Starting phenix.real_space_refine on Sat Sep 12 22:09:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lma_23437/09_2026/7lma_23437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lma_23437/09_2026/7lma_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lma_23437/09_2026/7lma_23437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lma_23437/09_2026/7lma_23437.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lma_23437/09_2026/7lma_23437.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lma_23437/09_2026/7lma_23437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lma_23437/09_2026/7lma_23437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lma_23437/09_2026/7lma_23437.map" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'GLU:plan': 4, 'ASP:plan': 7, 'GLN:plan1': 3, 'TYR:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4} 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: {'RNAv2': 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: 3.21, per 1000 atoms: 0.17 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 - 3.00 Amino acid : True - 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: 1.15 Conformation dependent library (CDL) restraints added in 616.1 milliseconds 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: 1.89 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: 3.98 Time building geometry restraints manager: 1.48 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=" C1' DT C 21 " pdb=" N1 DT C 21 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.30e+01 bond pdb=" C3' DG C 23 " pdb=" C2' DG C 23 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.98e+00 bond pdb=" N9 DG C 23 " pdb=" C4 DG C 23 " ideal model delta sigma weight residual 1.375 1.392 -0.017 8.00e-03 1.56e+04 4.63e+00 bond pdb=" C4' DG C 25 " pdb=" C3' DG C 25 " ideal model delta sigma weight residual 1.529 1.510 0.019 1.00e-02 1.00e+04 3.47e+00 bond pdb=" C4' DG C 30 " pdb=" C3' DG C 30 " ideal model delta sigma weight residual 1.529 1.511 0.018 1.00e-02 1.00e+04 3.40e+00 ... (remaining 19362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 25826 1.65 - 3.31: 867 3.31 - 4.96: 167 4.96 - 6.62: 25 6.62 - 8.27: 6 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 - 34.43: 10745 34.43 - 68.86: 547 68.86 - 103.28: 69 103.28 - 137.71: 0 137.71 - 172.14: 1 Dihedral angle restraints: 11362 sinusoidal: 5884 harmonic: 5478 Sorted by residual: dihedral pdb=" C4' A B 111 " pdb=" C3' A B 111 " pdb=" C2' A B 111 " pdb=" C1' A B 111 " ideal model delta sinusoidal sigma weight residual 36.35 -39.07 75.42 1 3.10e+00 1.04e-01 7.47e+02 dihedral pdb=" C4' A B 67 " pdb=" C3' A B 67 " pdb=" C2' A B 67 " pdb=" C1' A B 67 " ideal model delta sinusoidal sigma weight residual 36.34 -37.63 73.98 1 3.10e+00 1.04e-01 7.23e+02 dihedral pdb=" C4' U B 42 " pdb=" C3' U B 42 " pdb=" C2' U B 42 " pdb=" C1' U B 42 " ideal model delta sinusoidal sigma weight residual 36.34 -37.20 73.54 1 3.10e+00 1.04e-01 7.16e+02 ... (remaining 11359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2534 0.064 - 0.128: 316 0.128 - 0.192: 20 0.192 - 0.256: 175 0.256 - 0.321: 57 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=" C2' C B 75 " pdb=" C3' C B 75 " pdb=" O2' C B 75 " pdb=" C1' C B 75 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C3' A B 111 " pdb=" C4' A B 111 " pdb=" O3' A B 111 " pdb=" C2' A B 111 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.23e+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 3.040 nonbonded pdb=" OH TYR A1061 " pdb=" O2' G B 61 " model vdw 2.220 3.040 nonbonded pdb=" N6 A B 67 " pdb=" O2' U B 87 " model vdw 2.235 3.120 nonbonded pdb=" O SER F 111 " pdb=" OG SER F 115 " model vdw 2.239 3.040 nonbonded pdb=" O2' A B 111 " pdb=" N7 A B 112 " model vdw 2.243 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 19.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.770 ------------------------------------------------------------------------------- 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 : 0.005 0.415 19371 Z= 0.228 Angle : 0.731 13.434 26897 Z= 0.377 Chirality : 0.078 0.321 3102 Planarity : 0.003 0.042 2817 Dihedral : 18.550 172.138 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 % Allowed : 3.21 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.013 0.001 TYR G 112 PHE 0.013 0.001 PHE A 729 TRP 0.016 0.001 TRP A 496 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.19 (19367) covalent geometry : angle 0.71967 / 0.38 (26891) hydrogen bonds : bond 0.12819 / 8.83 ( 795) hydrogen bonds : angle 5.86182 / 4.14 ( 2246) metal coordination : bond 0.24061 / 11.70 ( 4) metal coordination : angle 8.46272 / 4.97 ( 6) *********************** 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 to be fit. rotamer outliers: 15 poor density : 323 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 401 HIS