Starting phenix.real_space_refine on Sat Sep 12 22:21:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uy6_26865/09_2026/7uy6_26865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uy6_26865/09_2026/7uy6_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_26865/09_2026/7uy6_26865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uy6_26865/09_2026/7uy6_26865.map" model { file = "/net/cci-nas-00/data/ceres_data/7uy6_26865/09_2026/7uy6_26865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uy6_26865/09_2026/7uy6_26865.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7uy6_26865/09_2026/7uy6_26865.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uy6_26865/09_2026/7uy6_26865.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 4, 'ASP:plan': 7, 'GLN:plan1': 3, 'TYR:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8542 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 22, 'TRANS': 989} Chain breaks: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "E" Number of atoms: 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: {'RNAv2': 156} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 24, 'rna3p_pur': 62, 'rna3p_pyr': 57} Link IDs: {'rna2p': 36, 'rna3p': 119} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10290 SG CYS D 555 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: 4.39, per 1000 atoms: 0.23 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: 1.84 Conformation dependent library (CDL) restraints added in 676.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 900 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 572 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 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: 2.11 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: 4.14 Time building geometry restraints manager: 2.38 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=" C1' DT C 51 " pdb=" N1 DT C 51 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.70e+00 bond pdb=" C3' DG C 53 " pdb=" C2' DG C 53 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.40e+00 bond pdb=" C3' DT C 50 " pdb=" C2' DT C 50 " ideal model delta sigma weight residual 1.516 1.532 -0.016 8.00e-03 1.56e+04 4.24e+00 bond pdb=" C3' DG C 55 " pdb=" C2' DG C 55 " ideal model delta sigma weight residual 1.516 1.531 -0.015 8.00e-03 1.56e+04 3.47e+00 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 ... (remaining 19440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 25828 1.27 - 2.53: 673 2.53 - 3.80: 391 3.80 - 5.06: 95 5.06 - 6.33: 15 Bond angle restraints: 27002 Sorted by residual: angle pdb=" N3 DT C 56 " pdb=" C4 DT C 56 " pdb=" O4 DT C 56 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C 57 " pdb=" C4 DT C 57 " pdb=" O4 DT C 57 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 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=" N3 DT C 51 " pdb=" C4 DT C 51 " pdb=" O4 DT C 51 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.62e+01 angle pdb=" N3 DT C 50 " pdb=" C4 DT C 50 " pdb=" O4 DT C 50 " ideal model delta sigma weight residual 119.90 122.28 -2.38 6.00e-01 2.78e+00 1.58e+01 ... (remaining 26997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.09: 10809 34.09 - 68.18: 534 68.18 - 102.27: 68 102.27 - 136.36: 0 136.36 - 170.45: 1 Dihedral angle restraints: 11412 sinusoidal: 5904 harmonic: 5508 Sorted by residual: dihedral pdb=" C4' U B 137 " pdb=" C3' U B 137 " pdb=" C2' U B 137 " pdb=" C1' U B 137 " ideal model delta sinusoidal sigma weight residual 36.34 -37.91 74.25 1 3.10e+00 1.04e-01 7.28e+02 dihedral pdb=" C4' A B 67 " pdb=" C3' A B 67 " pdb=" C2' A B 67 " pdb=" C1' A B 67 " ideal model delta sinusoidal sigma weight residual 36.34 -36.64 72.99 1 3.10e+00 1.04e-01 7.07e+02 dihedral pdb=" C4' A B 58 " pdb=" C3' A B 58 " pdb=" C2' A B 58 " pdb=" C1' A B 58 " ideal model delta sinusoidal sigma weight residual 36.34 -36.49 72.84 1 3.10e+00 1.04e-01 7.04e+02 ... (remaining 11409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2531 0.058 - 0.116: 328 0.116 - 0.174: 21 0.174 - 0.231: 73 0.231 - 0.289: 160 Chirality restraints: 3113 Sorted by residual: chirality pdb=" C2' G B 146 " pdb=" C3' G B 146 " pdb=" O2' G B 146 " pdb=" C1' G B 146 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" P C B 75 " pdb=" OP1 C B 