Starting phenix.real_space_refine on Mon Jun 16 16:13:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uy6_26865/06_2025/7uy6_26865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uy6_26865/06_2025/7uy6_26865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uy6_26865/06_2025/7uy6_26865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uy6_26865/06_2025/7uy6_26865.map" model { file = "/net/cci-nas-00/data/ceres_data/7uy6_26865/06_2025/7uy6_26865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uy6_26865/06_2025/7uy6_26865.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 170 5.49 5 S 65 5.16 5 C 11367 2.51 5 N 3166 2.21 5 O 3977 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18746 Number of models: 1 Model: "" Number of chains: 9 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1367 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8542 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 22, 'TRANS': 989} Chain breaks: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "E" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1195 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 952 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1542 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 1, 'TRANS': 182} Chain: "B" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3293 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 24, 'rna3p_pur': 62, 'rna3p_pyr': 57} Link IDs: {'rna2p': 36, 'rna3p': 119} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10290 SG CYS D 555 76.519 71.540 85.390 1.00102.65 S ATOM 10303 SG CYS D 557 74.797 69.232 87.751 1.00107.36 S ATOM 10423 SG CYS D 572 72.846 70.796 84.821 1.00101.57 S ATOM 10444 SG CYS D 575 73.748 72.898 87.764 1.00108.23 S Time building chain proxies: 12.03, per 1000 atoms: 0.64 Number of scatterers: 18746 At special positions: 0 Unit cell: (151.8, 158.4, 115.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 65 16.00 P 170 15.00 O 3977 8.00 N 3166 7.00 C 11367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 4.65 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 900 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 572 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 557 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 555 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 575 " Number of angles added : 6 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 16 sheets defined 49.4% alpha, 21.4% beta 28 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 7.65 Creating SS restraints... Processing helix chain 'H' and resid 115 through 130 Processing helix chain 'H' and resid 131 through 139 removed outlier: 3.836A pdb=" N HIS H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'H' and resid 157 through 161 removed outlier: 3.560A pdb=" N LYS H 160 " --> pdb=" O VAL H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 Processing helix chain 'H' and resid 203 through 216 removed outlier: 4.323A pdb=" N GLU H 216 " --> pdb=" O ASP H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 391 through 400 removed outlier: 3.620A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 403 No H-bonds generated for 'chain 'H' and resid 401 through 403' Processing helix chain 'H' and resid 469 through 480 removed outlier: 4.093A pdb=" N ARG H 473 " --> pdb=" O SER H 469 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN H 477 " --> pdb=" O ARG H 473 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS H 478 " --> pdb=" O LEU H 474 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU H 480 " --> pdb=" O ILE H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 531 Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.533A pdb=" N GLY A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.503A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 144 through 155 removed outlier: 4.292A pdb=" N TYR A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.634A pdb=" N PHE A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.877A pdb=" N SER A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.508A pdb=" N ARG A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.616A pdb=" N ASN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.809A pdb=" N LYS A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 425 through 426 No H-bonds generated for 'chain 'A' and resid 425 through 426' Processing helix chain 'A' and resid 427 through 431 Processing helix chain 'A' and resid 444 through 467 removed outlier: 3.540A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.920A pdb=" N GLU A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 553 through 557 removed outlier: 3.964A pdb=" N ASN A 556 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 557 " --> pdb=" O GLN A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 557' Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 565 through 579 removed outlier: 3.701A pdb=" N ASP A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N MET A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.880A pdb=" N ILE A 626 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.735A pdb=" N LYS A 717 " --> pdb=" O GLN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 793 removed outlier: 3.608A pdb=" N LEU A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 804 removed outlier: 4.092A pdb=" N LYS A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLN A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.520A pdb=" N GLN A 901 " --> pdb=" O GLN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 911 through 926 Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.687A pdb=" N MET A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 966 through 967 No H-bonds generated for 'chain 'A' and resid 966 through 967' Processing helix chain 'A' and resid 968 through 971 removed outlier: 3.641A pdb=" N LYS A 971 " --> pdb=" O ASP A 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 