/12_2022/7lma_23437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lma_23437/12_2022/7lma_23437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lma_23437/12_2022/7lma_23437.pdb" } resolution = 3.3 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= 0.006 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 Residue "H ARG 465": "NH1" <-> "NH2" Residue "H GLU 471": "OE1" <-> "OE2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "A TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A ARG 1055": "NH1" <-> "NH2" Residue "A ARG 1058": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ARG 554": "NH1" <-> "NH2" Residue "D ARG 588": "NH1" <-> "NH2" Residue "D GLU 622": "OE1" <-> "OE2" Residue "D GLU 632": "OE1" <-> "OE2" Residue "D GLU 692": "OE1" <-> "OE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G ARG 131": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18672 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: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1188 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 885 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 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 77.254 73.406 83.988 1.00156.42 S ATOM 10303 SG CYS D 557 75.835 70.694 86.662 1.00165.86 S ATOM 10423 SG CYS D 572 73.613 72.987 83.625 1.00167.66 S ATOM 10444 SG CYS D 575 74.813 75.100 86.767 1.00174.71 S Time building chain proxies: 10.68, per 1000 atoms: 0.57 Number of scatterers: 18672 At special positions: 0 Unit cell: (148.24, 160.48, 116.96, 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 3959 8.00 N 3153 7.00 C 11324 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: 8.48 Conformation dependent library (CDL) restraints added in 2.4 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 575 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 555 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 557 " Number of angles added : 6 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3562 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 19 sheets defined 47.0% alpha, 17.7% beta 40 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'H' and resid 115 through 131 Processing helix chain 'H' and resid 133 through 138 Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 203 through 216 Processing helix chain 'H' and resid 391 through 401 removed outlier: 4.099A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 469 through 480 removed outlier: 3.968A pdb=" N ARG H 473 " --> pdb=" O SER H 469 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN H 477 " --> pdb=" O ARG H 473 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS H 478 " --> pdb=" O LEU H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 531 removed outlier: 3.662A pdb=" N ARG H 522 " --> pdb=" O LYS H 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 27 removed outlier: 3.767A pdb=" N GLN A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) 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: 3.933A pdb=" N VAL A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.558A 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: 4.562A pdb=" N TYR A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.911A pdb=" N PHE A 178 " --> pdb=" O ASN A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.560A pdb=" N GLN A 228 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 300 through 319 Processing helix chain 'A' and resid 322 through 330 removed outlier: 3.566A pdb=" N LEU A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.775A pdb=" N ASN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.518A pdb=" N LYS A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.933A pdb=" N TYR A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 475 removed outlier: 3.930A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 560 through 577 removed outlier: 5.547A pdb=" N ASP A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.549A 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 794 removed outlier: 3.509A pdb=" N LEU A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER A 783 " --> pdb=" O GLY A 779 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 800 removed outlier: 4.028A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 removed outlier: 3.502A pdb=" N ALA A 827 " --> pdb=" O SER A 823 " (cutoff:3.500A) 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 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 removed outlier: 3.638A pdb=" N LYS A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.764A 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 972 through 980 removed outlier: 4.655A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1009 removed outlier: 3.827A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1038 removed outlier: 3.795A pdb=" N LYS A1018 " --> pdb=" O ASN A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1075 removed outlier: 3.782A pdb=" N LEU A1050 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1094 removed outlier: 3.669A pdb=" N ASN A1094 " --> pdb=" O PHE A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 4.398A pdb=" N THR A1102 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1109 removed outlier: 3.744A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 525 removed outlier: 3.554A pdb=" N ILE D 520 " --> pdb=" O SER