75 " pdb=" OP2 C B 75 " pdb=" O5' C B 75 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' A B 11 " pdb=" C3' A B 11 " pdb=" O2' A B 11 " pdb=" C1' A B 11 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (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: 4.950 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: 0.030 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.480 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19449 Z= 0.142 Angle : 0.637 6.325 27008 Z= 0.312 Chirality : 0.076 0.289 3113 Planarity : 0.003 0.041 2835 Dihedral : 17.835 170.449 7832 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.02 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (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 ARG 0.006 0.000 ARG D 588 TYR 0.015 0.001 TYR A 490 PHE 0.018 0.001 PHE A 924 TRP 0.013 0.001 TRP A 496 HIS 0.003 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (19445) covalent geometry : angle 0.63572 / 0.31 (27002) hydrogen bonds : bond 0.19097 / 13.53 ( 799) hydrogen bonds : angle 6.67151 / 4.70 ( 2292) metal coordination : bond 0.00299 / 0.15 ( 4) metal coordination : angle 2.61945 / 1.30 ( 6) *********************** 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 : 0.706 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: 0.7072 time to fit residues: 208.4925 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 : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 484 ASN H 512 ASN A 55 GLN A 102 ASN A 294 GLN A 734 GLN A 865 HIS D 693 HIS E 169 GLN F 7 GLN F 31 ASN F 110 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.169548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.115795 restraints weight = 24011.284| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.00 r_work: 0.3109 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 19449 Z= 0.192 Angle : 1.214 21.146 27008 Z= 0.496 Chirality : 0.120 1.462 3113 Planarity : 0.004 0.028 2835 Dihedral : 16.074 160.204 3989 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.87 % Allowed : 8.13 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1823 helix: 2.14 (0.19), residues: 800 sheet: 0.29 (0.32), residues: 278 loop : -0.33 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 49 TYR 0.019 0.001 TYR A 490 PHE 0.019 0.001 PHE H 525 TRP 0.014 0.002 TRP A 496 HIS 0.009 0.001 HIS D 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (19445) covalent geometry : angle 1.21320 / 0.50 (27002) hydrogen bonds : bond 0.05719 / 4.07 ( 799) hydrogen bonds : angle 4.63918 / 3.24 ( 2292) metal coordination : bond 0.00721 / 0.36 ( 4) metal coordination : angle 3.25498 / 1.70 ( 6) *********************** 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 228 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.747 Fit side-chains REVERT: H 385 ASN cc_start: 0.4802 (p0) cc_final: 0.4517 (p0) REVERT: H 472 GLN cc_start: 0.4141 (tp40) cc_final: 0.3506 (tm130) REVERT: H 521 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.4570 (m-10) REVERT: A 566 MET cc_start: 0.8176 (tpp) cc_final: 0.7779 (mmp) REVERT: A 589 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7893 (p0) REVERT: A 643 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7723 (t0) REVERT: A 897 GLN cc_start: 0.8271 (mp-120) cc_final: 0.8069 (tm-30) REVERT: D 588 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7305 (mtm-85) REVERT: E 86 MET cc_start: 0.8117 (mmt) cc_final: 0.7884 (mmm) REVERT: E 119 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7465 (tm-30) REVERT: E 169 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7738 (mt0) outliers start: 31 outliers final: 13 residues processed: 211 average time/residue: 0.6703 time to fit residues: 158.5204 Evaluate side-chains 204 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 31 LYS 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 D residue 522 GLN 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 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 Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 81 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 484 ASN A 55 GLN A 865 HIS D 619 HIS D 693 HIS E 40 ASN F 81 ASN F 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.168649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114426 