cc_start: 0.7778 (t-170) cc_final: 0.7456 (t-90) REVERT: H 405 GLU cc_start: 0.2926 (pm20) cc_final: 0.2498 (pm20) REVERT: H 471 GLU cc_start: 0.6018 (mm-30) cc_final: 0.5719 (pt0) REVERT: H 511 TRP cc_start: 0.5830 (m-10) cc_final: 0.4171 (m100) REVERT: H 518 LYS cc_start: 0.4680 (ttmt) cc_final: 0.4201 (ttpt) REVERT: A 292 GLU cc_start: 0.7976 (mp0) cc_final: 0.7763 (mp0) REVERT: A 368 ASP cc_start: 0.7935 (t0) cc_final: 0.7496 (t0) REVERT: A 395 LYS cc_start: 0.7993 (tptm) cc_final: 0.7612 (ttpt) REVERT: A 508 GLU cc_start: 0.7853 (tt0) cc_final: 0.7634 (tt0) REVERT: A 513 GLU cc_start: 0.7737 (pt0) cc_final: 0.7525 (pt0) REVERT: A 566 MET cc_start: 0.7460 (tpp) cc_final: 0.7225 (tpp) REVERT: A 578 MET cc_start: 0.8567 (mtm) cc_final: 0.8261 (mtp) REVERT: A 618 ASP cc_start: 0.8274 (p0) cc_final: 0.7923 (p0) REVERT: A 687 MET cc_start: 0.6408 (tpp) cc_final: 0.5589 (mtp) REVERT: A 862 ASN cc_start: 0.7657 (m110) cc_final: 0.7274 (t0) REVERT: A 921 ARG cc_start: 0.8591 (ttt90) cc_final: 0.8206 (ttt-90) REVERT: A 955 MET cc_start: 0.8909 (mtt) cc_final: 0.8686 (mtp) REVERT: D 536 TYR cc_start: 0.8017 (m-80) cc_final: 0.7769 (m-80) REVERT: D 693 HIS cc_start: 0.7784 (t70) cc_final: 0.6597 (m-70) REVERT: E 49 ASN cc_start: 0.7038 (m110) cc_final: 0.6739 (m110) REVERT: E 84 LYS cc_start: 0.7509 (mttp) cc_final: 0.6853 (pttt) REVERT: E 91 ASP cc_start: 0.8668 (t0) cc_final: 0.8275 (t0) REVERT: E 143 GLN cc_start: 0.7968 (mt0) cc_final: 0.7719 (mt0) REVERT: E 155 GLU cc_start: 0.7354 (tp30) cc_final: 0.6965 (mm-30) REVERT: F 16 GLU cc_start: 0.8374 (pm20) cc_final: 0.8015 (pm20) REVERT: F 61 ARG cc_start: 0.7150 (tpt90) cc_final: 0.6744 (tpt90) REVERT: F 72 GLU cc_start: 0.7927 (tt0) cc_final: 0.7510 (tt0) REVERT: F 98 ASP cc_start: 0.8158 (t70) cc_final: 0.7869 (t0) REVERT: F 120 ASP cc_start: 0.7840 (p0) cc_final: 0.7502 (p0) outliers start: 15 outliers final: 5 residues processed: 332 average time/residue: 0.1570 time to fit residues: 78.3966 Evaluate side-chains 223 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 53 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 472 GLN H 488 GLN A 26 GLN A 55 GLN A 77 GLN A 102 ASN A 105 ASN A 123 ASN A 135 ASN A 176 GLN A 297 ASN A 320 ASN A 324 ASN A 364 ASN A 382 GLN A 636 ASN A 642 GLN A 734 GLN A 746 HIS A 747 ASN A 748 HIS A 761 ASN A 896 GLN A 918 ASN A1095 ASN D 545 GLN D 584 HIS D 629 ASN 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: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.156333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109294 restraints weight = 26786.503| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.89 r_work: 0.3095 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19371 Z= 0.207 Angle : 1.227 26.418 26897 Z= 0.499 Chirality : 0.122 1.820 3102 Planarity : 0.004 0.039 2817 Dihedral : 17.377 162.341 3990 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.45 % Allowed : 9.45 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.19), residues: 1809 helix: 0.63 (0.18), residues: 755 sheet: -1.69 (0.28), residues: 281 loop : -2.01 (0.21), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 60 TYR 0.017 0.001 TYR F 59 PHE 0.018 0.001 PHE A 442 TRP 0.015 0.001 TRP A 496 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (19367) covalent geometry : angle 1.22526 / 0.50 (26891) hydrogen bonds : bond 0.05035 / 3.53 ( 795) hydrogen bonds : angle 4.75755 / 3.38 ( 2246) metal coordination : bond 0.00682 / 0.33 ( 4) metal coordination : angle 4.65971 / 2.75 ( 6) *********************** 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 274 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.4975 (pttt) cc_final: 0.3658 (mttt) REVERT: H 401 HIS cc_start: 0.7678 (t-170) cc_final: 0.7323 (t-90) REVERT: H 405 GLU cc_start: 0.3078 (pm20) cc_final: 0.2623 (mt-10) REVERT: H 471 GLU cc_start: 0.6098 (mm-30) cc_final: 0.5880 (pt0) REVERT: H 497 ASP cc_start: 0.7003 (t70) cc_final: 0.6551 (m-30) REVERT: H 510 TYR cc_start: 0.6969 (t80) cc_final: 0.6252 (t80) REVERT: H 511 TRP cc_start: 0.5835 (m-10) cc_final: 0.4113 (m100) REVERT: H 518 LYS cc_start: 0.5334 (ttmt) cc_final: 0.4898 (ttpt) REVERT: H 529 LYS cc_start: 0.4919 (mttp) cc_final: 0.4096 (pptt) REVERT: A 74 ASN cc_start: 0.9137 (m110) cc_final: 0.8912 (m-40) REVERT: A 235 MET cc_start: 0.8485 (ttm) cc_final: 0.8248 (ttt) REVERT: A 292 GLU cc_start: 0.8350 (mp0) cc_final: 0.7869 (mp0) REVERT: A 357 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 368 ASP cc_start: 0.8770 (t0) cc_final: 0.8304 (t0) REVERT: A 395 LYS cc_start: 0.8614 (tptm) cc_final: 0.7902 (ttpp) REVERT: A 618 ASP cc_start: 0.8577 (p0) cc_final: 0.8313 (p0) REVERT: A 687 MET cc_start: 0.6723 (tpp) cc_final: 0.5674 (mtp) REVERT: A 862 ASN cc_start: 0.7928 (m110) cc_final: 0.7422 (t0) REVERT: D 536 TYR cc_start: 0.8435 (m-80) cc_final: 0.8087 (m-80) REVERT: D 693 HIS cc_start: 0.8015 (t70) cc_final: 0.6478 (m170) REVERT: E 49 ASN cc_start: 0.6866 (m110) cc_final: 0.6542 (m110) REVERT: E 167 TYR cc_start: 0.8795 (t80) cc_final: 0.8547 (t80) REVERT: F 16 GLU cc_start: 0.8493 (pm20) cc_final: 0.8091 (pm20) REVERT: F 25 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7052 (mtpp) REVERT: F 72 GLU cc_start: 0.7851 (tt0) cc_final: 0.7504 (tt0) REVERT: F 87 GLU cc_start: 0.7395 (tp30) cc_final: 0.7152 (tp30) REVERT: F 88 LEU cc_start: 0.5875 (tp) cc_final: 0.5013 (tp) REVERT: F 98 ASP cc_start: 0.8514 (t70) cc_final: 0.8232 (t0) REVERT: F 120 ASP cc_start: 0.8026 (p0) cc_final: 0.7641 (p0) REVERT: G 2 LYS cc_start: 0.9298 (tttt) cc_final: 0.9068 (ttmt) REVERT: G 121 PHE cc_start: 0.8075 (m-80) cc_final: 0.7829 (m-80) outliers start: 24 outliers final: 18 residues processed: 261 average time/residue: 0.1506 time to fit residues: 59.5271 Evaluate side-chains 231 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 397 LEU Chi-restraints excluded: chain H residue 479 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 494 GLN Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 80 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN A 319 HIS A 633 ASN D 635 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107920 restraints weight = 26880.906| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.90 r_work: 0.3069 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19371 Z= 0.179 Angle : 0.935 18.363 26897 Z= 0.399 Chirality : 0.084 1.014 3102 Planarity : 0.003 0.039 2817 Dihedral : 17.439 161.653 3982 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.88 % Allowed : 11.08 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.19), residues: 1809 helix: 1.01 (0.19), residues: 767 sheet: -1.42 (0.29), residues: 283 loop : -1.89 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 60 TYR 0.026 0.001 TYR H 510 PHE 0.021 0.001 PHE H 524 TRP 0.015 0.002 TRP A 496 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (19367) covalent geometry : angle 0.93350 / 0.40 (26891) hydrogen bonds : bond 0.05183 / 3.63 ( 795) hydrogen bonds : angle 4.57799 / 3.26 ( 2246) metal coordination : bond 0.00301 / 0.15 ( 4) metal coordination : angle 3.26157 / 1.88 ( 6) *********************** 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 256 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.4939 (pttt) cc_final: 0.3665 (mttt) REVERT: H 401 HIS cc_start: 0.7573 (t-170) cc_final: 0.7365 (t70) REVERT: H 405 GLU cc_start: 0.2997 (pm20) cc_final: 0.2579 (mt-10) REVERT: H 463 MET cc_start: 0.5346 (ttp) cc_final: 0.5023 (ttt) REVERT: H 466 PHE cc_start: 0.5470 (m-80) cc_final: 0.5254 (m-80) REVERT: H 468 ASN cc_start: 0.6209 (m-40) cc_final: 0.5730 (m-40) REVERT: H 479 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6832 (mm) REVERT: H 497 ASP cc_start: 0.7030 (t70) cc_final: 0.6569 (m-30) REVERT: H 516 PHE cc_start: 0.6677 (t80) cc_final: 0.6406 (t80) REVERT: H 518 LYS cc_start: 0.5385 (ttmt) cc_final: 0.4927 (ttpt) REVERT: H 520 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: H 529 LYS cc_start: 0.4992 (mttp) cc_final: 0.4154 (pptt) REVERT: A 74 ASN cc_start: 0.8970 (m110) cc_final: 0.8722 (m-40) REVERT: A 292 GLU cc_start: 0.8411 (mp0) cc_final: 0.8102 (mp0) REVERT: A 357 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 368 ASP cc_start: 0.8453 (t0) cc_final: 0.7968 (t0) REVERT: A 618 ASP cc_start: 0.8419 (p0) cc_final: 0.8177 (p0) REVERT: A 687 MET cc_start: 0.6755 (tpp) cc_final: 0.5772 (mtp) REVERT: A 862 ASN cc_start: 0.7729 (m110) cc_final: 0.7297 (t0) REVERT: A 1060 PHE cc_start: 0.9092 (t80) cc_final: 0.8876 (t80) REVERT: D 536 TYR cc_start: 0.8243 (m-80) cc_final: 0.7661 (m-80) REVERT: D 693 HIS cc_start: 0.8066 (t70) cc_final: 0.6513 (m170) REVERT: E 49 ASN cc_start: 0.6818 (m110) cc_final: 0.6527 (m110) REVERT: F 16 GLU cc_start: 0.8603 (pm20) cc_final: 0.8198 (pm20) REVERT: F 25 LYS cc_start: 0.7580 (mtmm) cc_final: 0.6911 (mtpp) REVERT: F 72 GLU cc_start: 0.7654 (tt0) cc_final: 0.7423 (tt0) REVERT: F 98 ASP cc_start: 0.8279 (t70) cc_final: 0.7985 (t0) REVERT: F 120 ASP cc_start: 0.8164 (p0) cc_final: 0.7790 (p0) REVERT: G 2 LYS cc_start: 0.9230 (tttt) cc_final: 0.9017 (ttmt) REVERT: G 121 PHE cc_start: 0.8087 (m-80) cc_final: 0.7812 (m-80) outliers start: 31 outliers final: 27 residues processed: 240 average time/residue: 0.1477 time to fit residues: 53.5045 Evaluate side-chains 236 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 397 LEU Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 479 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 494 GLN Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 520 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 894 GLN D 531 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.155371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107719 