968 through 971' Processing helix chain 'A' and resid 972 through 980 removed outlier: 4.543A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1009 Processing helix chain 'A' and resid 1014 through 1038 Processing helix chain 'A' and resid 1045 through 1075 removed outlier: 3.959A pdb=" N LYS A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A1050 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1094 Processing helix chain 'A' and resid 1103 through 1108 Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 603 through 615 Processing helix chain 'D' and resid 621 through 634 removed outlier: 4.583A pdb=" N GLN D 625 " --> pdb=" O GLN D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 679 through 697 removed outlier: 4.320A pdb=" N GLU D 683 " --> pdb=" O ASN D 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 110 through 123 removed outlier: 3.540A pdb=" N TYR E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 175 removed outlier: 4.140A pdb=" N SER E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 22 removed outlier: 3.519A pdb=" N MET F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 Processing helix chain 'F' and resid 114 through 119 removed outlier: 3.836A pdb=" N PHE F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.774A pdb=" N LYS G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 removed outlier: 3.623A pdb=" N ILE G 41 " --> pdb=" O LYS G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 removed outlier: 4.037A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 94 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 157 removed outlier: 3.606A pdb=" N LYS G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 184 Processing sheet with id=AA1, first strand: chain 'H' and resid 220 through 221 removed outlier: 3.779A pdb=" N LYS H 230 " --> pdb=" O LYS H 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 406 through 411 removed outlier: 4.085A pdb=" N LYS H 382 " --> pdb=" O ILE H 499 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.747A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ALA A 170 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.747A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ALA A 170 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 115 Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.776A pdb=" N GLY A 531 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 808 through 813 removed outlier: 3.554A pdb=" N LEU A 617 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASP A 618 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS A 849 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 850 " --> pdb=" O SER A 869 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 874 through 876 Processing sheet with id=AB1, first strand: chain 'D' and resid 532 through 545 removed outlier: 5.617A pdb=" N LEU D 541 " --> pdb=" O GLN D 592 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN D 592 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER D 543 " --> pdb=" O PHE D 590 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE D 590 " --> pdb=" O SER D 543 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG D 588 " --> pdb=" O GLN D 545 " (cutoff:3.500A) removed outlier: 13.501A pdb=" N THR D 597 " --> pdb=" O ILE D 668 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N TYR D 670 " --> pdb=" O THR D 597 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL D 672 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET D 601 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LYS D 674 " --> pdb=" O MET D 601 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLU D 654 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE D 675 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE D 652 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 649 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 533 " --> pdb=" O PHE D 657 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 551 through 554 removed outlier: 3.588A pdb=" N GLN D 582 " --> pdb=" O ARG D 554 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 562 through 564 removed outlier: 3.897A pdb=" N PHE D 571 " --> pdb=" O LEU D 563 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 66 through 76 removed outlier: 4.257A pdb=" N MET E 86 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 98 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE E 142 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLN E 101 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N TYR E 146 " --> pdb=" O GLN E 101 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR E 146 " --> pdb=" O MET E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 87 through 91 removed outlier: 3.809A pdb=" N GLU F 72 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N VAL F 83 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 55 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU F 41 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL F 26 " --> pdb=" O GLY F 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 71 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 46 through 51 removed outlier: 7.144A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER G 103 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE G 58 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN G 73 " --> pdb=" O GLN G 63 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N HIS G 65 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 71 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 46 through 51 removed outlier: 7.144A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N SER G 103 " --> pdb=" O ASP G 134 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP G 134 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL G 105 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS G 132 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 107 " --> pdb=" O