Starting phenix.real_space_refine on Thu Mar 5 03:23:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lma_23437/03_2026/7lma_23437.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lma_23437/03_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_23437/03_2026/7lma_23437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lma_23437/03_2026/7lma_23437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lma_23437/03_2026/7lma_23437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lma_23437/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 156} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 24, 'rna3p_pur': 62, 'rna3p_pyr': 57} Link IDs: {'rna2p': 36, 'rna3p': 119} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10290 SG CYS D 555 77.254 73.406 83.988 1.00156.42 S ATOM 10303 SG CYS D 557 75.835 70.694 86.662 1.00165.86 S ATOM 10423 SG CYS D 572 73.613 72.987 83.625 1.00167.66 S ATOM 10444 SG CYS D 575 74.813 75.100 86.767 1.00174.71 S Time building chain proxies: 4.50, per 1000 atoms: 0.24 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: 1.59 Conformation dependent library (CDL) restraints added in 815.4 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: 2.95 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: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4519 1.33 - 1.45: 4587 1.45 - 1.57: 9826 1.57 - 1.69: 338 1.69 - 1.81: 97 Bond restraints: 19367 Sorted by residual: bond pdb=" N ASN A 904 " pdb=" CA ASN A 904 " ideal model delta sigma weight residual 1.459 1.439 0.021 1.27e-02 6.20e+03 2.68e+00 bond pdb=" CA LYS E 104 " pdb=" C LYS E 104 " ideal model delta sigma weight residual 1.524 1.544 -0.020 1.29e-02 6.01e+03 2.52e+00 bond pdb=" N LYS A 493 " pdb=" CA LYS A 493 " ideal model delta sigma weight residual 1.462 1.475 -0.013 8.50e-03 1.38e+04 2.48e+00 bond pdb=" N ASP A 523 " pdb=" CA ASP A 523 " ideal model delta sigma weight residual 1.459 1.478 -0.018 1.19e-02 7.06e+03 2.38e+00 bond pdb=" CA GLU A 122 " pdb=" C GLU A 122 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.31e-02 5.83e+03 2.03e+00 ... (remaining 19362 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 26389 1.65 - 3.31: 436 3.31 - 4.96: 44 4.96 - 6.62: 16 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 - 35.67: 11211 35.67 - 71.34: 535 71.34 - 107.01: 69 107.01 - 142.68: 3 142.68 - 178.36: 6 Dihedral angle restraints: 11824 sinusoidal: 6346 harmonic: 5478 Sorted by residual: dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 200.00 64.83 135.17 1 1.50e+01 4.44e-03 7.29e+01 dihedral pdb=" O4' C B 43 " pdb=" C1' C B 43 " pdb=" N1 C B 43 " pdb=" C2 C B 43 " ideal model delta sinusoidal sigma weight residual -160.00 -33.23 -126.77 1 1.50e+01 4.44e-03 6.82e+01 dihedral pdb=" O4' U B 158 " pdb=" C1' U B 158 " pdb=" N1 U B 158 " pdb=" C2 U B 158 " ideal model delta sinusoidal sigma weight residual 232.00 53.64 178.36 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2772 0.064 - 0.128: 308 0.128 - 0.192: 19 0.192 - 0.256: 1 0.256 - 0.321: 2 Chirality restraints: 3102 Sorted by residual: chirality pdb=" CA LYS A 582 " pdb=" N LYS A 582 " pdb=" C LYS A 582 " pdb=" CB LYS A 582 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA LYS A 438 " pdb=" N LYS A 438 " pdb=" C LYS A 438 " pdb=" CB LYS A 438 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ARG G 86 " pdb=" N ARG G 86 " pdb=" C ARG G 86 " pdb=" CB ARG G 86 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3099 not shown) Planarity restraints: 2817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 52 " -0.027 2.00e-02 2.50e+03 1.29e-02 4.61e+00 pdb=" N9 A B 52 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A B 52 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 52 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A B 52 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A B 52 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B 52 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A B 52 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B 52 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 52 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 52 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 103 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C SER E 103 " 0.036 2.00e-02 2.50e+03 pdb=" O SER E 103 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS E 104 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 16 " 0.028 2.00e-02 2.50e+03 1.25e-02 4.31e+00 pdb=" N9 A B 16 " -0.028 2.00e-02 2.50e+03 pdb=" C8 A B 16 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A B 16 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A B 16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 16 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A B 16 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A B 16 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A B 16 