restraints weight = 26871.171| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.90 r_work: 0.3061 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19371 Z= 0.172 Angle : 0.849 16.749 26897 Z= 0.367 Chirality : 0.074 1.002 3102 Planarity : 0.003 0.039 2817 Dihedral : 17.359 166.335 3982 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.12 % Allowed : 12.72 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.20), residues: 1809 helix: 1.08 (0.19), residues: 790 sheet: -1.28 (0.30), residues: 274 loop : -1.83 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 60 TYR 0.027 0.002 TYR D 536 PHE 0.015 0.002 PHE H 524 TRP 0.015 0.002 TRP A 496 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (19367) covalent geometry : angle 0.84800 / 0.37 (26891) hydrogen bonds : bond 0.05012 / 3.46 ( 795) hydrogen bonds : angle 4.43746 / 3.16 ( 2246) metal coordination : bond 0.00343 / 0.18 ( 4) metal coordination : angle 2.82074 / 1.61 ( 6) *********************** 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 259 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.4957 (pttt) cc_final: 0.3727 (mttt) REVERT: H 401 HIS cc_start: 0.7386 (t-170) cc_final: 0.7037 (t-90) REVERT: H 405 GLU cc_start: 0.4533 (pm20) cc_final: 0.4064 (mt-10) REVERT: H 463 MET cc_start: 0.5354 (ttp) cc_final: 0.4575 (ttt) REVERT: H 479 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6828 (mm) REVERT: H 483 ASN cc_start: 0.1941 (OUTLIER) cc_final: 0.1326 (p0) REVERT: H 496 CYS cc_start: 0.5034 (m) cc_final: 0.4702 (p) REVERT: H 497 ASP cc_start: 0.7069 (t70) cc_final: 0.6570 (m-30) REVERT: H 520 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: H 529 LYS cc_start: 0.4843 (mttp) cc_final: 0.3745 (pttp) REVERT: A 74 ASN cc_start: 0.8961 (m110) cc_final: 0.8702 (m-40) REVERT: A 235 MET cc_start: 0.8300 (ttm) cc_final: 0.8015 (ttt) REVERT: A 292 GLU cc_start: 0.8456 (mp0) cc_final: 0.8126 (mp0) REVERT: A 357 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7641 (tm-30) REVERT: A 368 ASP cc_start: 0.8476 (t0) cc_final: 0.7969 (t0) REVERT: A 395 LYS cc_start: 0.8480 (tptm) cc_final: 0.8231 (tttm) REVERT: A 687 MET cc_start: 0.6763 (tpp) cc_final: 0.5756 (mtp) REVERT: A 862 ASN cc_start: 0.7783 (m110) cc_final: 0.7297 (t0) REVERT: D 571 PHE cc_start: 0.5777 (t80) cc_final: 0.5435 (t80) REVERT: D 693 HIS cc_start: 0.8086 (t70) cc_final: 0.6448 (m170) REVERT: E 49 ASN cc_start: 0.6810 (m110) cc_final: 0.6513 (m110) REVERT: E 143 GLN cc_start: 0.8288 (mt0) cc_final: 0.7865 (mm-40) REVERT: F 16 GLU cc_start: 0.8600 (pm20) cc_final: 0.8218 (pm20) REVERT: F 72 GLU cc_start: 0.7695 (tt0) cc_final: 0.7398 (tt0) REVERT: F 98 ASP cc_start: 0.8273 (t70) cc_final: 0.7962 (t0) REVERT: G 40 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7172 (ttm) REVERT: G 121 PHE cc_start: 0.8163 (m-80) cc_final: 0.7904 (m-80) outliers start: 35 outliers final: 23 residues processed: 245 average time/residue: 0.1406 time to fit residues: 53.1370 Evaluate side-chains 230 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 397 LEU Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 479 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASN Chi-restraints excluded: chain H residue 494 GLN Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 520 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 177 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 848 GLN D 580 ASN E 159 HIS F 7 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.157334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110168 restraints weight = 26669.329| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.87 r_work: 0.3102 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19371 Z= 0.126 Angle : 0.774 14.075 26897 Z= 0.338 Chirality : 0.066 0.879 3102 Planarity : 0.003 0.042 2817 Dihedral : 17.422 177.456 3982 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.54 % Allowed : 13.69 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1809 helix: 1.34 (0.19), residues: 790 sheet: -1.24 (0.30), residues: 283 loop : -1.59 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 60 TYR 0.018 0.001 TYR E 167 PHE 0.025 0.001 PHE H 524 TRP 0.015 0.001 TRP A 496 HIS 0.003 0.001 HIS A 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (19367) covalent geometry : angle 0.77368 / 0.34 (26891) hydrogen bonds : bond 0.04461 / 3.08 ( 795) hydrogen bonds : angle 4.28586 / 3.05 ( 2246) metal coordination : bond 0.00275 / 0.14 ( 4) metal coordination : angle 2.38793 / 1.34 ( 6) *********************** 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 262 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5150 (pttt) cc_final: 0.3692 (mttt) REVERT: H 405 GLU cc_start: 0.4874 (pm20) cc_final: 0.4204 (mt-10) REVERT: H 463 MET cc_start: 0.5577 (OUTLIER) cc_final: 0.5319 (ttt) REVERT: H 483 ASN cc_start: 0.1487 (OUTLIER) cc_final: 0.0896 (p0) REVERT: H 490 GLU cc_start: 0.6671 (tp30) cc_final: 0.6414 (tp30) REVERT: H 497 ASP cc_start: 0.6983 (t70) cc_final: 0.6536 (m-30) REVERT: H 529 LYS cc_start: 0.4823 (mttp) cc_final: 0.3777 (pttp) REVERT: A 235 MET cc_start: 0.8152 (ttm) cc_final: 0.7891 (ttt) REVERT: A 357 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7545 (tm-30) REVERT: A 368 ASP cc_start: 0.8436 (t0) cc_final: 0.7943 (t0) REVERT: A 374 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8333 (mttm) REVERT: A 395 LYS cc_start: 0.8366 (tptm) cc_final: 0.8055 (tttm) REVERT: A 687 MET cc_start: 0.6747 (tpp) cc_final: 0.5724 (mtp) REVERT: A 862 ASN cc_start: 0.7769 (m110) cc_final: 0.7339 (t0) REVERT: D 536 TYR cc_start: 0.7547 (m-80) cc_final: 0.7244 (m-80) REVERT: D 571 PHE cc_start: 0.5682 (t80) cc_final: 0.5371 (t80) REVERT: D 693 HIS cc_start: 0.8056 (t70) cc_final: 0.6459 (m170) REVERT: E 49 ASN cc_start: 0.6632 (m110) cc_final: 0.6338 (m110) REVERT: E 143 GLN cc_start: 0.8269 (mt0) cc_final: 0.7865 (mm-40) REVERT: F 16 GLU cc_start: 0.8623 (pm20) cc_final: 0.8245 (pm20) REVERT: F 98 ASP cc_start: 0.8191 (t70) cc_final: 0.7888 (t0) REVERT: G 40 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7109 (ttm) REVERT: G 121 PHE cc_start: 0.8106 (m-80) cc_final: 0.7856 (m-80) outliers start: 42 outliers final: 25 residues processed: 246 average time/residue: 0.1427 time to fit residues: 53.4423 Evaluate side-chains 227 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 479 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASN Chi-restraints excluded: chain H residue 494 GLN Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain A residue 374 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 122 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.156153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.108917 restraints weight = 26716.334| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.84 r_work: 0.3071 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19371 Z= 0.168 Angle : 0.777 12.616 26897 Z= 0.343 Chirality : 0.065 0.768 3102 Planarity : 0.003 0.042 2817 Dihedral : 17.409 177.328 3982 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.60 % Allowed : 14.84 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.20), residues: 1809 helix: 1.35 (0.19), residues: 790 sheet: -1.28 (0.29), residues: 293 loop : -1.54 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 60 TYR 0.030 0.001 TYR D 536 PHE 0.019 0.002 PHE H 521 TRP 0.014 0.002 TRP A 496 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (19367) covalent geometry : angle 0.77579 / 0.34 (26891) hydrogen bonds : bond 0.04860 / 3.36 ( 795) hydrogen bonds : angle 4.29694 / 3.05 ( 2246) metal coordination : bond 0.02140 / 1.05 ( 4) metal coordination : angle 2.97959 / 1.73 ( 6) *********************** 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 247 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5058 (pttt) cc_final: 0.3883 (mttt) REVERT: H 405 GLU cc_start: 0.5023 (pm20) cc_final: 0.4396 (mt-10) REVERT: H 463 MET cc_start: 0.5439 (OUTLIER) cc_final: 0.5101 (ttt) REVERT: H 483 ASN cc_start: 0.1431 (OUTLIER) cc_final: 0.0865 (p0) REVERT: H 490 GLU cc_start: 0.6678 (tp30) cc_final: 0.6465 (tp30) REVERT: H 497 ASP cc_start: 0.6981 (t70) cc_final: 0.6567 (m-30) REVERT: H 516 PHE cc_start: 0.6541 (t80) cc_final: 0.6100 (t80) REVERT: H 520 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: H 529 LYS cc_start: 0.4465 (mttp) cc_final: 0.3481 (pttp) REVERT: A 235 MET cc_start: 0.8253 (ttm) cc_final: 0.7978 (ttt) REVERT: A 357 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7571 (tm-30) REVERT: A 368 ASP cc_start: 0.8493 (t0) cc_final: 0.7972 (t0) REVERT: A 395 LYS cc_start: 0.8550 (tptm) cc_final: 0.8239 (tttm) REVERT: A 687 MET cc_start: 0.6702 (tpp) cc_final: 0.5738 (mtp) REVERT: A 862 ASN cc_start: 0.7829 (m110) cc_final: 0.7318 (t0) REVERT: D 536 TYR cc_start: 0.7892 (m-80) cc_final: 0.7652 (m-10) REVERT: D 571 PHE cc_start: 0.5765 (t80) cc_final: 0.5531 (t80) REVERT: D 693 HIS cc_start: 0.8093 (t70) cc_final: 0.6435 (m170) REVERT: E 49 ASN cc_start: 0.6691 (m110) cc_final: 0.6381 (m110) REVERT: E 143 GLN cc_start: 0.8310 (mt0) cc_final: 0.7883 (mt0) REVERT: F 16 GLU cc_start: 0.8635 (pm20) cc_final: 0.8264 (pm20) REVERT: F 98 ASP cc_start: 0.8160 (t70) cc_final: 0.7814 (t0) REVERT: G 121 PHE cc_start: 0.8194 (m-80) cc_final: 0.7942 (m-80) outliers start: 43 outliers final: 33 residues processed: 229 average time/residue: 0.1449 time to fit residues: 51.2263 Evaluate side-chains 237 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 409 ASP Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 479 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASN Chi-restraints excluded: chain H residue 494 GLN Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 