MET G 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN G 109 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 21.376A pdb=" N LYS G 80 " --> pdb=" O PHE G 121 " (cutoff:3.500A) removed outlier: 16.095A pdb=" N ILE G 123 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N ILE G 82 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU G 125 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) 754 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 8.90 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4358 1.33 - 1.45: 4756 1.45 - 1.57: 9896 1.57 - 1.69: 338 1.69 - 1.81: 97 Bond restraints: 19445 Sorted by residual: bond pdb=" C THR A 814 " pdb=" O THR A 814 " ideal model delta sigma weight residual 1.243 1.226 0.017 9.50e-03 1.11e+04 3.38e+00 bond pdb=" CG1 ILE A 376 " pdb=" CD1 ILE A 376 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.77e+00 bond pdb=" CA THR A 814 " pdb=" CB THR A 814 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.53e-02 4.27e+03 1.28e+00 bond pdb=" CA ILE A1104 " pdb=" CB ILE A1104 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.05e+00 bond pdb=" CB PRO E 28 " pdb=" CG PRO E 28 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.18e-01 ... (remaining 19440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 26472 1.27 - 2.53: 434 2.53 - 3.80: 60 3.80 - 5.06: 23 5.06 - 6.33: 13 Bond angle restraints: 27002 Sorted by residual: angle pdb=" CA THR A 814 " pdb=" C THR A 814 " pdb=" N ASP A 815 " ideal model delta sigma weight residual 119.98 116.56 3.42 8.50e-01 1.38e+00 1.62e+01 angle pdb=" N ASP A 816 " pdb=" CA ASP A 816 " pdb=" C ASP A 816 " ideal model delta sigma weight residual 109.24 114.57 -5.33 1.63e+00 3.76e-01 1.07e+01 angle pdb=" N LEU A 813 " pdb=" CA LEU A 813 " pdb=" C LEU A 813 " ideal model delta sigma weight residual 108.52 103.45 5.07 1.63e+00 3.76e-01 9.66e+00 angle pdb=" C THR A 814 " pdb=" CA THR A 814 " pdb=" CB THR A 814 " ideal model delta sigma weight residual 117.23 113.42 3.81 1.36e+00 5.41e-01 7.83e+00 angle pdb=" C TRP A 876 " pdb=" N ILE A 877 " pdb=" CA ILE A 877 " ideal model delta sigma weight residual 121.97 126.43 -4.46 1.80e+00 3.09e-01 6.14e+00 ... (remaining 26997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.72: 11318 35.72 - 71.44: 487 71.44 - 107.16: 61 107.16 - 142.88: 0 142.88 - 178.60: 8 Dihedral angle restraints: 11874 sinusoidal: 6366 harmonic: 5508 Sorted by residual: dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 200.00 21.40 178.60 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C B 43 " pdb=" C1' C B 43 " pdb=" N1 C B 43 " pdb=" C2 C B 43 " ideal model delta sinusoidal sigma weight residual 200.00 39.35 160.65 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" O4' U B 158 " pdb=" C1' U B 158 " pdb=" N1 U B 158 " pdb=" C2 U B 158 " ideal model delta sinusoidal sigma weight residual -128.00 50.10 -178.10 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2484 0.041 - 0.082: 475 0.082 - 0.123: 142 0.123 - 0.164: 9 0.164 - 0.205: 3 Chirality restraints: 3113 Sorted by residual: chirality pdb=" CG LEU A 920 " pdb=" CB LEU A 920 " pdb=" CD1 LEU A 920 " pdb=" CD2 LEU A 920 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU A 813 " pdb=" N LEU A 813 " pdb=" C LEU A 813 " pdb=" CB LEU A 813 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA THR A 814 " pdb=" N THR A 814 " pdb=" C THR A 814 " pdb=" CB THR A 814 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 3110 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1104 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A1105 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A1105 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1105 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 588 " -0.092 9.50e-02 1.11e+02 4.14e-02 1.18e+00 pdb=" NE ARG D 588 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG D 588 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG D 588 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 588 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 924 " -0.008 2.00e-02 2.50e+03 7.74e-03 1.05e+00 pdb=" CG PHE A 924 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE A 924 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 924 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 924 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 924 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 924 " -0.002 2.00e-02 2.50e+03 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2114 2.75 - 3.29: 17264 3.29 - 3.83: 30683 3.83 - 4.36: 36344 4.36 - 4.90: 60190 Nonbonded interactions: 146595 Sorted by model distance: nonbonded pdb=" OH TYR A1061 " pdb=" O2' G B 61 " model vdw 2.215 3.040 nonbonded pdb=" O GLN A 228 " pdb=" NH1 ARG A 473 " model vdw 2.245 3.120 nonbonded pdb=" O2' U B 41 " pdb=" OP1 C B 43 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLN A1008 " pdb=" OH TYR A1025 " model vdw 2.272 3.040 nonbonded pdb=" OE1 GLN A 417 " pdb=" OH TYR A 422 " model vdw 2.283 3.040 ... (remaining 146590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 55.990 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19449 Z= 0.103 Angle : 0.444 6.325 27008 Z= 0.243 Chirality : 0.036 0.205 3113 Planarity : 0.003 0.041 2835 Dihedral : 18.325 178.601 8294 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.06 % Allowed : 0.30 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1823 helix: 2.06 (0.19), residues: 790 sheet: 0.07 (0.31), residues: 287 loop : -0.24 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 496 HIS 0.003 0.001 HIS A 482 PHE 0.018 0.001 PHE A 924 TYR 0.015 0.001 TYR A 490 ARG 0.006 0.000 ARG D 588 Details of bonding type rmsd hydrogen bonds : bond 0.19097 ( 799) hydrogen bonds : angle 6.67151 ( 2292) metal coordination : bond 0.00299 ( 4) metal coordination : angle 2.61945 ( 6) covalent geometry : bond 0.00215 (19445) covalent geometry : angle 0.44253 (27002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 1.941 Fit side-chains revert: symmetry clash REVERT: H 472 GLN cc_start: 0.3963 (tp40) cc_final: 0.3237 (tm130) REVERT: A 689 ASN cc_start: 0.7768 (m-40) cc_final: 0.7475 (p0) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 1.4871 time to fit residues: 437.5758 Evaluate side-chains 191 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 154 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 484 ASN H 512 ASN A 55 GLN A 102 ASN A 294 GLN A 734 GLN A 865 HIS D 619 HIS D 693 HIS E 169 GLN F 7 GLN F 31 ASN F 110 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.168459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113513 restraints weight = 23856.977| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.05 r_work: 0.3074 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 19449 Z= 0.131 Angle : 0.516 6.432 27008 Z= 0.278 Chirality : 0.038 0.153 3113 Planarity : 0.003 0.030 2835 Dihedral : 19.253 178.798 4451 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.87 % Allowed : 8.92 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1823 helix: 2.15 (0.19), residues: 801 sheet: 0.23 (0.32), residues: 278 loop : -0.31 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 496 HIS 0.009 0.001 HIS D 693 PHE 0.015 0.001 PHE H 525 TYR 0.019 0.001 TYR A 490 ARG 0.008 0.000 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.05422 ( 799) hydrogen bonds : angle 4.47896 ( 2292) metal coordination : bond 0.00525 ( 4) metal coordination : angle 3.29041 ( 6) covalent geometry : bond 0.00292 (19445) covalent geometry : angle 0.51397 (27002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 2.103 Fit side-chains REVERT: H 385 ASN cc_start: 0.4811 (p0) cc_final: 0.4534 (p0) REVERT: H 472 GLN cc_start: 0.4126 (tp40) cc_final: 0.3507 (tm130) REVERT: H 490 GLU cc_start: 0.5433 (tp30) cc_final: 0.5198 (tp30) REVERT: H 521 PHE cc_start: 0.5051 (OUTLIER) cc_final: 0.4365 (m-10) REVERT: A 566 MET cc_start: 0.8170 (tpp) cc_final: 0.7805 (mmp) REVERT: A 589 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7894 (p0) REVERT: A 643 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7792 (t0) REVERT: A 897 GLN cc_start: 0.8326 (mp-120) cc_final: 0.8095 (tm-30) REVERT: D 588 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7813 (mtm180) REVERT: E 86 MET cc_start: 0.8100 (mmt) cc_final: 0.7837 (mmm) REVERT: E 119 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7475 (tm-30) REVERT: E 148 SER cc_start: 0.8602 (p) cc_final: 0.8345 (m) REVERT: E 169 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7758 (mt0) outliers start: 31 outliers final: 12 residues processed: 218 average time/residue: 1.4195 time to fit residues: 346.6635 Evaluate side-chains 211 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 109 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 158 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 156 optimal weight: 0.0020 chunk 113 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 179 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 461 GLN H 467 GLN H 484 ASN A 55 GLN A 865 HIS D 619 HIS D 693 HIS F 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.169133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115063 restraints weight = 23937.756| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.08 r_work: 0.3085 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 19449 Z= 0.108 Angle : 0.482 7.081 27008 Z= 0.259 Chirality : 0.037 0.150 3113 Planarity : 0.003 0.025 2835 Dihedral : 19.204 179.557 4451 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.17 % Allowed : 10.72 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1823 helix: 2.23 (0.19), residues: 801 sheet: 0.15 (0.30), residues: 288 loop : -0.32 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 496 HIS 0.006 0.001 HIS D 693 PHE 0.017 0.001 PHE H 526 TYR 0.018 0.001 TYR A 490 ARG 0.006 0.000 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 799) hydrogen bonds : angle 4.12780 ( 2292) metal coordination : bond 0.00592 ( 4) metal coordination : angle 3.30512 ( 6) covalent geometry : bond 0.00234 (19445) covalent geometry : angle 0.47924 (27002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 385 ASN cc_start: 0.4662 (OUTLIER) cc_final: 0.4417 (p0) REVERT: H 396 VAL cc_start: 0.6609 (OUTLIER) cc_final: 0.6401 (p) REVERT: H 472 GLN cc_start: 0.4274 (tp40) cc_final: 0.3640 (tm130) REVERT: H 490 GLU cc_start: 0.5605 (tp30) cc_final: 0.5292 (tp30) REVERT: H 521 PHE cc_start: 0.5198 (OUTLIER) cc_final: 0.4556 (m-10) REVERT: A 566 MET cc_start: 0.8244 (tpp) cc_final: 0.7931 (mmp) REVERT: A 643 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7889 (t70) REVERT: A 848 GLN cc_start: 0.7878 (mm-40) cc_final: 0.7557 (mp-120) REVERT: D 588 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7812 (mtm-85) REVERT: D 661 GLU cc_start: 0.8039 (tt0) cc_final: 0.7575 (mm-30) REVERT: E 86 MET cc_start: 0.8116 (mmt) cc_final: 0.7802 (mmm) REVERT: E 119 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7327 (tm-30) REVERT: G 120 THR cc_start: 0.7889 (t) cc_final: 0.7576 (t) outliers start: 36 outliers final: 12 residues processed: 221 average time/residue: 1.3486 time to fit residues: 334.5261 Evaluate side-chains 207 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 385 ASN Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 791 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 104 LYS Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 163 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 188 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 467 GLN H 468 ASN H 484 ASN A 55 GLN A 865 HIS D 619 HIS D 693 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.168847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113514 restraints weight = 24008.216| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.02 r_work: 0.3078 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 