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 16 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A B 16 " -0.006 2.00e-02 2.50e+03 ... (remaining 2814 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1856 2.74 - 3.28: 18449 3.28 - 3.82: 30392 3.82 - 4.36: 36338 4.36 - 4.90: 59368 Nonbonded interactions: 146403 Sorted by model distance: nonbonded pdb=" O2 U B 42 " pdb=" O2' C B 43 " model vdw 2.202 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: 1.520 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.900 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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= 0.205 Angle : 0.569 13.434 26897 Z= 0.325 Chirality : 0.040 0.321 3102 Planarity : 0.003 0.042 2817 Dihedral : 19.035 178.355 8262 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 covalent geometry : bond 0.00353 (19367) covalent geometry : angle 0.55503 (26891) hydrogen bonds : bond 0.12819 ( 795) hydrogen bonds : angle 5.86182 ( 2246) metal coordination : bond 0.24061 ( 4) metal coordination : angle 8.46272 ( 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 : 0.654 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: 0.1459 time to fit residues: 72.0398 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 : 0.588 ------------------------------------------------------------------------------- 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: 10.0000 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... Flipped N/Q/H residues before XYZ refinement: H 472 GLN H 488 GLN A 26 GLN A 55 GLN A 77 GLN A 102 ASN A 135 ASN A 297 ASN A 320 ASN A 324 ASN A 364 ASN A 382 GLN A 633 ASN 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 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.156042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108865 restraints weight = 26785.193| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.90 r_work: 0.3096 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1408 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= 0.122 Angle : 0.516 7.090 26897 Z= 0.273 Chirality : 0.038 0.155 3102 Planarity : 0.003 0.042 2817 Dihedral : 20.332 179.006 4452 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.39 % Allowed : 9.51 % 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: -1.12 (0.19), residues: 1809 helix: 0.77 (0.19), residues: 764 sheet: -1.60 (0.30), residues: 267 loop : -1.98 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 554 TYR 0.015 0.001 TYR A 958 PHE 0.013 0.001 PHE H 524 TRP 0.014 0.001 TRP A 496 HIS 0.002 0.001 HIS A 751 Details of bonding type rmsd covalent geometry : bond 0.00270 (19367) covalent geometry : angle 0.51430 (26891) hydrogen bonds : bond 0.04648 ( 795) hydrogen bonds : angle 4.54684 ( 2246) metal coordination : bond 0.00776 ( 4) metal coordination : angle 3.01235 ( 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 271 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5022 (pttt) cc_final: 0.3618 (mttt) REVERT: H 401 HIS cc_start: 0.7668 (t-170) cc_final: 0.7313 (t-90) REVERT: H 405 GLU cc_start: 0.2705 (pm20) cc_final: 0.2237 (pm20) REVERT: H 497 ASP cc_start: 0.6909 (t70) cc_final: 0.6547 (m-30) REVERT: H 510 TYR cc_start: 0.6801 (t80) cc_final: 0.6244 (t80) REVERT: H 511 TRP cc_start: 0.5912 (m-10) cc_final: 0.4152 (m100) REVERT: H 518 LYS cc_start: 0.5282 (ttmt) cc_final: 0.4741 (ttpt) REVERT: H 529 LYS cc_start: 0.4912 (mttp) cc_final: 0.4091 (pptt) REVERT: A 74 ASN cc_start: 0.9187 (m110) cc_final: 0.8866 (m-40) REVERT: A 235 MET cc_start: 0.8539 (ttm) cc_final: 0.8314 (ttt) REVERT: A 292 GLU cc_start: 0.8437 (mp0) cc_final: 0.7974 (mp0) REVERT: A 357 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7308 (tm-30) REVERT: A 368 ASP cc_start: 0.8813 (t0) cc_final: 0.8347 (t0) REVERT: A 395 LYS cc_start: 0.8587 (tptm) cc_final: 0.7914 (ttpp) REVERT: A 546 MET cc_start: 0.8810 (mtt) cc_final: 0.8606 (mtt) REVERT: A 618 ASP cc_start: 0.8580 (p0) cc_final: 0.8313 (p0) REVERT: A 687 MET cc_start: 0.6676 (tpp) cc_final: 0.5653 (mtp) REVERT: A 708 TYR cc_start: 0.7655 (m-10) cc_final: 0.7258 (m-10) REVERT: A 862 ASN cc_start: 0.7904 (m110) cc_final: 0.7396 (t0) REVERT: D 536 TYR cc_start: 0.8353 (m-80) cc_final: 0.7869 (m-80) REVERT: D 549 LYS cc_start: 0.9094 (ptmt) cc_final: 0.8691 (ptmm) REVERT: D 693 HIS cc_start: 0.8021 (t70) cc_final: 0.6442 (m170) REVERT: E 49 ASN cc_start: 0.6849 (m110) cc_final: 0.6494 (m110) REVERT: E 126 ARG cc_start: 0.7777 (mtt-85) cc_final: 0.7440 (mtt-85) REVERT: F 16 GLU cc_start: 0.8676 (pm20) cc_final: 0.8201 (pm20) REVERT: F 25 LYS cc_start: 0.7662 (mtmm) cc_final: 0.7038 (mtpp) REVERT: F 72 GLU cc_start: 0.7869 (tt0) cc_final: 0.7517 (tt0) REVERT: F 88 LEU cc_start: 0.5479 (tp) cc_final: 0.4846 (tp) REVERT: F 98 ASP cc_start: 0.8507 (t70) cc_final: 0.8238 (t0) REVERT: F 120 ASP cc_start: 0.7973 (p0) cc_final: 0.7586 (p0) REVERT: G 86 ARG cc_start: 0.8179 (ttp-170) cc_final: 0.7972 (ttp-170) REVERT: G 121 PHE cc_start: 0.8145 (m-80) cc_final: 0.7810 (m-80) REVERT: G 129 GLU cc_start: 0.8882 (tp30) cc_final: 0.8681 (tt0) outliers start: 23 outliers final: 17 residues processed: 260 average time/residue: 0.1451 time to fit residues: 55.9697 Evaluate side-chains 226 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 167 optimal weight: 0.0770 chunk 124 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 467 GLN A 319 HIS A 848 GLN A 894 GLN D 531 GLN ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.155668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108150 restraints weight = 26860.502| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.91 r_work: 0.3073 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19371 Z= 0.132 Angle : 0.506 7.363 26897 Z= 0.268 Chirality : 0.038 0.155 3102 Planarity : 0.003 0.039 2817 Dihedral : 20.221 179.928 4444 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.94 % Allowed : 10.78 % Favored : 87.28 % 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: -0.62 (0.20), residues: 1809 helix: 1.23 (0.19), residues: 776 sheet: -1.39 (0.29), residues: 281 loop : -1.78 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 60 TYR 0.013 0.001 TYR G 29 PHE 0.015 0.001 PHE H 521 TRP 0.015 0.002 TRP A 496 HIS 0.003 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00303 (19367) covalent geometry : angle 0.50466 (26891) hydrogen bonds : bond 0.04615 ( 795) hydrogen bonds : angle 4.35884 ( 2246) metal coordination : bond 0.00321 ( 4) metal coordination : angle 2.46005 ( 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 264 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5044 (pttt) cc_final: 0.3640 (mttt) REVERT: H 405 GLU cc_start: 0.2524 (pm20) cc_final: 0.2263 (pm20) REVERT: H 406 PHE cc_start: 0.5829 (p90) cc_final: 0.5409 (p90) REVERT: H 466 PHE cc_start: 0.5600 (m-80) cc_final: 0.5213 (m-80) REVERT: H 483 ASN cc_start: 0.1518 (OUTLIER) cc_final: 0.0957 (p0) REVERT: H 497 ASP cc_start: 0.7079 (t70) cc_final: 0.6616 (m-30) REVERT: H 511 TRP cc_start: 0.5888 (m-10) cc_final: 0.4543 (m100) REVERT: H 520 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: H 521 PHE cc_start: 0.7062 (m-80) cc_final: 0.6706 (m-80) REVERT: H 529 LYS cc_start: 0.4389 (mttp) cc_final: 0.3533 (pptt) REVERT: A 235 MET cc_start: 0.8263 (ttm) cc_final: 0.8016 (ttt) REVERT: A 292 GLU cc_start: 0.8422 (mp0) cc_final: 0.7987 (mp0) REVERT: A 357 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7378 (tm-30) REVERT: A 368 ASP cc_start: 0.8470 (t0) cc_final: 0.7979 (t0) REVERT: A 618 ASP cc_start: 0.8428 (p0) cc_final: 0.8186 (p0) REVERT: A 687 MET cc_start: 0.6684 (tpp) cc_final: 0.5756 (mtp) REVERT: A 862 ASN cc_start: 0.7676 (m110) cc_final: 0.7262 (t0) REVERT: D 571 PHE cc_start: 0.5807 (t80) cc_final: 0.5521 (t80) REVERT: D 619 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7630 (t-90) REVERT: D 693 HIS cc_start: 0.8024 (t70) cc_final: 0.6414 (m170) REVERT: E 49 ASN cc_start: 0.6810 (m110) cc_final: 0.6476 (m110) REVERT: E 93 THR cc_start: 0.8613 (p) cc_final: 0.8273 (p) REVERT: E 126 ARG cc_start: 0.7678 (mtt-85) cc_final: 0.7353 (mtt-85) REVERT: F 16 GLU cc_start: 0.8613 (pm20) cc_final: 0.8199 (pm20) REVERT: F 72 GLU cc_start: 0.7666 (tt0) cc_final: 0.7350 (tt0) REVERT: F 98 ASP cc_start: 0.8303 (t70) cc_final: 0.8040 (t0) REVERT: F 120 ASP cc_start: 0.8028 (p0) cc_final: 0.7659 (p0) REVERT: G 2 LYS cc_start: 0.9217 (tttt) cc_final: 0.9003 (ttmt) REVERT: G 38 PHE cc_start: 0.7588 (t80) cc_final: 0.7120 (t80) REVERT: G 121 PHE cc_start: 0.8097 (m-80) cc_final: 0.7810 (m-80) outliers start: 32 outliers final: 22 residues processed: 249 average time/residue: 0.1380 time to fit residues: 52.3440 Evaluate side-chains 233 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 411 ILE 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 809 LEU Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain D residue 619 HIS Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 SER 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 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 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: 0.8980 chunk 13 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 401 HIS ** D 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.155154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107471 restraints weight = 26875.870| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.85 r_work: 0.3069 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19371 Z= 0.147 Angle : 0.514 8.392 26897 Z= 0.272 Chirality : 0.038 0.161 3102 Planarity : 0.003 0.038 2817 Dihedral : 20.167 179.665 4444 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.48 % Allowed : 12.48 % Favored : 85.04 % 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: -0.47 (0.20), residues: 