518 LYS Chi-restraints excluded: chain H residue 520 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 118 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 192 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 174 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 176 GLN A 530 GLN ** 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 = 0.3922 r_free = 0.3922 target = 0.153277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105762 restraints weight = 26799.073| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.87 r_work: 0.3026 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19371 Z= 0.243 Angle : 0.825 11.077 26897 Z= 0.372 Chirality : 0.067 0.682 3102 Planarity : 0.004 0.039 2817 Dihedral : 17.449 174.468 3982 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.79 % Allowed : 14.84 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1809 helix: 1.13 (0.19), residues: 781 sheet: -1.23 (0.30), residues: 290 loop : -1.53 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 60 TYR 0.024 0.002 TYR D 536 PHE 0.027 0.002 PHE H 406 TRP 0.011 0.002 TRP A 496 HIS 0.004 0.001 HIS A 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (19367) covalent geometry : angle 0.82410 / 0.37 (26891) hydrogen bonds : bond 0.05722 / 3.98 ( 795) hydrogen bonds : angle 4.48030 / 3.18 ( 2246) metal coordination : bond 0.01093 / 0.52 ( 4) metal coordination : angle 3.05994 / 1.71 ( 6) *********************** 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 252 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 206 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5085 (pttt) cc_final: 0.3817 (mttt) REVERT: H 405 GLU cc_start: 0.5037 (pm20) cc_final: 0.4404 (mt-10) REVERT: H 463 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.4649 (ttt) REVERT: H 483 ASN cc_start: 0.1326 (OUTLIER) cc_final: 0.0790 (p0) REVERT: H 497 ASP cc_start: 0.6957 (t70) cc_final: 0.6398 (m-30) REVERT: H 520 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: H 529 LYS cc_start: 0.4446 (mttp) cc_final: 0.3470 (pttp) REVERT: A 235 MET cc_start: 0.8353 (ttm) cc_final: 0.8057 (ttt) REVERT: A 357 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7415 (tm-30) REVERT: A 368 ASP cc_start: 0.8578 (t0) cc_final: 0.8053 (t0) REVERT: A 395 LYS cc_start: 0.8473 (tptm) cc_final: 0.8166 (tttm) REVERT: A 687 MET cc_start: 0.6739 (tpp) cc_final: 0.5777 (mtp) REVERT: A 862 ASN cc_start: 0.7809 (m110) cc_final: 0.7330 (t0) REVERT: D 536 TYR cc_start: 0.7893 (m-80) cc_final: 0.7656 (m-10) REVERT: D 571 PHE cc_start: 0.5622 (t80) cc_final: 0.5394 (t80) REVERT: D 693 HIS cc_start: 0.8396 (t70) cc_final: 0.6542 (m170) REVERT: E 34 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9058 (pp) REVERT: E 49 ASN cc_start: 0.6744 (m110) cc_final: 0.6420 (m110) REVERT: E 143 GLN cc_start: 0.8350 (mt0) cc_final: 0.7931 (mt0) REVERT: F 16 GLU cc_start: 0.8667 (pm20) cc_final: 0.8271 (pm20) REVERT: F 98 ASP cc_start: 0.8320 (t70) cc_final: 0.7969 (t0) REVERT: G 121 PHE cc_start: 0.8303 (m-80) cc_final: 0.8091 (m-80) outliers start: 46 outliers final: 37 residues processed: 236 average time/residue: 0.1429 time to fit residues: 51.8931 Evaluate side-chains 236 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 479 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASN Chi-restraints excluded: chain H residue 494 GLN Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 518 LYS Chi-restraints excluded: chain H residue 520 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 155 optimal weight: 0.0470 chunk 191 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.155990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109478 restraints weight = 26706.399| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.86 r_work: 0.3077 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19371 Z= 0.136 Angle : 0.746 11.311 26897 Z= 0.334 Chirality : 0.062 0.618 3102 Planarity : 0.003 0.042 2817 Dihedral : 17.395 173.588 3982 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.30 % Allowed : 15.38 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1809 helix: 1.43 (0.19), residues: 785 sheet: -1.18 (0.30), residues: 289 loop : -1.44 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 60 TYR 0.017 0.001 TYR D 536 PHE 0.022 0.001 PHE H 524 TRP 0.018 0.002 TRP A 496 HIS 0.003 0.001 HIS A 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (19367) covalent geometry : angle 0.74529 / 0.33 (26891) hydrogen bonds : bond 0.04693 / 3.26 ( 795) hydrogen bonds : angle 4.27892 / 3.03 ( 2246) metal coordination : bond 0.00305 / 0.15 ( 4) metal coordination : angle 1.90086 / 1.09 ( 6) *********************** 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 253 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5094 (pttt) cc_final: 0.3895 (mttt) REVERT: H 405 GLU cc_start: 0.5169 (pm20) cc_final: 0.4641 (mt-10) REVERT: H 463 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.4645 (ttt) REVERT: H 483 ASN cc_start: 0.1293 (OUTLIER) cc_final: 0.0780 (p0) REVERT: H 497 ASP cc_start: 0.6953 (t70) cc_final: 0.6456 (m-30) REVERT: H 506 GLU cc_start: 0.5052 (tp30) cc_final: 0.4848 (tp30) REVERT: H 521 PHE cc_start: 0.7124 (m-80) cc_final: 0.6871 (m-80) REVERT: H 529 LYS cc_start: 0.4215 (mttp) cc_final: 0.3206 (pttp) REVERT: A 357 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 368 ASP cc_start: 0.8494 (t0) cc_final: 0.7990 (t0) REVERT: A 374 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8395 (mttm) REVERT: A 395 LYS cc_start: 0.8544 (tptm) cc_final: 0.8223 (tttm) REVERT: A 574 ASN cc_start: 0.8945 (t0) cc_final: 0.8709 (t0) REVERT: A 687 MET cc_start: 0.6655 (tpp) cc_final: 0.5781 (mtt) REVERT: A 862 ASN cc_start: 0.7833 (m110) cc_final: 0.7359 (t0) REVERT: D 571 PHE cc_start: 0.5682 (t80) cc_final: 0.5457 (t80) REVERT: D 693 HIS cc_start: 0.8273 (t70) cc_final: 0.6434 (m170) REVERT: E 34 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8951 (pp) REVERT: E 49 ASN cc_start: 0.6605 (m110) cc_final: 0.6294 (m110) REVERT: E 143 GLN cc_start: 0.8343 (mt0) cc_final: 0.7895 (mm-40) REVERT: F 16 GLU cc_start: 0.8647 (pm20) cc_final: 0.8260 (pm20) REVERT: F 98 ASP cc_start: 0.8205 (t70) cc_final: 0.7875 (t0) REVERT: G 147 ASP cc_start: 0.8389 (t0) cc_final: 0.8113 (t0) outliers start: 38 outliers final: 30 residues processed: 235 average time/residue: 0.1397 time to fit residues: 50.5433 Evaluate side-chains 234 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 479 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASN Chi-restraints excluded: chain H residue 494 GLN Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 518 LYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 166 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 140 optimal weight: 0.0670 chunk 2 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 154 optimal weight: 5.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 GLN A 751 HIS ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.110023 restraints weight = 26819.741| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.88 r_work: 0.3090 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19371 Z= 0.128 Angle : 0.730 11.776 26897 Z= 0.329 Chirality : 0.061 0.580 3102 Planarity : 0.003 0.044 2817 Dihedral : 17.317 174.616 3982 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.06 % Allowed : 15.87 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1809 helix: 1.53 (0.19), residues: 785 sheet: -1.19 (0.30), residues: 291 loop : -1.35 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 60 TYR 0.034 0.001 TYR D 536 PHE 0.022 0.001 PHE H 524 TRP 0.018 0.002 TRP A 496 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (19367) covalent geometry : angle 0.72987 / 0.33 (26891) hydrogen bonds : bond 0.04464 / 3.08 ( 795) hydrogen bonds : angle 4.22110 / 2.99 ( 2246) metal coordination : bond 0.00244 / 0.12 ( 4) metal coordination : angle 1.72524 / 0.96 ( 6) *********************** 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 240 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5080 (pttt) cc_final: 0.3894 (mttt) REVERT: H 405 GLU cc_start: 0.5084 (pm20) cc_final: 0.4755 (mt-10) REVERT: H 463 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.4868 (ttt) REVERT: H 471 GLU cc_start: 0.6393 (tp30) cc_final: 0.4682 (tt0) REVERT: H 483 ASN cc_start: 0.1200 (OUTLIER) cc_final: 0.0736 (p0) REVERT: H 497 ASP cc_start: 0.6765 (t70) cc_final: 0.6521 (m-30) REVERT: H 521 PHE cc_start: 0.7038 (m-80) cc_final: 0.6776 (m-80) REVERT: H 526 PHE cc_start: 0.6773 (m-10) cc_final: 0.6194 (m-80) REVERT: A 357 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 368 ASP cc_start: 0.8506 (t0) cc_final: 0.8000 (t0) REVERT: A 374 LYS cc_start: 0.8576 (mmtm) cc_final: 0.8369 (mttm) REVERT: A 395 LYS cc_start: 0.8502 (tptm) cc_final: 0.8202 (tttm) REVERT: A 574 ASN cc_start: 0.8975 (t0) cc_final: 0.8766 (t0) REVERT: A 687 MET cc_start: 0.6655 (tpp) cc_final: 0.5655 (mtp) REVERT: A 862 ASN cc_start: 0.7754 (m110) cc_final: 0.7279 (t0) REVERT: D 536 TYR cc_start: 0.7866 (m-10) cc_final: 0.7567 (m-10) REVERT: D 549 LYS cc_start: 0.8962 (ptmt) cc_final: 0.8617 (ptmm) REVERT: D 693 HIS cc_start: 0.8208 (t70) cc_final: 0.6500 (m-70) REVERT: E 34 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8932 (pp) REVERT: E 49 ASN cc_start: 0.6594 (m110) cc_final: 0.6241 (m110) REVERT: E 143 GLN cc_start: 0.8334 (mt0) cc_final: 0.7909 (mm-40) REVERT: F 16 GLU cc_start: 0.8635 (pm20) cc_final: 0.8249 (pm20) REVERT: F 98 ASP cc_start: 0.8182 (t70) cc_final: 0.7842 (t0) REVERT: G 121 PHE cc_start: 0.8320 (m-80) cc_final: 0.8028 (m-80) REVERT: G 147 ASP cc_start: 0.8380 (t0) cc_final: 0.8102 (t0) outliers start: 34 outliers