restraints weight = 24018.331| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.00 r_work: 0.3078 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19449 Z= 0.170 Angle : 0.905 20.343 27008 Z= 0.387 Chirality : 0.085 1.373 3113 Planarity : 0.003 0.034 2835 Dihedral : 16.801 170.690 3989 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.29 % Allowed : 10.30 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1823 helix: 2.04 (0.19), residues: 804 sheet: 0.21 (0.30), residues: 283 loop : -0.34 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 49 TYR 0.018 0.002 TYR A 490 PHE 0.014 0.001 PHE A 143 TRP 0.015 0.002 TRP A 496 HIS 0.021 0.002 HIS D 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (19445) covalent geometry : angle 0.90418 / 0.39 (27002) hydrogen bonds : bond 0.05568 / 3.99 ( 799) hydrogen bonds : angle 4.39226 / 3.04 ( 2292) metal coordination : bond 0.00673 / 0.34 ( 4) metal coordination : angle 3.18544 / 1.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 385 ASN cc_start: 0.4544 (OUTLIER) cc_final: 0.4272 (p0) REVERT: H 402 LEU cc_start: 0.6573 (mm) cc_final: 0.6354 (mt) REVERT: H 472 GLN cc_start: 0.4087 (tp40) cc_final: 0.3547 (tm130) REVERT: H 490 GLU cc_start: 0.5741 (tp30) cc_final: 0.5392 (tp30) REVERT: H 521 PHE cc_start: 0.5353 (OUTLIER) cc_final: 0.4649 (m-10) REVERT: A 41 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8280 (mp) REVERT: A 566 MET cc_start: 0.8168 (tpp) cc_final: 0.7794 (mmp) REVERT: A 602 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: A 643 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7789 (t0) REVERT: A 897 GLN cc_start: 0.8351 (mp-120) cc_final: 0.8145 (tm-30) REVERT: D 549 LYS cc_start: 0.8239 (tptp) cc_final: 0.7907 (tptp) REVERT: D 588 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7277 (mtm-85) REVERT: E 86 MET cc_start: 0.8121 (mmt) cc_final: 0.7870 (mmm) REVERT: E 119 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7398 (tm-30) REVERT: E 148 SER cc_start: 0.8663 (p) cc_final: 0.8360 (m) outliers start: 38 outliers final: 15 residues processed: 220 average time/residue: 0.6642 time to fit residues: 163.5175 Evaluate side-chains 213 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 41 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 602 GLU 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 522 GLN 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 178 optimal weight: 0.1980 chunk 169 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 468 ASN H 484 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS A 911 ASN D 693 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.168696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113637 restraints weight = 23966.851| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.06 r_work: 0.3067 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 19449 Z= 0.145 Angle : 0.823 20.486 27008 Z= 0.355 Chirality : 0.075 1.205 3113 Planarity : 0.003 0.030 2835 Dihedral : 16.920 174.744 3989 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.77 % Allowed : 11.75 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1823 helix: 2.13 (0.19), residues: 803 sheet: 0.20 (0.30), residues: 284 loop : -0.38 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 49 TYR 0.017 0.001 TYR A 490 PHE 0.015 0.001 PHE A 143 TRP 0.016 0.002 TRP A 496 HIS 0.021 0.001 HIS D 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (19445) covalent geometry : angle 0.82126 / 0.35 (27002) hydrogen bonds : bond 0.05033 / 3.61 ( 799) hydrogen bonds : angle 4.18209 / 2.90 ( 2292) metal coordination : bond 0.00685 / 0.34 ( 4) metal coordination : angle 3.43203 / 1.83 ( 6) *********************** 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 238 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 192 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 396 VAL cc_start: 0.6666 (OUTLIER) cc_final: 0.6430 (p) REVERT: H 402 LEU cc_start: 0.6594 (mm) cc_final: 0.6072 (mt) REVERT: H 472 GLN cc_start: 0.4204 (tp40) cc_final: 0.3517 (tm130) REVERT: H 479 LEU cc_start: 0.5321 (tt) cc_final: 0.4874 (mt) REVERT: H 490 GLU cc_start: 0.5853 (tp30) cc_final: 0.5500 (tp30) REVERT: H 521 PHE cc_start: 0.5342 (OUTLIER) cc_final: 0.4639 (m-10) REVERT: H 531 GLN cc_start: 0.3368 (mt0) cc_final: 