1809 helix: 1.27 (0.19), residues: 794 sheet: -1.30 (0.29), residues: 288 loop : -1.67 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 60 TYR 0.018 0.001 TYR E 167 PHE 0.016 0.001 PHE H 524 TRP 0.016 0.002 TRP A 496 HIS 0.011 0.001 HIS H 401 Details of bonding type rmsd covalent geometry : bond 0.00343 (19367) covalent geometry : angle 0.51336 (26891) hydrogen bonds : bond 0.04686 ( 795) hydrogen bonds : angle 4.30834 ( 2246) metal coordination : bond 0.00282 ( 4) metal coordination : angle 2.05132 ( 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 268 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5098 (pttt) cc_final: 0.3691 (mttt) REVERT: H 406 PHE cc_start: 0.5665 (p90) cc_final: 0.5170 (p90) REVERT: H 490 GLU cc_start: 0.6697 (tp30) cc_final: 0.6458 (tp30) REVERT: H 497 ASP cc_start: 0.7154 (t70) cc_final: 0.6547 (m-30) REVERT: H 521 PHE cc_start: 0.7170 (m-80) cc_final: 0.6956 (m-80) REVERT: H 529 LYS cc_start: 0.4639 (mttp) cc_final: 0.3666 (pptt) REVERT: A 357 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7357 (tm-30) REVERT: A 368 ASP cc_start: 0.8514 (t0) cc_final: 0.7996 (t0) REVERT: A 395 LYS cc_start: 0.8426 (tptm) cc_final: 0.8164 (tttm) REVERT: A 574 ASN cc_start: 0.9084 (t0) cc_final: 0.8830 (t0) REVERT: A 687 MET cc_start: 0.6593 (tpp) cc_final: 0.5676 (mtp) REVERT: A 708 TYR cc_start: 0.7489 (m-10) cc_final: 0.7271 (m-10) REVERT: A 849 LYS cc_start: 0.7967 (ptpp) cc_final: 0.7722 (mttm) REVERT: A 862 ASN cc_start: 0.7731 (m110) cc_final: 0.7272 (t0) REVERT: D 549 LYS cc_start: 0.8998 (ptmt) cc_final: 0.8625 (ptmm) REVERT: D 571 PHE cc_start: 0.5714 (t80) cc_final: 0.5450 (t80) REVERT: D 619 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7680 (t-90) REVERT: D 693 HIS cc_start: 0.8136 (t70) cc_final: 0.6437 (m170) REVERT: E 49 ASN cc_start: 0.6701 (m110) cc_final: 0.6351 (m110) REVERT: E 93 THR cc_start: 0.8601 (p) cc_final: 0.8172 (p) REVERT: E 143 GLN cc_start: 0.8281 (mt0) cc_final: 0.7879 (mm-40) REVERT: F 16 GLU cc_start: 0.8682 (pm20) cc_final: 0.8276 (pm20) REVERT: F 98 ASP cc_start: 0.8253 (t70) cc_final: 0.7993 (t0) REVERT: G 40 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7394 (ttm) REVERT: G 121 PHE cc_start: 0.8171 (m-80) cc_final: 0.7905 (m-80) outliers start: 41 outliers final: 31 residues processed: 249 average time/residue: 0.1341 time to fit residues: 50.8953 Evaluate side-chains 238 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 119 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 310 PHE 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 D residue 619 HIS Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 92 SER 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 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: 0.5980 chunk 92 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 401 HIS D 584 HIS F 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.157115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109954 restraints weight = 26734.213| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.90 r_work: 0.3104 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19371 Z= 0.108 Angle : 0.510 17.497 26897 Z= 0.259 Chirality : 0.037 0.149 3102 Planarity : 0.003 0.039 2817 Dihedral : 20.066 179.265 4444 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.48 % Allowed : 14.35 % Favored : 83.16 % 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: -0.16 (0.20), residues: 1809 helix: 1.55 (0.19), residues: 787 sheet: -1.24 (0.30), residues: 284 loop : -1.47 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 60 TYR 0.020 0.001 TYR E 167 PHE 0.019 0.001 PHE H 524 TRP 0.014 0.001 TRP A 496 HIS 0.008 0.001 HIS H 401 Details of bonding type rmsd covalent geometry : bond 0.00240 (19367) covalent geometry : angle 0.48481 (26891) hydrogen bonds : bond 0.04126 ( 795) hydrogen bonds : angle 4.11058 ( 2246) metal coordination : bond 0.00846 ( 4) metal coordination : angle 10.57685 ( 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 264 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5207 (pttt) cc_final: 0.3825 (mttt) REVERT: H 463 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5345 (ppp) REVERT: H 483 ASN cc_start: 0.1232 (OUTLIER) cc_final: 0.0737 (p0) REVERT: H 497 ASP cc_start: 0.6882 (t70) cc_final: 0.6523 (m-30) REVERT: H 516 PHE cc_start: 0.6509 (t80) cc_final: 0.6305 (t80) REVERT: H 521 PHE cc_start: 0.6998 (m-80) cc_final: 0.6648 (m-80) REVERT: H 526 PHE cc_start: 0.6882 (m-10) cc_final: 0.6540 (m-80) REVERT: A 357 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7348 (tm-30) REVERT: A 368 ASP cc_start: 0.8880 (t0) cc_final: 0.8349 (t0) REVERT: A 395 LYS cc_start: 0.8584 (tptm) cc_final: 0.8157 (tttp) REVERT: A 687 MET cc_start: 0.6599 (tpp) cc_final: 0.5602 (mtp) REVERT: A 849 LYS cc_start: 0.8217 (ptpp) cc_final: 0.7920 (mttm) REVERT: A 862 ASN cc_start: 0.7917 (m110) cc_final: 