D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 615 Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 679 through 697 removed outlier: 3.662A pdb=" N LYS D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 110 through 124 removed outlier: 3.819A pdb=" N TYR E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 175 removed outlier: 3.695A pdb=" N SER E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 22 removed outlier: 4.063A pdb=" N ALA F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG F 22 " --> pdb=" O MET F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 114 through 119 removed outlier: 4.169A pdb=" N PHE F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 114 through 119' Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.779A pdb=" N LYS G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 87 through 94 removed outlier: 3.984A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 94 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 157 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: 3.595A pdb=" N LYS H 230 " --> pdb=" O LYS H 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 407 through 411 removed outlier: 3.815A 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: 6.877A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 10.253A 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: 6.877A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 10.253A 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 513 through 514 removed outlier: 6.563A pdb=" N GLY A 531 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 613 through 615 Processing sheet with id=AA9, first strand: chain 'A' and resid 849 through 852 removed outlier: 6.063A pdb=" N ILE A 850 " --> pdb=" O SER A 869 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 532 through 537 removed outlier: 6.412A pdb=" N ILE D 652 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE D 675 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU D 654 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N TYR D 670 " --> pdb=" O THR D 597 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL D 672 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N MET D 601 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N LYS D 674 " --> pdb=" O MET D 601 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA D 649 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 552 through 554 removed outlier: 3.594A pdb=" N GLN D 582 " --> pdb=" O ARG D 554 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 563 through 564 removed outlier: 3.607A pdb=" N LEU D 563 " --> pdb=" O PHE D 571 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE D 571 " --> pdb=" O LEU D 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 661 through 662 Processing sheet with id=AB5, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.475A pdb=" N VAL E 32 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR E 70 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 96 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.475A pdb=" N VAL E 32 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR E 70 " --> pdb=" O VAL E 32 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 85 through 86 removed outlier: 3.619A pdb=" N ILE E 85 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 25 through 32 removed outlier: 4.429A pdb=" N HIS F 53 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N VAL F 83 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE F 56 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N CYS F 85 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 76 " --> pdb=" O SER F 84 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG F 74 " --> pdb=" O GLU F 86 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU F 88 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU F 72 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU F 90 " --> pdb=" O PHE F 70 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE F 70 " --> pdb=" O GLU F 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 48 through 51 removed outlier: 3.882A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER G 103 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN G 61 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN G 73 " --> pdb=" O GLN G 63 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS G 65 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G 71 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 79 " --> pdb=" O ASP G 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 48 through 51 removed outlier: 3.882A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N SER G 103 " --> pdb=" O ASP G 134 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP G 134 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL G 105 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS G 132 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE G 107 " --> pdb=" O MET G 130 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN G 109 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 15.995A pdb=" N LYS G 80 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 12.702A pdb=" N LEU G 125 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ILE G 82 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N ILE G 127 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN G 84 " --> pdb=" O ILE G 127 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLU G 129 " --> pdb=" O ASN G 84 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2058 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 99 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 8.49 Time building geometry restraints manager: 8.98 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: 4519 1.33 - 1.45: 4587 1.45 - 1.57: 9826 1.57 - 1.69: 338 1.69 - 1.81: 97 Bond restraints: 19367 Sorted by residual: bond pdb=" N ASN A 904 " pdb=" CA ASN A 904 " ideal model delta sigma weight residual 1.459 1.439 0.021 1.27e-02 6.20e+03 2.68e+00 bond pdb=" CA LYS E 104 " pdb=" C LYS E 104 " ideal model delta sigma weight residual 1.524 1.544 -0.020 1.29e-02 6.01e+03 2.52e+00 bond pdb=" N LYS A 493 " pdb=" CA LYS A 493 " ideal model delta sigma weight residual 1.462 1.475 -0.013 8.50e-03 1.38e+04 2.48e+00 bond pdb=" N ASP A 523 " pdb=" CA ASP A 523 " ideal model delta sigma weight residual 1.459 1.478 -0.018 1.19e-02 7.06e+03 2.38e+00 bond pdb=" CA GLU A 122 " pdb=" C GLU A 122 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.31e-02 5.83e+03 2.03e+00 ... (remaining 19362 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.79: 1192 106.79 - 113.59: 10728 113.59 - 120.39: 7446 120.39 - 127.20: 7117 127.20 - 134.00: 408 Bond angle restraints: 26891 Sorted by residual: angle pdb=" N ARG G 86 " pdb=" CA ARG G 86 " pdb=" C ARG G 86 " ideal model delta sigma weight residual 111.28 118.85 -7.57 1.09e+00 8.42e-01 4.83e+01 angle pdb=" N LYS A 582 " pdb=" CA LYS A 582 " pdb=" C LYS A 582 " ideal model delta sigma weight residual 113.12 121.09 -7.97 1.25e+00 6.40e-01 4.07e+01 angle pdb=" N LYS A 438 " pdb=" CA LYS A 438 " pdb=" C LYS A 438 " ideal model delta sigma weight residual 113.17 120.37 -7.20 1.26e+00 6.30e-01 3.27e+01 angle pdb=" N LYS E 104 " pdb=" CA LYS E 104 " pdb=" C LYS E 104 " ideal model delta sigma weight residual 111.36 117.38 -6.02 1.09e+00 8.42e-01 3.05e+01 angle pdb=" N GLU A 407 " pdb=" CA GLU A 407 " pdb=" C GLU A 407 " ideal model delta sigma weight residual 111.28 105.73 5.55 1.09e+00 8.42e-01 2.59e+01 ... (remaining 26886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 10978 35.67 - 71.34: 337 71.34 - 107.01: 38 107.01 - 142.68: 3 142.68 - 178.36: 6 Dihedral angle restraints: 11362 sinusoidal: 5884 harmonic: 5478 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 64.83 135.17 1 1.50e+01 4.44e-03 7.29e+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 -160.00 -33.23 -126.77 1 1.50e+01 4.44e-03 6.82e+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 232.00 53.64 178.36 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2772 0.064 - 0.128: 308 0.128 - 0.192: 19 0.192 - 0.256: 1 0.256 - 0.321: 2 Chirality restraints: 3102 Sorted by residual: chirality pdb=" CA LYS A 582 " pdb=" N LYS A 582 " pdb=" C LYS A 582 " pdb=" CB LYS A 582 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA LYS A 438 " pdb=" N LYS A 438 " pdb=" C LYS A 438 " pdb=" CB LYS A 438 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ARG G 86 " pdb=" N ARG G 86 " pdb=" C ARG G 86 " pdb=" CB ARG G 86 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3099 not shown) Planarity restraints: 2817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 52 " -0.027 2.00e-02 2.50e+03 1.29e-02 4.61e+00 pdb=" N9 A B 52 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A B 52 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 52 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 52 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B 52 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B 52 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 52 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B 52 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 52 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 52 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 103 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C SER E 103 " 0.036 2.00e-02 2.50e+03 pdb=" O SER E 103 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS E 104 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 16 " 0.028 2.00e-02 2.50e+03 1.25e-02 4.31e+00 pdb=" N9 A B 16 " -0.028 2.00e-02 2.50e+03 pdb=" C8 A B 16 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A B 16 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 16 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 16 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A B 16 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A B 16 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 16 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A B 16 " -0.006 2.00e-02 2.50e+03 ... (remaining 2814 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1856 2.74 - 3.28: 18449 3.28 - 3.82: 30392 3.82 - 4.36: 36338 4.36 - 4.90: 59368 Nonbonded interactions: 146403 Sorted by model distance: nonbonded pdb=" O2 U B 42 " pdb=" O2' C B 43 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR A1061 " pdb=" O2' G B 61 " model vdw 2.220 2.440 nonbonded pdb=" N6 A B 67 " pdb=" O2' U B 87 " model vdw 2.235 2.520 nonbonded pdb=" O SER F 111 " pdb=" OG SER F 115 " model vdw 2.239 2.440 nonbonded pdb=" O2' A B 111 " pdb=" N7 A B 112 " model vdw 2.243 2.520 ... (remaining 146398 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 