0.3128 (mt0) REVERT: A 41 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 566 MET cc_start: 0.8160 (tpp) cc_final: 0.7824 (mmp) REVERT: A 629 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8070 (mmp) REVERT: A 643 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7898 (t70) REVERT: A 848 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7648 (mp-120) REVERT: D 588 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7830 (mtm-85) REVERT: D 633 ASN cc_start: 0.7335 (m110) cc_final: 0.6786 (OUTLIER) REVERT: D 661 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: E 86 MET cc_start: 0.8137 (mmt) cc_final: 0.7836 (mmm) REVERT: E 105 MET cc_start: 0.5079 (pmm) cc_final: 0.3614 (tpp) REVERT: E 119 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7393 (tm-30) REVERT: E 148 SER cc_start: 0.8599 (p) cc_final: 0.8317 (m) REVERT: F 66 ASN cc_start: 0.7683 (p0) cc_final: 0.7467 (p0) REVERT: G 120 THR cc_start: 0.7905 (t) cc_final: 0.7601 (t) outliers start: 46 outliers final: 21 residues processed: 218 average time/residue: 0.6661 time to fit residues: 162.7175 Evaluate side-chains 216 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 41 LEU 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 578 MET 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 791 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 522 GLN 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 92 SER Chi-restraints excluded: chain E residue 104 LYS 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 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 21 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 95 optimal weight: 0.0870 chunk 111 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 461 GLN H 468 ASN H 484 ASN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 619 HIS D 693 HIS F 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 = 0.4067 r_free = 0.4067 target = 0.168721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113513 restraints weight = 23871.474| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.00 r_work: 0.3078 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19449 Z= 0.141 Angle : 0.776 17.826 27008 Z= 0.337 Chirality : 0.070 1.112 3113 Planarity : 0.003 0.028 2835 Dihedral : 17.008 177.699 3989 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.07 % Allowed : 11.99 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.20), residues: 1823 helix: 2.16 (0.19), residues: 803 sheet: 0.18 (0.30), residues: 280 loop : -0.37 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1058 TYR 0.016 0.001 TYR A 490 PHE 0.021 0.001 PHE H 526 TRP 0.016 0.002 TRP A 496 HIS 0.011 0.001 HIS D 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (19445) covalent geometry : angle 0.77393 / 0.34 (27002) hydrogen bonds : bond 0.04930 / 3.53 ( 799) hydrogen bonds : angle 4.10788 / 2.85 ( 2292) metal coordination : bond 0.00692 / 0.34 ( 4) metal coordination : angle 3.51534 / 1.87 ( 6) *********************** 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 244 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: H 396 VAL cc_start: 0.6610 (OUTLIER) cc_final: 0.6378 (p) REVERT: H 402 LEU cc_start: 0.6735 (mm) cc_final: 0.6196 (mt) REVERT: H 472 GLN cc_start: 0.4075 (tp40) cc_final: 0.3342 (tm130) REVERT: H 479 LEU cc_start: 0.5250 (tt) cc_final: 0.4846 (mt) REVERT: H 490 GLU cc_start: 0.5779 (tp30) cc_final: 0.5449 (tp30) REVERT: H 521 PHE cc_start: 0.5351 (OUTLIER) cc_final: 0.4654 (m-10) REVERT: H 531 GLN cc_start: 0.3279 (mt0) cc_final: 0.2979 (mt0) REVERT: A 31 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8514 (mptt) REVERT: A 41 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8262 (mp) REVERT: A 223 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8337 (tt0) REVERT: A 510 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6980 (pt0) REVERT: A 566 MET cc_start: 0.8202 (tpp) cc_final: 0.7896 (mmp) REVERT: A 629 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8038 (mmp) REVERT: A 643 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7873 (t70) REVERT: A 848 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7763 (mp-120) REVERT: D 588 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7834 (mtm-85) REVERT: D 633 ASN cc_start: 0.7327 (m110) cc_final: 0.6780 (t0) REVERT: D 661 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7706 (mm-30) REVERT: E 34 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8280 (pp) REVERT: E 86 MET cc_start: 0.8099 (mmt) cc_final: 0.7790 (mmm) REVERT: E 119 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7360 (tm-30) REVERT: E 148 SER cc_start: 0.8567 (p) cc_final: 0.8291 (m) REVERT: F 66 ASN cc_start: 0.7694 (p0) cc_final: 0.7474 (p0) REVERT: G 120 THR cc_start: 0.7881 (t) cc_final: 0.7548 (t) outliers start: 51 outliers final: 24 residues processed: 222 average time/residue: 0.6602 time to fit residues: 164.5008 Evaluate side-chains 224 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 31 LYS Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 578 MET 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 791 GLU Chi-restraints excluded: chain A residue 907 ILE 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 522 GLN 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 34 LEU 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 44 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 128 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 158 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS D 693 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.169628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.115060 restraints weight = 23842.666| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.89 r_work: 0.3103 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19449 Z= 0.124 Angle : 0.740 16.110 27008 Z= 0.323 Chirality : 0.067 0.979 3113 Planarity : 0.003 0.030 2835 Dihedral : 17.023 175.409 3989 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.95 % Allowed : 12.95 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1823 helix: 2.20 (0.19), residues: 803 sheet: 0.17 (0.30), residues: 280 loop : -0.37 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 492 TYR 0.020 0.001 TYR A 249 PHE 0.012 0.001 PHE D 657 TRP 0.015 0.002 TRP A 496 HIS 0.006 0.001 HIS D 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19445) covalent geometry : angle 0.73793 / 0.32 (27002) hydrogen bonds : bond 0.04587 / 3.29 ( 799) hydrogen bonds : angle 4.01837 / 2.79 ( 2292) metal coordination : bond 0.00582 / 0.29 ( 4) metal coordination : angle 3.53260 / 1.88 ( 6) *********************** 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 251 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: H 396 VAL cc_start: 0.6682 (OUTLIER) cc_final: 0.6470 (p) REVERT: H 402 LEU cc_start: 0.6748 (mm) cc_final: 0.6289 (mt) REVERT: H 472 GLN cc_start: 0.4065 (tp40) cc_final: 0.3258 (tm130) REVERT: H 479 LEU cc_start: 0.5153 (tt) cc_final: 0.4765 (mt) REVERT: H 490 GLU cc_start: 0.5764 (tp30) cc_final: 0.5435 (tp30) REVERT: H 521 PHE cc_start: 0.5355 (OUTLIER) cc_final: 0.4653 (m-10) REVERT: H 531 GLN cc_start: 0.3443 (mt0) cc_final: 0.3195 (mt0) REVERT: A 31 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8488 (mptt) REVERT: A 566 MET cc_start: 0.8282 (tpp) cc_final: 0.7998 (mmt) REVERT: A 602 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: A 629 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8047 (mmp) REVERT: A 643 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7912 (t70) REVERT: A 662 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.6082 (mm-40) REVERT: A 848 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7913 (mp-120) REVERT: A 991 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8233 (t0) REVERT: D 588 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7829 (mtm180) REVERT: D 633 ASN cc_start: 0.7333 (m110) cc_final: 0.6759 (t0) REVERT: D 661 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: E 34 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8305 (pp) REVERT: E 86 MET cc_start: 0.8077 (mmt) cc_final: 0.7616 (mmp) REVERT: E 105 MET cc_start: 0.5038 (pmm) cc_final: 0.3437 (tpp) REVERT: E 119 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7339 (tm-30) REVERT: E 148 SER cc_start: 0.8548 (p) cc_final: 0.8300 (m) REVERT: F 66 ASN cc_start: 0.7652 (p0) cc_final: 0.7417 (p0) REVERT: G 120 THR cc_start: 0.7877 (t) cc_final: 0.7543 (t) outliers start: 49 outliers final: 25 residues processed: 232 average time/residue: 0.6583 time to fit residues: 