0.7362 (t0) REVERT: D 536 TYR cc_start: 0.7900 (m-80) cc_final: 0.7620 (m-10) REVERT: D 693 HIS cc_start: 0.8097 (t70) cc_final: 0.6461 (m170) REVERT: E 34 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8845 (pp) REVERT: E 49 ASN cc_start: 0.6644 (m110) cc_final: 0.6242 (m110) REVERT: E 93 THR cc_start: 0.8530 (p) cc_final: 0.8245 (p) REVERT: E 143 GLN cc_start: 0.8483 (mt0) cc_final: 0.8105 (mm-40) REVERT: F 16 GLU cc_start: 0.8756 (pm20) cc_final: 0.8311 (pm20) REVERT: F 90 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: F 98 ASP cc_start: 0.8288 (t70) cc_final: 0.7923 (t0) REVERT: F 110 GLN cc_start: 0.8051 (mp10) cc_final: 0.7844 (mp10) REVERT: G 38 PHE cc_start: 0.7642 (t80) cc_final: 0.7398 (t80) REVERT: G 121 PHE cc_start: 0.8250 (m-80) cc_final: 0.7991 (m-80) outliers start: 41 outliers final: 28 residues processed: 247 average time/residue: 0.1244 time to fit residues: 47.8903 Evaluate side-chains 235 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 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 907 ILE 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 92 SER 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 89 THR Chi-restraints excluded: chain F residue 90 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 122 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 584 HIS ** D 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109719 restraints weight = 26653.275| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.88 r_work: 0.3104 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19371 Z= 0.115 Angle : 0.510 14.469 26897 Z= 0.263 Chirality : 0.037 0.187 3102 Planarity : 0.003 0.039 2817 Dihedral : 20.017 179.411 4444 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.73 % Allowed : 14.90 % 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: -0.02 (0.20), residues: 1809 helix: 1.69 (0.19), residues: 787 sheet: -1.18 (0.29), residues: 290 loop : -1.41 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 60 TYR 0.020 0.001 TYR E 167 PHE 0.020 0.001 PHE H 524 TRP 0.014 0.002 TRP A 496 HIS 0.002 0.001 HIS A 751 Details of bonding type rmsd covalent geometry : bond 0.00260 (19367) covalent geometry : angle 0.49192 (26891) hydrogen bonds : bond 0.04160 ( 795) hydrogen bonds : angle 4.08213 ( 2246) metal coordination : bond 0.00273 ( 4) metal coordination : angle 8.93014 ( 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 253 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5268 (pttt) cc_final: 0.3867 (mttt) REVERT: H 463 MET cc_start: 0.5981 (OUTLIER) cc_final: 0.5413 (ppp) REVERT: H 497 ASP cc_start: 0.6916 (t70) cc_final: 0.6559 (m-30) REVERT: H 516 PHE cc_start: 0.6441 (t80) cc_final: 0.6054 (t80) REVERT: H 521 PHE cc_start: 0.7113 (m-80) cc_final: 0.6812 (m-80) REVERT: H 526 PHE cc_start: 0.6877 (m-10) cc_final: 0.6570 (m-80) REVERT: A 312 GLU cc_start: 0.7774 (tt0) cc_final: 0.7520 (mt-10) REVERT: A 357 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7799 (tm-30) REVERT: A 368 ASP cc_start: 0.8888 (t0) cc_final: 0.8421 (t0) REVERT: A 395 LYS cc_start: 0.8577 (tptm) cc_final: 0.8134 (tttp) REVERT: A 687 MET cc_start: 0.6668 (tpp) cc_final: 0.5678 (mtp) REVERT: A 862 ASN cc_start: 0.7924 (m110) cc_final: 0.7375 (t0) REVERT: D 619 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7849 (t-90) REVERT: D 657 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8741 (p90) REVERT: D 693 HIS cc_start: 0.8177 (t70) cc_final: 0.6456 (m170) REVERT: E 34 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8810 (pp) REVERT: E 49 ASN cc_start: 0.6666 (m110) cc_final: 0.6249 (m110) REVERT: E 93 THR cc_start: 0.8631 (p) cc_final: 0.8298 (p) REVERT: E 143 GLN cc_start: 0.8489 (mt0) cc_final: 0.8103 (mm-40) REVERT: F 16 GLU cc_start: 0.8749 (pm20) cc_final: 0.8284 (pm20) REVERT: F 90 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: F 98 ASP cc_start: 0.8321 (t70) cc_final: 0.7956 (t0) REVERT: F 110 GLN cc_start: 0.8071 (mp10) cc_final: 0.7777 (mp10) REVERT: G 76 ASP cc_start: 0.8590 (p0) cc_final: 0.8360 (p0) REVERT: G 121 PHE cc_start: 0.8264 (m-80) cc_final: 0.8006 (m-80) outliers start: 45 outliers final: 30 residues processed: 234 average time/residue: 0.1249 time to fit residues: 45.5988 Evaluate side-chains 232 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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 851 THR Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain D residue 619 HIS Chi-restraints excluded: chain D residue 657 PHE 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 92 SER 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 90 GLU Chi-restraints excluded: chain F residue 91 PHE 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: 2.9990 chunk 122 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 174 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 GLN ** D 