11324 2.51 5 N 3153 2.21 5 O 3959 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: 0.550 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: 5.430 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.140 Process input model: 59.320 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.004 0.031 19367 Z= 0.224 Angle : 0.555 8.271 26891 Z= 0.324 Chirality : 0.040 0.321 3102 Planarity : 0.003 0.042 2817 Dihedral : 16.767 178.355 7800 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.18), residues: 1809 helix: -0.79 (0.17), residues: 762 sheet: -2.36 (0.27), residues: 286 loop : -2.43 (0.21), residues: 761 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 323 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 332 average time/residue: 0.3265 time to fit residues: 160.7999 Evaluate side-chains 213 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 208 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1867 time to fit residues: 4.4340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 0.0670 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 472 GLN H 488 GLN A 26 GLN A 55 GLN A 77 GLN A 102 ASN A 123 ASN A 135 ASN A 297 ASN A 320 ASN ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN A 633 ASN A 636 ASN A 734 GLN A 746 HIS A 747 ASN A 748 HIS A 761 ASN A 896 GLN A 918 ASN A1095 ASN D 531 GLN ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 HIS E 139 ASN E 141 GLN E 151 ASN E 172 HIS F 20 GLN G 12 GLN G 34 GLN G 84 ASN G 150 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 19367 Z= 0.146 Angle : 0.487 6.794 26891 Z= 0.258 Chirality : 0.037 0.154 3102 Planarity : 0.003 0.040 2817 Dihedral : 16.292 179.866 3977 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.45 % 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: -1.03 (0.20), residues: 1809 helix: 0.86 (0.19), residues: 777 sheet: -1.58 (0.30), residues: 268 loop : -1.98 (0.21), residues: 764 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 246 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 257 average time/residue: 0.3357 time to fit residues: 128.3367 Evaluate side-chains 227 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 2.082 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1752 time to fit residues: 7.5677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 0.0870 chunk 148 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 158 optimal weight: 0.0010 chunk 176 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN A 848 GLN A 894 GLN D 580 ASN ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 19367 Z= 0.129 Angle : 0.465 7.117 26891 Z= 0.245 Chirality : 0.036 0.151 3102 Planarity : 0.003 0.038 2817 Dihedral : 16.084 179.347 3977 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.03 % 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: -0.46 (0.20), residues: 1809 helix: 1.40 (0.19), residues: 786 sheet: -1.42 (0.30), residues: 284 loop : -1.73 (0.21), residues: 739 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 240 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 248 average time/residue: 0.3058 time to fit residues: 115.9748 Evaluate side-chains 219 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1652 time to fit residues: 5.5254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 324 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 ASN ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN G 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19367 Z= 0.211 Angle : 0.500 8.318 26891 Z= 0.264 Chirality : 0.038 0.165 3102 Planarity : 0.003 0.037 2817 Dihedral : 16.077 179.715 3977 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 1.51 % 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: -0.34 (0.20), residues: 1809 helix: 1.41 (0.19), residues: 789 sheet: -1.16 (0.30), residues: 282 loop : -1.66 (0.21), residues: 738 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 15 residues processed: 238 average time/residue: 0.2988 time to fit residues: 110.0580 Evaluate side-chains 217 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1705 time to fit residues: 7.4687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.0470 chunk 0 optimal weight: 40.0000 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 361 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN G 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 19367 Z= 0.170 Angle : 0.483 8.102 26891 Z= 0.255 Chirality : 0.037 0.151 3102 Planarity : 0.003 0.036 2817 Dihedral : 16.005 179.886 3977 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 0.97 % 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: -0.17 (0.20), residues: 1809 helix: 1.56 (0.19), residues: 787 sheet: -1.18 (0.30), residues: 290 loop : -1.53 (0.22), residues: 732 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 222 average time/residue: 0.2987 time to fit residues: 103.1735 Evaluate side-chains 214 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 2.224 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1830 time to fit residues: 5.6855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.0470 chunk 170 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 189 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 GLN A 839 ASN D 584 HIS E 57 HIS E 114 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 19367 