171.4041 Evaluate side-chains 229 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 396 VAL 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 578 MET Chi-restraints excluded: chain A residue 602 GLU 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 662 GLN Chi-restraints excluded: chain A residue 791 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 522 GLN 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 34 LEU Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 104 LYS 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 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 93 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS A1048 ASN 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 = 0.4081 r_free = 0.4081 target = 0.169916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114564 restraints weight = 24002.984| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.02 r_work: 0.3084 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 0.056 19449 Z= 0.124 Angle : 0.727 15.284 27008 Z= 0.321 Chirality : 0.065 0.886 3113 Planarity : 0.003 0.047 2835 Dihedral : 16.962 171.546 3989 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.41 % Allowed : 14.34 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1823 helix: 2.29 (0.19), residues: 796 sheet: 0.10 (0.30), residues: 291 loop : -0.33 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 49 TYR 0.014 0.001 TYR A 490 PHE 0.024 0.001 PHE H 526 TRP 0.015 0.002 TRP A 496 HIS 0.004 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (19445) covalent geometry : angle 0.72499 / 0.32 (27002) hydrogen bonds : bond 0.04489 / 3.21 ( 799) hydrogen bonds : angle 3.96726 / 2.76 ( 2292) metal coordination : bond 0.00561 / 0.28 ( 4) metal coordination : angle 3.64363 / 1.93 ( 6) *********************** 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 236 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 196 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: H 396 VAL cc_start: 0.6664 (OUTLIER) cc_final: 0.6457 (p) REVERT: H 402 LEU cc_start: 0.6691 (mm) cc_final: 0.6298 (mt) REVERT: H 472 GLN cc_start: 0.3975 (tp40) cc_final: 0.3151 (tm130) REVERT: H 479 LEU cc_start: 0.5031 (tt) cc_final: 0.4676 (mt) REVERT: H 490 GLU cc_start: 0.5803 (tp30) cc_final: 0.5458 (tp30) REVERT: H 521 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.4612 (m-10) REVERT: A 31 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8431 (mptt) REVERT: A 566 MET cc_start: 0.8315 (tpp) cc_final: 0.8044 (mmp) REVERT: A 602 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: A 629 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8096 (mmp) REVERT: A 643 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7971 (t70) REVERT: A 662 GLN cc_start: 0.6776 (mm-40) cc_final: 0.6120 (mm-40) REVERT: A 848 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7932 (mp-120) REVERT: A 991 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8239 (t0) REVERT: D 588 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7887 (mtm-85) REVERT: D 633 ASN cc_start: 0.7375 (m110) cc_final: 0.6787 (t0) REVERT: D 661 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7714 (mm-30) REVERT: E 34 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8305 (pp) REVERT: E 86 MET cc_start: 0.8091 (mmt) cc_final: 0.7628 (mmp) REVERT: E 119 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7335 (tm-30) REVERT: E 148 SER cc_start: 0.8544 (p) cc_final: 0.8305 (m) REVERT: F 66 ASN cc_start: 0.7678 (p0) cc_final: 0.7419 (p0) REVERT: G 120 THR cc_start: 0.7893 (t) cc_final: 0.7580 (t) outliers start: 40 outliers final: 24 residues processed: 218 average time/residue: 0.6507 time to fit residues: 159.2993 Evaluate side-chains 225 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 602 GLU 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 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 522 GLN 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 92 SER 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 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 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 24 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 102 optimal weight: 0.0470 