19449 Z= 0.112 Angle : 0.481 9.032 27008 Z= 0.258 Chirality : 0.037 0.149 3113 Planarity : 0.003 0.025 2835 Dihedral : 19.183 179.102 4451 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.83 % Allowed : 11.63 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1823 helix: 2.26 (0.19), residues: 802 sheet: 0.14 (0.30), residues: 290 loop : -0.31 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 496 HIS 0.009 0.001 HIS D 693 PHE 0.011 0.001 PHE G 85 TYR 0.021 0.001 TYR A 249 ARG 0.003 0.000 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 799) hydrogen bonds : angle 4.00073 ( 2292) metal coordination : bond 0.00589 ( 4) metal coordination : angle 3.59581 ( 6) covalent geometry : bond 0.00248 (19445) covalent geometry : angle 0.47826 (27002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 1.858 Fit side-chains revert: symmetry clash REVERT: H 396 VAL cc_start: 0.6677 (OUTLIER) cc_final: 0.6467 (p) REVERT: H 472 GLN cc_start: 0.4225 (tp40) cc_final: 0.3573 (tm130) REVERT: H 490 GLU cc_start: 0.5325 (tp30) cc_final: 0.5074 (tp30) REVERT: H 521 PHE cc_start: 0.5187 (OUTLIER) cc_final: 0.4469 (m-10) REVERT: A 41 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8315 (mp) REVERT: A 589 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7819 (p0) REVERT: A 643 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7897 (t70) REVERT: A 848 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7902 (mp-120) REVERT: A 859 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7443 (pm20) REVERT: D 588 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7843 (mtm180) REVERT: D 633 ASN cc_start: 0.7262 (m110) cc_final: 0.6739 (t0) REVERT: D 661 GLU cc_start: 0.8015 (tt0) cc_final: 0.7649 (mm-30) REVERT: E 86 MET cc_start: 0.8123 (mmt) cc_final: 0.7631 (mmp) REVERT: E 108 GLU cc_start: 0.6030 (pm20) cc_final: 0.5820 (pm20) REVERT: E 119 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7410 (tm-30) REVERT: G 120 THR cc_start: 0.7910 (t) cc_final: 0.7547 (t) outliers start: 47 outliers final: 17 residues processed: 224 average time/residue: 1.4304 time to fit residues: 358.2693 Evaluate side-chains 211 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 87 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 86 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 155 optimal weight: 0.0770 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 619 HIS D 693 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.168576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114025 restraints weight = 24121.556| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.06 r_work: 0.3075 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19449 Z= 0.116 Angle : 0.483 7.514 27008 Z= 0.259 Chirality : 0.037 0.150 3113 Planarity : 0.003 0.039 2835 Dihedral : 19.181 178.825 4451 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.01 % Allowed : 12.29 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1823 helix: 2.25 (0.19), residues: 804 sheet: 0.12 (0.30), residues: 295 loop : -0.34 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 496 HIS 0.013 0.001 HIS D 693 PHE 0.018 0.001 PHE H 526 TYR 0.016 0.001 TYR A 490 ARG 0.008 0.000 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 799) hydrogen bonds : angle 3.97112 ( 2292) metal coordination : bond 0.00605 ( 4) metal coordination : angle 3.65275 ( 6) covalent geometry : bond 0.00262 (19445) covalent geometry : angle 0.48030 (27002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 2.051 Fit side-chains revert: symmetry clash REVERT: H 396 VAL cc_start: 0.6633 (OUTLIER) cc_final: 0.6425 (p) REVERT: H 402 LEU cc_start: 0.6655 (mm) cc_final: 0.6024 (mt) REVERT: H 471 GLU cc_start: 0.5356 (OUTLIER) cc_final: 0.4229 (mt-10) REVERT: H 472 GLN cc_start: 0.4140 (tp40) cc_final: 0.3447 (tm130) REVERT: H 479 LEU cc_start: 0.5166 (tt) cc_final: 0.4803 (mt) REVERT: H 490 GLU cc_start: 0.5239 (tp30) cc_final: 0.4965 (tp30) REVERT: H 521 PHE cc_start: 0.5221 (OUTLIER) cc_final: 0.4514 (m-10) REVERT: A 31 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8537 (mptt) REVERT: A 566 MET cc_start: 0.8348 (tpp) cc_final: 0.8077 (mmt) REVERT: A 589 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7824 (p0) REVERT: A 629 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8060 (mmp) REVERT: A 643 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7911 (t70) REVERT: A 848 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7950 (mp-120) REVERT: A 859 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7382 (pm20) REVERT: A 991 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8252 (t0) REVERT: D 588 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7903 (mtm-85) REVERT: D 633 ASN cc_start: 0.7173 (m110) cc_final: 0.6603 (t0) REVERT: D 661 GLU cc_start: 0.8069 (tt0) cc_final: 0.7706 (mm-30) REVERT: E 34 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8336 (pp) REVERT: E 86 MET cc_start: 0.8113 (mmt) cc_final: 0.7619 (mmp) REVERT: E 108 GLU cc_start: 0.6202 (pm20) cc_final: 0.5966 (pm20) REVERT: E 119 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7365 (tm-30) REVERT: G 120 THR cc_start: 0.7893 (t) cc_final: 0.7532 (t) outliers start: 50 outliers final: 20 residues processed: 227 average time/residue: 1.2925 time to fit residues: 329.9302 Evaluate side-chains 219 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 396 VAL Chi-restraints excluded: chain H residue 471 GLU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 74 optimal weight: 0.8980 chunk 178 optimal weight: 0.0970 chunk 137 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 chunk 130 optimal weight: 0.0270 chunk 187 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 619 HIS D 693 HIS F 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.113987 restraints weight = 24158.880| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.04 r_work: 0.3082 