Z= 0.118 Angle : 0.459 8.793 26891 Z= 0.241 Chirality : 0.036 0.151 3102 Planarity : 0.003 0.037 2817 Dihedral : 15.798 179.928 3977 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.61 % 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: 0.16 (0.20), residues: 1809 helix: 1.81 (0.19), residues: 788 sheet: -0.96 (0.31), residues: 284 loop : -1.35 (0.22), residues: 737 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 225 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 230 average time/residue: 0.3008 time to fit residues: 107.5354 Evaluate side-chains 204 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 2.056 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1826 time to fit residues: 4.0291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 188 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 19367 Z= 0.195 Angle : 0.499 9.976 26891 Z= 0.264 Chirality : 0.037 0.197 3102 Planarity : 0.003 0.037 2817 Dihedral : 15.809 179.575 3977 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.91 % 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: 0.14 (0.20), residues: 1809 helix: 1.80 (0.19), residues: 786 sheet: -1.04 (0.30), residues: 292 loop : -1.33 (0.22), residues: 731 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 2.207 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 210 average time/residue: 0.3084 time to fit residues: 101.3848 Evaluate side-chains 204 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 197 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1735 time to fit residues: 5.0118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 0.0570 chunk 93 optimal weight: 0.0970 chunk 17 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 19367 Z= 0.248 Angle : 0.533 9.908 26891 Z= 0.283 Chirality : 0.039 0.184 3102 Planarity : 0.003 0.037 2817 Dihedral : 15.889 179.398 3977 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1809 helix: 1.67 (0.19), residues: 786 sheet: -1.02 (0.30), residues: 291 loop : -1.30 (0.22), residues: 732 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 2.071 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 208 average time/residue: 0.3047 time to fit residues: 98.7063 Evaluate side-chains 201 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 193 time to evaluate : 2.060 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1771 time to fit residues: 5.3796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9990 chunk 180 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 HIS ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 19367 Z= 0.176 Angle : 0.506 10.294 26891 Z= 0.269 Chirality : 0.037 0.172 3102 Planarity : 0.003 0.039 2817 Dihedral : 15.815 179.785 3977 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1809 helix: 1.80 (0.19), residues: 785 sheet: -1.04 (0.30), residues: 292 loop : -1.27 (0.22), residues: 732 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 203 time to evaluate : 1.915 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 206 average time/residue: 0.3116 time to fit residues: 99.8121 Evaluate side-chains 201 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 2.050 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1759 time to fit residues: 4.0603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 3.9990 chunk 186 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 195 optimal weight: 10.0000 chunk 179 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 95 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 19367 Z= 0.153 Angle : 0.500 10.396 26891 Z= 0.265 Chirality : 0.037 0.205 3102 Planarity : 0.003 0.040 2817 Dihedral : 15.708 179.254 3977 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1809 helix: 1.88 (0.19), residues: 788 sheet: -1.02 (0.30), residues: 293 loop : -1.19 (0.22), residues: 728 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 201 time to evaluate : 2.096 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 201 average time/residue: 0.3052 time to fit residues: 94.9202 Evaluate side-chains 197 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 2.109 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1771 time to fit residues: 3.4311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 8.9990 chunk 165 optimal weight: 0.0270 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 159 optimal weight: 0.0060 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 481 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 HIS E 114 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.160235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113522 restraints weight = 26630.856| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.87 r_work: 0.3135 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 19367 Z= 0.142 Angle : 0.489 11.452 26891 Z= 0.260 Chirality : 0.036 0.191 3102 Planarity : 0.003 0.040 2817 Dihedral : 15.602 179.512 3977 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 0.18 % 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: 0.36 (0.20), residues: 1809 helix: 1.96 (0.19), residues: 788 sheet: -1.06 (0.30), residues: 294 loop : -1.13 (0.22), residues: 727 =============================================================================== Job complete usr+sys time: 3433.99 seconds wall clock time: 63 minutes 32.21 seconds (3812.21 seconds total)