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.153939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.106000 restraints weight = 26730.383| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.87 r_work: 0.3042 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19371 Z= 0.199 Angle : 0.578 13.137 26897 Z= 0.300 Chirality : 0.040 0.159 3102 Planarity : 0.003 0.039 2817 Dihedral : 20.096 178.847 4444 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.73 % Allowed : 15.69 % Favored : 81.59 % 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: 1.41 (0.19), residues: 794 sheet: -1.19 (0.29), residues: 288 loop : -1.47 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 60 TYR 0.030 0.002 TYR D 536 PHE 0.020 0.002 PHE H 524 TRP 0.011 0.002 TRP A 496 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00477 (19367) covalent geometry : angle 0.56431 (26891) hydrogen bonds : bond 0.05269 ( 795) hydrogen bonds : angle 4.30685 ( 2246) metal coordination : bond 0.00312 ( 4) metal coordination : angle 8.34463 ( 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 245 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5285 (pttt) cc_final: 0.3784 (mttt) REVERT: H 463 MET cc_start: 0.5632 (OUTLIER) cc_final: 0.5407 (ppp) REVERT: H 497 ASP cc_start: 0.6993 (t70) cc_final: 0.6623 (m-30) REVERT: H 521 PHE cc_start: 0.7269 (m-80) cc_final: 0.6946 (m-80) REVERT: H 526 PHE cc_start: 0.6975 (m-10) cc_final: 0.6670 (m-80) REVERT: A 357 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 368 ASP cc_start: 0.8618 (t0) cc_final: 0.8137 (t0) REVERT: A 395 LYS cc_start: 0.8431 (tptm) cc_final: 0.8132 (tttm) REVERT: A 687 MET cc_start: 0.6645 (tpp) cc_final: 0.5860 (mtt) REVERT: A 862 ASN cc_start: 0.7693 (m110) cc_final: 0.7268 (t0) REVERT: D 619 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7722 (t-90) REVERT: D 657 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8709 (p90) REVERT: D 693 HIS cc_start: 0.8373 (t70) cc_final: 0.6602 (m-70) REVERT: E 34 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8961 (pp) REVERT: E 49 ASN cc_start: 0.6716 (m110) cc_final: 0.6340 (m110) REVERT: E 143 GLN cc_start: 0.8321 (mt0) cc_final: 0.7921 (mt0) REVERT: F 16 GLU cc_start: 0.8654 (pm20) cc_final: 0.8222 (pm20) REVERT: F 90 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: F 98 ASP cc_start: 0.8350 (t70) cc_final: 0.8032 (t0) REVERT: G 121 PHE cc_start: 0.8333 (m-80) cc_final: 0.8092 (m-80) outliers start: 45 outliers final: 31 residues processed: 226 average time/residue: 0.1278 time to fit residues: 45.0646 Evaluate side-chains 229 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 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 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 907 ILE Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain D residue 619 HIS Chi-restraints excluded: chain D residue 657 PHE 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 90 GLU Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 28 THR 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: 0.0040 chunk 123 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109863 restraints weight = 26681.869| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.88 r_work: 0.3102 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 19371 Z= 0.109 Angle : 0.513 11.083 26897 Z= 0.267 Chirality : 0.037 0.169 3102 Planarity : 0.003 0.043 2817 Dihedral : 19.990 179.208 4444 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.06 % Allowed : 16.66 % Favored : 81.28 % 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: 1.76 (0.19), residues: 789 sheet: -1.03 (0.30), residues: 278 loop : -1.28 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 60 TYR 0.023 0.001 TYR D 536 PHE 0.029 0.001 PHE H 524 TRP 0.014 0.001 TRP A 496 HIS 0.002 0.000 HIS A 751 Details of bonding type rmsd covalent geometry : bond 0.00239 (19367) covalent geometry : angle 0.50014 (26891) hydrogen bonds : bond 0.04014 ( 795) hydrogen bonds : angle 4.10205 ( 2246) metal coordination : bond 0.00130 ( 4) metal coordination : angle 7.60419 ( 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 246 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.5238 (pttt) cc_final: 0.3848 (mttt) REVERT: H 463 MET cc_start: 0.5138 (OUTLIER) cc_final: 0.4885 (ppp) REVERT: H 497 ASP cc_start: 0.7048 (t70) cc_final: 0.6705 (m-30) REVERT: H 521 PHE cc_start: 0.7284 (m-80) cc_final: 0.6760 (m-80) REVERT: H 526 PHE cc_start: 0.6946 (m-10) cc_final: 0.6600 (m-80) REVERT: A 293 TYR cc_start: 0.8177 (t80) cc_final: 0.7926 (t80) REVERT: A 357 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 368 ASP cc_start: 0.8545 (t0) cc_final: 0.8024 (t0) REVERT: A 395 LYS cc_start: 0.8324 (tptm) cc_final: 0.7876 (tttp) REVERT: A 687 MET cc_start: 0.6609 (tpp) cc_final: 0.5822 (mtt) REVERT: A 862 ASN cc_start: 0.7704 (m110) cc_final: 0.7239 (t0) REVERT: D 536 TYR cc_start: 0.7758 (m-10) cc_final: 0.7479 (m-80) REVERT: D 657 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8711 (p90) REVERT: D 693 HIS cc_start: 0.8183 (t70) cc_final: 0.6517 (m170) REVERT: E 34 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8820 (pp) REVERT: E 49 ASN cc_start: 0.6576 (m110) cc_final: 0.6185 (m110) REVERT: E 126 ARG cc_start: 0.7442 (mtt-85) cc_final: 0.7161 (mtt-85) REVERT: E 143 GLN cc_start: 0.8288 (mt0) cc_final: 0.7894 (mm-40) REVERT: F 16 GLU cc_start: 0.8588 (pm20) cc_final: 0.8176 (pm20) REVERT: F 98 ASP cc_start: 0.8200 (t70) cc_final: 0.7843 (t0) REVERT: G 121 PHE cc_start: 0.8263 (m-80) cc_final: 0.8030 (m-80) REVERT: G 147 ASP cc_start: 0.8344 (t0) cc_final: 0.8116 (t0) outliers start: 34 outliers final: 26 residues processed: 229 average time/residue: 0.1182 time to fit residues: 42.5475 Evaluate side-chains 231 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 395 VAL 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 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 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 657 PHE 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 27 ASP Chi-restraints excluded: chain G residue 53 SER 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: 0.2980 chunk 64 optimal weight: 0.3980 chunk 140 optimal weight: 0.0970 chunk 2 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 95 optimal weight: 0.0570 chunk 71 optimal weight: 0.6980 chunk 1 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 GLN A 733 ASN D 580 ASN ** D 584 HIS ** 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 = 0.4008 r_free = 0.4008 target = 0.160871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113372 restraints weight = 26734.804| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.93 r_work: 0.3146 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 19371 Z= 0.098 Angle : 0.500 10.563 26897 Z= 0.262 Chirality : 0.037 0.183 3102 Planarity : 0.003 0.046 2817 Dihedral : 19.836 179.416 4444 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.00 % Allowed : 16.66 % Favored : 81.34 % 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: 0.38 (0.20), residues: 1809 helix: 1.94 (0.19), residues: 789 sheet: -0.86 (0.31), residues: 271 loop : -1.17 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 60 TYR 0.023 0.001 TYR E 167 PHE 0.019 0.001 PHE H 524 TRP 0.012 0.001 TRP A 604 HIS 0.002 0.000 HIS H 482 Details of bonding type rmsd covalent geometry : bond 0.00207 (19367) covalent geometry : angle 0.48968 (26891) hydrogen bonds : bond 0.03587 ( 795) hydrogen bonds : angle 3.98851 ( 2246) metal coordination : bond 0.00103 ( 4) metal coordination : angle 6.90592 ( 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 250 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 382 LYS cc_start: 0.4965 (pttt) cc_final: 0.3710 (mttt) REVERT: H 405 GLU cc_start: 0.2923 (OUTLIER) cc_final: 0.2383 (pp20) REVERT: H 463 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.4877 (ppp) REVERT: H 497 ASP cc_start: 0.7114 (t70) cc_final: 0.6753 (m-30) REVERT: H 521 PHE cc_start: 0.7266 (m-80) cc_final: 0.6466 (m-80) REVERT: H 526 PHE cc_start: 0.6886 (m-10) cc_final: 0.6502 (m-80) REVERT: A 293 TYR cc_start: 0.8166 (t80) cc_final: 0.7948 (t80) REVERT: A 357 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 368 ASP cc_start: 0.8497 (t0) cc_final: 0.7967 (t0) REVERT: A 687 MET cc_start: 0.6631 (tpp) cc_final: 0.5691 (mtp) REVERT: A 862 ASN cc_start: 0.8019 (m110) cc_final: 0.7384 (t0) REVERT: D 549 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7809 (pttt) REVERT: D 586 MET cc_start: 0.7755 (tmm) cc_final: 0.7493 (ttp) REVERT: D 657 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8650 (p90) REVERT: D 693 HIS cc_start: 0.7967 (t70) cc_final: 0.6524 (m170) REVERT: E 34 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8771 (pp) REVERT: E 49 ASN cc_start: 0.6586 (m110) cc_final: 0.6175 (m110) REVERT: E 143 GLN cc_start: 0.8324 (mt0) cc_final: 0.7931 (mm-40) REVERT: F 16 GLU cc_start: 0.8563 (pm20) cc_final: 0.8182 (pm20) REVERT: F 110 GLN cc_start: 0.8335 (mp10) cc_final: 0.8117 (mp10) REVERT: G 26 TYR cc_start: 0.7153 (t80) cc_final: 0.6776 (t80) REVERT: G 121 PHE cc_start: 0.8197 (m-80) cc_final: 0.7972 (m-80) REVERT: G 147 ASP cc_start: 0.8288 (t0) cc_final: 0.8024 (t0) outliers start: 33 outliers final: 20 residues processed: 239 average time/residue: 0.1229 time to fit residues: 45.7658 Evaluate side-chains 224 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 405 GLU 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 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 809 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 657 PHE Chi-restraints excluded: chain E residue 34 LEU 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 27 ASP 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: 0.9990 chunk 10 