final: 29 residues processed: 228 average time/residue: 0.1432 time to fit residues: 50.5764 Evaluate side-chains 233 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 479 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASN Chi-restraints excluded: chain H residue 494 GLN Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 139 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108827 restraints weight = 26689.315| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.86 r_work: 0.3072 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19371 Z= 0.160 Angle : 0.748 12.453 26897 Z= 0.337 Chirality : 0.061 0.532 3102 Planarity : 0.003 0.044 2817 Dihedral : 17.272 175.190 3982 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.36 % Allowed : 15.99 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.20), residues: 1809 helix: 1.47 (0.19), residues: 786 sheet: -1.13 (0.30), residues: 290 loop : -1.38 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 60 TYR 0.032 0.001 TYR D 536 PHE 0.018 0.001 PHE H 524 TRP 0.016 0.002 TRP A 496 HIS 0.006 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (19367) covalent geometry : angle 0.74712 / 0.34 (26891) hydrogen bonds : bond 0.04818 / 3.34 ( 795) hydrogen bonds : angle 4.25816 / 3.01 ( 2246) metal coordination : bond 0.00271 / 0.13 ( 4) metal coordination : angle 1.78791 / 1.01 ( 6) ********************** 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 245 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5111 (pttt) cc_final: 0.3904 (mttt) REVERT: H 463 MET cc_start: 0.5643 (OUTLIER) cc_final: 0.4976 (ttt) REVERT: H 471 GLU cc_start: 0.6624 (tp30) cc_final: 0.4982 (tt0) REVERT: H 483 ASN cc_start: 0.1165 (OUTLIER) cc_final: 0.0706 (p0) REVERT: H 497 ASP cc_start: 0.6838 (t70) cc_final: 0.6609 (m-30) REVERT: H 521 PHE cc_start: 0.7237 (m-80) cc_final: 0.6921 (m-80) REVERT: H 526 PHE cc_start: 0.6766 (m-10) cc_final: 0.6202 (m-80) REVERT: A 357 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7701 (tm-30) REVERT: A 368 ASP cc_start: 0.8522 (t0) cc_final: 0.8014 (t0) REVERT: A 374 LYS cc_start: 0.8600 (mmtm) cc_final: 0.8396 (mttm) REVERT: A 395 LYS cc_start: 0.8535 (tptm) cc_final: 0.8240 (tttm) REVERT: A 687 MET cc_start: 0.6695 (tpp) cc_final: 0.5710 (mtp) REVERT: A 862 ASN cc_start: 0.7679 (m110) cc_final: 0.7193 (t0) REVERT: D 536 TYR cc_start: 0.7888 (m-10) cc_final: 0.7578 (m-10) REVERT: D 693 HIS cc_start: 0.8185 (t70) cc_final: 0.6380 (m-70) REVERT: E 34 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8978 (pp) REVERT: E 49 ASN cc_start: 0.6642 (m110) cc_final: 0.6288 (m110) REVERT: E 143 GLN cc_start: 0.8345 (mt0) cc_final: 0.7902 (mt0) REVERT: F 16 GLU cc_start: 0.8660 (pm20) cc_final: 0.8242 (pm20) REVERT: F 98 ASP cc_start: 0.8220 (t70) cc_final: 0.7876 (t0) REVERT: G 121 PHE cc_start: 0.8256 (m-80) cc_final: 0.7968 (m-80) REVERT: G 147 ASP cc_start: 0.8388 (t0) cc_final: 0.8101 (t0) outliers start: 39 outliers final: 33 residues processed: 228 average time/residue: 0.1418 time to fit residues: 50.2769 Evaluate side-chains 239 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 411 ILE Chi-restraints excluded: chain H residue 463 MET Chi-restraints excluded: chain H residue 479 LEU Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 483 ASN Chi-restraints excluded: chain H residue 494 GLN Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 520 GLU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 899 ILE Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain D residue 554 ARG Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain G residue 26 TYR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 7 GLN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.156923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109740 restraints weight = 26912.473| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.89 r_work: 0.3087 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19371 Z= 0.135 Angle : 0.724 11.814 26897 Z= 0.327 Chirality : 0.059 0.508 3102 Planarity : 0.003 0.045 2817 Dihedral : 17.232 175.966 3982 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.30 % Allowed : 16.05 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1809 helix: 1.60 (0.19), residues: 785 sheet: -1.15 (0.30), residues: 292 loop : -1.31 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 60 TYR 0.026 0.001 TYR E 167 PHE 0.029 0.001 PHE H 524 TRP 0.017 0.002 TRP A 496 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (19367) covalent geometry : angle 0.72327 / 0.33 (26891) hydrogen bonds : bond 0.04505 / 3.11 ( 795) hydrogen bonds : angle 4.17533 / 2.95 ( 2246) metal coordination : bond 0.00218 / 0.11 ( 4) metal coordination : angle 1.50990 / 0.85 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4280.79 seconds wall clock time: 74 minutes 22.06 seconds (4462.06 seconds total)