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.169409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113320 restraints weight = 23903.155| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.04 r_work: 0.3074 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19449 Z= 0.134 Angle : 0.724 13.219 27008 Z= 0.322 Chirality : 0.063 0.715 3113 Planarity : 0.003 0.031 2835 Dihedral : 16.967 173.691 3989 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.65 % Allowed : 14.58 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1823 helix: 2.23 (0.19), residues: 790 sheet: 0.11 (0.30), residues: 280 loop : -0.38 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 49 TYR 0.021 0.001 TYR A 249 PHE 0.022 0.001 PHE H 525 TRP 0.015 0.002 TRP A 496 HIS 0.005 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (19445) covalent geometry : angle 0.72135 / 0.32 (27002) hydrogen bonds : bond 0.04649 / 3.33 ( 799) hydrogen bonds : angle 3.99386 / 2.78 ( 2292) metal coordination : bond 0.00598 / 0.30 ( 4) metal coordination : angle 3.82961 / 2.03 ( 6) *********************** 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 243 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: H 396 VAL cc_start: 0.6741 (OUTLIER) cc_final: 0.6532 (p) REVERT: H 402 LEU cc_start: 0.6695 (mm) cc_final: 0.6317 (mt) REVERT: H 472 GLN cc_start: 0.4048 (tp40) cc_final: 0.3148 (tm130) REVERT: H 479 LEU cc_start: 0.5158 (tt) cc_final: 0.4805 (mt) REVERT: H 490 GLU cc_start: 0.5811 (tp30) cc_final: 0.5451 (tp30) REVERT: H 521 PHE cc_start: 0.5369 (OUTLIER) cc_final: 0.4684 (m-10) REVERT: H 528 LYS cc_start: 0.2879 (mtpp) cc_final: 0.2590 (mttt) REVERT: A 31 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8413 (mptt) REVERT: A 223 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: A 566 MET cc_start: 0.8301 (tpp) cc_final: 0.8030 (mmp) REVERT: A 602 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7843 (tt0) REVERT: A 629 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8087 (mmp) REVERT: A 643 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7967 (t70) REVERT: A 662 GLN cc_start: 0.6667 (mm-40) cc_final: 0.5975 (mm-40) REVERT: A 848 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7955 (mp-120) REVERT: A 859 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7385 (pm20) REVERT: A 991 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8252 (t0) REVERT: D 588 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7879 (mtm180) REVERT: D 633 ASN cc_start: 0.7312 (m110) cc_final: 0.6702 (t0) REVERT: D 661 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: D 693 HIS cc_start: 0.7936 (t-90) cc_final: 0.7717 (t-170) REVERT: E 86 MET cc_start: 0.8091 (mmt) cc_final: 0.7561 (mmp) REVERT: E 105 MET cc_start: 0.4950 (pmm) cc_final: 0.3263 (tpp) REVERT: E 108 GLU cc_start: 0.6305 (pm20) cc_final: 0.5909 (pm20) REVERT: E 119 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7431 (tm-30) REVERT: E 148 SER cc_start: 0.8554 (p) cc_final: 0.8306 (m) REVERT: F 66 ASN cc_start: 0.7715 (p0) cc_final: 0.7486 (p0) REVERT: G 120 THR cc_start: 0.7956 (t) cc_final: 0.7648 (t) outliers start: 44 outliers final: 26 residues processed: 224 average time/residue: 0.6593 time to fit residues: 166.1355 Evaluate side-chains 231 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 602 GLU 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 522 GLN Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain E residue 92 SER 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 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 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 122 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 482 HIS A 865 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114271 restraints weight = 23887.557| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.06 r_work: 0.3086 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19449 Z= 0.132 Angle : 0.715 13.141 27008 Z= 0.321 Chirality : 0.062 0.652 3113 Planarity : 0.003 0.035 2835 Dihedral : 16.984 176.643 3989 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.47 % Allowed : 14.70 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.20), residues: 1823 helix: 2.20 (0.19), residues: 789 sheet: 0.20 (0.31), residues: 272 loop : -0.40 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 