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 155 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 584 HIS ** 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 = 0.3991 r_free = 0.3991 target = 0.159440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111966 restraints weight = 26542.430| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.92 r_work: 0.3114 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19371 Z= 0.114 Angle : 0.520 10.790 26897 Z= 0.271 Chirality : 0.038 0.188 3102 Planarity : 0.003 0.046 2817 Dihedral : 19.807 179.658 4444 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.39 % Allowed : 17.44 % Favored : 81.16 % 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: 0.39 (0.20), residues: 1809 helix: 1.92 (0.19), residues: 789 sheet: -0.86 (0.31), residues: 278 loop : -1.13 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 60 TYR 0.022 0.001 TYR E 167 PHE 0.045 0.001 PHE H 524 TRP 0.015 0.002 TRP A 496 HIS 0.004 0.001 HIS D 584 Details of bonding type rmsd covalent geometry : bond 0.00258 (19367) covalent geometry : angle 0.51038 (26891) hydrogen bonds : bond 0.03930 ( 795) hydrogen bonds : angle 4.03857 ( 2246) metal coordination : bond 0.00125 ( 4) metal coordination : angle 6.58371 ( 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 226 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: H 382 LYS cc_start: 0.4984 (pttt) cc_final: 0.3660 (mttt) REVERT: H 463 MET cc_start: 0.5562 (OUTLIER) cc_final: 0.5232 (ppp) REVERT: H 467 GLN cc_start: 0.6611 (tm-30) cc_final: 0.5833 (tp40) REVERT: H 497 ASP cc_start: 0.7076 (t70) cc_final: 0.6782 (m-30) REVERT: H 521 PHE cc_start: 0.7219 (m-80) cc_final: 0.6513 (m-80) REVERT: H 526 PHE cc_start: 0.6830 (m-10) cc_final: 0.6287 (m-80) REVERT: A 293 TYR cc_start: 0.8200 (t80) cc_final: 0.7967 (t80) REVERT: A 357 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 368 ASP cc_start: 0.8482 (t0) cc_final: 0.8005 (t0) REVERT: A 687 MET cc_start: 0.6676 (tpp) cc_final: 0.5722 (mtp) REVERT: A 834 LEU cc_start: 0.8957 (mm) cc_final: 0.8669 (mt) REVERT: A 862 ASN cc_start: 0.7805 (m110) cc_final: 0.7293 (t0) REVERT: D 586 MET cc_start: 0.7765 (tmm) cc_final: 0.7505 (ttp) REVERT: D 657 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8629 (p90) REVERT: D 693 HIS cc_start: 0.8074 (t70) cc_final: 0.6514 (m170) REVERT: E 34 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8874 (pp) REVERT: E 49 ASN cc_start: 0.6644 (m110) cc_final: 0.6240 (m110) REVERT: E 143 GLN cc_start: 0.8364 (mt0) cc_final: 0.7958 (mt0) REVERT: F 16 GLU cc_start: 0.8505 (pm20) cc_final: 0.8230 (pm20) REVERT: F 110 GLN cc_start: 0.8297 (mp10) cc_final: 0.8011 (mp10) REVERT: G 26 TYR cc_start: 0.7297 (t80) cc_final: 0.6993 (t80) REVERT: G 121 PHE cc_start: 0.8268 (m-80) cc_final: 0.8052 (m-80) REVERT: G 147 ASP cc_start: 0.8332 (t0) cc_final: 0.8044 (t0) outliers start: 23 outliers final: 20 residues processed: 216 average time/residue: 0.1254 time to fit residues: 42.3333 Evaluate side-chains 221 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 395 VAL 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 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 809 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 887 GLU Chi-restraints excluded: chain D residue 657 PHE Chi-restraints excluded: chain E residue 34 LEU 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 27 ASP 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: 2.9990 chunk 65 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 chunk 116 optimal weight: 2.9990 chunk 175 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 481 ASN A 176 GLN ** D 584 HIS ** 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 = 0.3966 r_free = 0.3966 target = 0.157402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.109702 restraints weight = 26784.662| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.97 r_work: 0.3070 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19371 Z= 0.143 Angle : 0.546 11.281 26897 Z= 0.285 Chirality : 0.039 0.208 3102 Planarity : 0.003 0.045 2817 Dihedral : 19.810 179.914 4444 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.76 % Allowed : 17.14 % Favored : 81.10 % 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: 0.29 (0.20), residues: 1809 helix: 1.81 (0.19), residues: 786 sheet: -0.84 (0.31), residues: 276 loop : -1.16 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 60 TYR 0.023 0.001 TYR E 167 PHE 0.066 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 covalent geometry : bond 0.00335 (19367) covalent geometry : angle 0.53718 (26891) hydrogen bonds : bond 0.04459 ( 795) hydrogen bonds : angle 4.16595 ( 2246) metal coordination : bond 0.00172 ( 4) metal coordination : angle 6.49548 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4183.84 seconds wall clock time: 73 minutes 11.64 seconds (4391.64 seconds total)