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 19449 Z= 0.112 Angle : 0.480 8.121 27008 Z= 0.258 Chirality : 0.037 0.150 3113 Planarity : 0.003 0.031 2835 Dihedral : 19.174 178.818 4451 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.25 % Allowed : 13.01 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1823 helix: 2.28 (0.19), residues: 802 sheet: 0.12 (0.30), residues: 294 loop : -0.35 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 496 HIS 0.014 0.001 HIS D 693 PHE 0.011 0.001 PHE G 85 TYR 0.023 0.001 TYR A 249 ARG 0.008 0.000 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 799) hydrogen bonds : angle 3.95319 ( 2292) metal coordination : bond 0.00557 ( 4) metal coordination : angle 3.67472 ( 6) covalent geometry : bond 0.00250 (19445) covalent geometry : angle 0.47688 (27002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 1.873 Fit side-chains revert: symmetry clash REVERT: H 402 LEU cc_start: 0.6565 (mm) cc_final: 0.6073 (mt) REVERT: H 472 GLN cc_start: 0.4165 (tp40) cc_final: 0.3409 (tm130) REVERT: H 479 LEU cc_start: 0.5263 (tt) cc_final: 0.4915 (mt) REVERT: H 490 GLU cc_start: 0.5276 (tp30) cc_final: 0.4977 (tp30) REVERT: H 521 PHE cc_start: 0.5233 (OUTLIER) cc_final: 0.4509 (m-10) REVERT: A 31 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8482 (mptt) REVERT: A 218 GLN cc_start: 0.8147 (pm20) cc_final: 0.7433 (pt0) REVERT: A 589 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7832 (p0) REVERT: A 629 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8047 (mmp) REVERT: A 643 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7896 (t70) REVERT: A 848 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7972 (mp-120) REVERT: A 859 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7377 (pm20) REVERT: A 991 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8247 (t0) REVERT: D 588 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7838 (mtm-85) REVERT: D 633 ASN cc_start: 0.7240 (m110) cc_final: 0.6637 (t0) REVERT: D 661 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7700 (mm-30) REVERT: E 34 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8293 (pp) REVERT: E 86 MET cc_start: 0.8115 (mmt) cc_final: 0.7609 (mmp) REVERT: E 88 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7592 (tmtm) REVERT: E 108 GLU cc_start: 0.6190 (pm20) cc_final: 0.5937 (pm20) REVERT: E 119 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7319 (tm-30) REVERT: F 73 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7399 (mt) REVERT: G 120 THR cc_start: 0.7877 (t) cc_final: 0.7518 (t) outliers start: 54 outliers final: 20 residues processed: 229 average time/residue: 1.3317 time to fit residues: 344.6728 Evaluate side-chains 224 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 12 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 188 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 10 optimal weight: 0.0570 chunk 76 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 482 HIS A 865 HIS D 619 HIS D 693 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114647 restraints weight = 23894.927| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.04 r_work: 0.3082 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 19449 Z= 0.105 Angle : 0.473 8.318 27008 Z= 0.254 Chirality : 0.036 0.150 3113 Planarity : 0.003 0.028 2835 Dihedral : 19.150 179.356 4451 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.83 % Allowed : 13.73 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1823 helix: 2.33 (0.19), residues: 801 sheet: 0.23 (0.31), residues: 268 loop : -0.32 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 496 HIS 0.009 0.001 HIS D 693 PHE 0.022 0.001 PHE H 526 TYR 0.015 0.001 TYR A 490 ARG 0.007 0.000 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 799) hydrogen bonds : angle 3.90492 ( 2292) metal coordination : bond 0.00485 ( 4) metal coordination : angle 3.76859 ( 6) covalent geometry : bond 0.00231 (19445) covalent geometry : angle 0.46977 (27002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 2.116 Fit side-chains revert: symmetry clash REVERT: H 402 LEU cc_start: 0.6547 (mm) cc_final: 0.6036 (mt) REVERT: H 471 GLU cc_start: 0.5330 (OUTLIER) cc_final: 0.4485 (mt-10) REVERT: H 472 GLN cc_start: 0.4155 (tp40) cc_final: 0.3332 (tm130) REVERT: H 479 LEU cc_start: 0.5227 (tt) cc_final: 0.4882 (mt) REVERT: H 490 GLU cc_start: 0.5423 (tp30) cc_final: 0.5180 (tp30) REVERT: H 521 PHE cc_start: 0.5239 (OUTLIER) cc_final: 0.4497 (m-10) REVERT: A 31 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8454 (mptt) REVERT: A 589 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7793 (p0) REVERT: A 629 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8057 (mmp) REVERT: A 643 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7938 (t70) REVERT: A 848 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8029 (mp-120) REVERT: A 859 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7374 (pm20) REVERT: A 920 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 991 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8210 (t0) REVERT: D 588 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7925 (mtm-85) REVERT: D 633 ASN cc_start: 0.7271 (m110) cc_final: 0.6631 (t0) REVERT: D 661 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7702 (mm-30) REVERT: E 29 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: E 86 MET cc_start: 0.8121 (mmt) cc_final: 0.7523 (mmp) REVERT: E 88 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7633 (tmtm) REVERT: E 97 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: E 105 MET cc_start: 0.4919 (pmm) cc_final: 0.3401 (tpt) REVERT: E 108 GLU cc_start: 0.6253 (pm20) cc_final: 0.5917 (pm20) REVERT: E 119 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7290 (tm-30) REVERT: G 87 ASP cc_start: 0.8528 (p0) cc_final: 0.8187 (p0) REVERT: G 120 THR cc_start: 0.7838 (t) cc_final: 0.7470 (t) REVERT: G 153 LYS cc_start: 0.8584 (pttm) cc_final: 0.8356 (pttp) outliers start: 47 outliers final: 19 residues processed: 228 average time/residue: 1.3429 time to fit residues: 344.6787 Evaluate side-chains 224 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 383 ILE Chi-restraints excluded: chain H residue 471 GLU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 88 LYS Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 461 GLN ** H 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 494 GLN A 55 GLN A 440 GLN A 444 GLN A 865 HIS D 693 HIS F 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.166738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111731 restraints weight = 23898.822| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.04 r_work: 0.3042 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 19449 Z= 0.169 Angle : 0.543 8.384 27008 Z= 0.290 Chirality : 0.039 0.156 3113 Planarity : 0.003 0.031 2835 Dihedral : 19.240 177.666 4451 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.89 % Allowed : 14.16 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1823 helix: 2.07 (0.19), residues: 797 sheet: 0.17 (0.31), residues: 266 loop : -0.40 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 496 HIS 0.029 0.002 HIS D 693 PHE 0.016 0.002 PHE A 784 TYR 0.023 0.002 TYR A 249 ARG 0.006 0.001 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.05260 ( 799) hydrogen bonds : angle 4.11619 ( 2292) metal coordination : bond 0.00775 ( 4) metal coordination : angle 4.43761 ( 6) covalent geometry : bond 0.00401 (19445) covalent geometry : angle 0.53857 (27002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 193 time to evaluate : 2.005 Fit side-chains revert: symmetry clash REVERT: H 402 LEU cc_start: 0.6574 (mm) cc_final: 0.6154 (mt) REVERT: H 471 GLU cc_start: 0.5204 (OUTLIER) cc_final: 0.4647 (mt-10) REVERT: H 472 GLN cc_start: 0.4166 (tp40) cc_final: 0.3232 (tm130) REVERT: H 479 LEU cc_start: 0.5276 (tt) cc_final: 0.4937 (mt) REVERT: H 490 GLU cc_start: 0.5301 (tp30) cc_final: 0.4951 (tp30) REVERT: H 521 PHE cc_start: 0.5291 (OUTLIER) cc_final: 0.4529 (m-10) REVERT: H 531 GLN cc_start: 0.3400 (mt0) cc_final: 0.2874 (mp10) REVERT: A 31 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8479 (mptt) REVERT: A 41 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8337 (mp) REVERT: A 629 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8019 (mmp) REVERT: A 643 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7968 (t70) REVERT: A 848 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8008 (mp-120) REVERT: A 859 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7346 (pm20) REVERT: A 991 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8337 (t0) REVERT: D 588 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7985 (mtm-85) REVERT: D 661 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: D 664 ASN cc_start: 0.7083 (t0) cc_final: 0.6862 (t160) REVERT: E 29 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6402 (tm-30) REVERT: E 86 MET cc_start: 0.8138 (mmt) cc_final: 0.7603 (mmp) REVERT: E 97 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: E 108 GLU cc_start: 0.6388 (pm20) cc_final: 0.6145 (pm20) REVERT: E 119 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7335 (tm-30) outliers start: 48 outliers final: 21 residues processed: 219 average time/residue: 1.3020 time to fit residues: 320.9012 Evaluate side-chains 222 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 471 GLU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 157 optimal weight: 0.0770 chunk 177 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 82 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 461 GLN ** H 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 840 ASN A 865 HIS D 619 HIS D 693 HIS F 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.168703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114090 restraints weight = 24029.531| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.05 r_work: 0.3084 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 19449 Z= 0.108 Angle : 0.497 8.805 27008 Z= 0.267 Chirality : 0.037 0.151 3113 Planarity : 0.003 0.027 2835 Dihedral : 19.170 178.462 4451 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.29 % Allowed : 15.06 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1823 helix: 2.18 (0.19), residues: 801 sheet: 0.19 (0.31), residues: 276 loop : -0.39 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 496 HIS 0.004 0.001 HIS A 865 PHE 0.026 0.001 PHE H 526 TYR 0.015 0.001 TYR A 490 ARG 0.007 0.000 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 799) hydrogen bonds : angle 3.93355 ( 2292) metal coordination : bond 0.00500 ( 4) metal coordination : angle 4.03656 ( 6) covalent geometry : bond 0.00238 (19445) covalent geometry : angle 0.49379 (27002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 3.064 Fit side-chains REVERT: H 396 VAL cc_start: 0.6734 (t) cc_final: 0.6525 (p) REVERT: H 402 LEU cc_start: 0.6470 (mm) cc_final: 0.5968 (mt) REVERT: H 471 GLU cc_start: 0.5272 (OUTLIER) cc_final: 0.4792 (mt-10) REVERT: H 472 GLN cc_start: 0.4159 (tp40) cc_final: 0.3246 (tm130) REVERT: H 479 LEU cc_start: 0.5176 (tt) cc_final: 0.4848 (mt) REVERT: H 494 GLN cc_start: 0.3198 (pp30) cc_final: 0.2973 (pp30) REVERT: H 521 PHE cc_start: 0.5344 (OUTLIER) cc_final: 0.4568 (m-10) REVERT: A 31 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8462 (mptt) REVERT: A 308 LEU cc_start: 0.8425 (tp) cc_final: 0.8219 (mt) REVERT: A 566 MET cc_start: 0.8270 (tpp) cc_final: 0.8010 (mmt) REVERT: A 629 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8022 (mmp) REVERT: A 643 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7969 (t70) REVERT: A 859 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7375 (pm20) REVERT: A 920 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8561 (tt) REVERT: A 991 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8236 (t0) REVERT: D 588 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7906 (mtm-85) REVERT: D 633 ASN cc_start: 0.7356 (m110) cc_final: 0.6630 (t0) REVERT: E 86 MET cc_start: 0.8161 (mmt) cc_final: 0.7609 (mmp) REVERT: E 93 THR cc_start: 0.8748 (p) cc_final: 0.8529 (t) REVERT: E 97 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: E 105 MET cc_start: 0.5149 (pmm) cc_final: 0.3205 (tpp) REVERT: E 119 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7305 (tm-30) REVERT: F 72 GLU cc_start: 0.8349 (pt0) cc_final: 0.8100 (pp20) REVERT: F 73 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7385 (mt) REVERT: G 87 ASP cc_start: 0.8522 (p0) cc_final: 0.8178 (p0) REVERT: G 120 THR cc_start: 0.7777 (t) cc_final: 0.7430 (t) outliers start: 38 outliers final: 20 residues processed: 214 average time/residue: 1.7806 time to fit residues: 436.1378 Evaluate side-chains 221 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 471 GLU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 93 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 484 ASN A 55 GLN A 865 HIS D 664 ASN D 693 HIS F 110 GLN G 150 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.168126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113053 restraints weight = 23946.668| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.99 r_work: 0.3075 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19449 Z= 0.121 Angle : 0.512 8.669 27008 Z= 0.274 Chirality : 0.037 0.150 3113 Planarity : 0.003 0.026 2835 Dihedral : 19.172 178.270 4451 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 2.23 % Allowed : 15.30 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1823 helix: 2.17 (0.19), residues: 796 sheet: 0.19 (0.31), residues: 276 loop : -0.44 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 496 HIS 0.019 0.001 HIS D 693 PHE 0.016 0.001 PHE H 525 TYR 0.024 0.001 TYR A 249 ARG 0.006 0.000 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 799) hydrogen bonds : angle 3.96897 ( 2292) metal coordination : bond 0.00562 ( 4) metal coordination : angle 4.14514 ( 6) covalent geometry : bond 0.00275 (19445) covalent geometry : angle 0.50825 (27002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 1.953 Fit side-chains REVERT: H 396 VAL cc_start: 0.6703 (t) cc_final: 0.6493 (p) REVERT: H 402 LEU cc_start: 0.6465 (mm) cc_final: 0.5967 (mt) REVERT: H 471 GLU cc_start: 0.5271 (OUTLIER) cc_final: 0.4805 (mt-10) REVERT: H 472 GLN cc_start: 0.4161 (tp40) cc_final: 0.3252 (tm130) REVERT: H 479 LEU cc_start: 0.5188 (tt) cc_final: 0.4853 (mt) REVERT: H 494 GLN cc_start: 0.3341 (pp30) cc_final: 0.3042 (pp30) REVERT: H 521 PHE cc_start: 0.5360 (OUTLIER) cc_final: 0.4576 (m-10) REVERT: H 531 GLN cc_start: 0.3615 (mt0) cc_final: 0.3124 (mp10) REVERT: A 31 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8472 (mptt) REVERT: A 308 LEU cc_start: 0.8452 (tp) cc_final: 0.8230 (mt) REVERT: A 629 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8025 (mmp) REVERT: A 643 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8005 (t70) REVERT: A 859 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7372 (pm20) REVERT: A 991 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8252 (t0) REVERT: D 588 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7922 (mtm-85) REVERT: D 633 ASN cc_start: 0.7385 (m110) cc_final: 0.6640 (t0) REVERT: E 29 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.6483 (tm-30) REVERT: E 86 MET cc_start: 0.8166 (mmt) cc_final: 0.7627 (mmp) REVERT: E 93 THR cc_start: 0.8754 (p) cc_final: 0.8522 (t) REVERT: E 97 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: E 105 MET cc_start: 0.5117 (pmm) cc_final: 0.3315 (tpp) REVERT: E 119 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7256 (tm-30) REVERT: F 72 GLU cc_start: 0.8334 (pt0) cc_final: 0.8043 (pp20) REVERT: F 73 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7374 (mt) REVERT: G 120 THR cc_start: 0.7795 (t) cc_final: 0.7454 (t) outliers start: 37 outliers final: 24 residues processed: 204 average time/residue: 1.3115 time to fit residues: 302.0030 Evaluate side-chains 220 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 471 GLU Chi-restraints excluded: chain H residue 490 GLU Chi-restraints excluded: chain H residue 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 687 MET Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 693 HIS Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 44 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 184 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 chunk 146 optimal weight: 0.0000 chunk 85 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 75 optimal weight: 0.0870 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 865 HIS D 664 ASN D 693 HIS F 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.170164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.115908 restraints weight = 24118.382| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.02 r_work: 0.3108 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19449 Z= 0.097 Angle : 0.480 8.668 27008 Z= 0.257 Chirality : 0.036 0.147 3113 Planarity : 0.003 0.027 2835 Dihedral : 19.123 179.690 4451 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 1.63 % Allowed : 15.96 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1823 helix: 2.28 (0.19), residues: 807 sheet: 0.11 (0.30), residues: 287 loop : -0.33 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 496 HIS 0.018 0.001 HIS D 693 PHE 0.030 0.001 PHE H 526 TYR 0.014 0.001 TYR A 490 ARG 0.007 0.000 ARG G 49 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 799) hydrogen bonds : angle 3.84589 ( 2292) metal coordination : bond 0.00349 ( 4) metal coordination : angle 3.73562 ( 6) covalent geometry : bond 0.00203 (19445) covalent geometry : angle 0.47729 (27002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16289.40 seconds wall clock time: 280 minutes 48.65 seconds (16848.65 seconds total)