49 TYR 0.014 0.001 TYR A 490 PHE 0.025 0.001 PHE H 526 TRP 0.015 0.002 TRP A 496 HIS 0.004 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (19445) covalent geometry : angle 0.71312 / 0.32 (27002) hydrogen bonds : bond 0.04597 / 3.30 ( 799) hydrogen bonds : angle 3.99934 / 2.79 ( 2292) metal coordination : bond 0.00581 / 0.29 ( 4) metal coordination : angle 3.87858 / 2.05 ( 6) *********************** 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 234 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.712 Fit side-chains REVERT: H 396 VAL cc_start: 0.6844 (OUTLIER) cc_final: 0.6642 (p) REVERT: H 402 LEU cc_start: 0.6714 (mm) cc_final: 0.6336 (mt) REVERT: H 472 GLN cc_start: 0.4170 (tp40) cc_final: 0.3204 (tm130) REVERT: H 479 LEU cc_start: 0.5133 (tt) cc_final: 0.4778 (mt) REVERT: H 490 GLU cc_start: 0.5786 (tp30) cc_final: 0.5447 (tp30) REVERT: H 521 PHE cc_start: 0.5377 (OUTLIER) cc_final: 0.4672 (m-10) REVERT: H 528 LYS cc_start: 0.2682 (mtpp) cc_final: 0.2340 (mttt) REVERT: A 31 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8399 (mptt) REVERT: A 41 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 566 MET cc_start: 0.8269 (tpp) cc_final: 0.7994 (mmt) REVERT: A 602 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: A 629 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8046 (mmp) REVERT: A 643 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.7950 (t70) REVERT: A 662 GLN cc_start: 0.6622 (mm-40) cc_final: 0.5931 (mm-40) REVERT: A 848 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7961 (mp-120) REVERT: A 991 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8235 (t0) REVERT: D 588 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7929 (mtm-85) REVERT: D 633 ASN cc_start: 0.7330 (m110) cc_final: 0.6697 (t0) REVERT: D 661 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7676 (mm-30) REVERT: D 693 HIS cc_start: 0.7900 (t-90) cc_final: 0.7672 (t-170) REVERT: E 86 MET cc_start: 0.8074 (mmt) cc_final: 0.7559 (mmp) REVERT: E 108 GLU cc_start: 0.6440 (pm20) cc_final: 0.6025 (pm20) REVERT: E 119 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7430 (tm-30) REVERT: E 148 SER cc_start: 0.8539 (p) cc_final: 0.8287 (m) REVERT: F 66 ASN cc_start: 0.7714 (p0) cc_final: 0.7463 (p0) REVERT: G 120 THR cc_start: 0.7837 (t) cc_final: 0.7550 (t) outliers start: 41 outliers final: 26 residues processed: 217 average time/residue: 0.6478 time to fit residues: 158.3594 Evaluate side-chains 226 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 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 428 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 602 GLU 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 522 GLN Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain E residue 92 SER 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 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 Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 301 GLN A 440 GLN A 444 GLN A 865 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 = 0.4063 r_free = 0.4063 target = 0.168580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112762 restraints weight = 23816.587| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.04 r_work: 0.3057 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19449 Z= 0.153 Angle : 0.732 13.374 27008 Z= 0.330 Chirality : 0.063 0.660 3113 Planarity : 0.003 0.030 2835 Dihedral : 17.016 178.951 3989 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 2.35 % Allowed : 14.94 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1823 helix: 2.15 (0.19), residues: 789 sheet: 0.27 (0.32), residues: 259 loop : -0.45 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 49 TYR 0.021 0.002 TYR A 249 PHE 0.017 0.001 PHE H 525 TRP 0.015 0.002 TRP A 496 HIS 0.004 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (19445) covalent geometry : angle 0.72901 / 0.33 (27002) hydrogen bonds : bond 0.05001 / 3.59 ( 799) hydrogen bonds : angle 4.06827 / 2.83 ( 2292) metal coordination : bond 0.00686 / 0.34 ( 4) metal coordination : angle 4.17923 / 2.22 ( 6) ********************** 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 234 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: H 402 LEU cc_start: 0.6714 (mm) cc_final: 0.6358 (mt) REVERT: H 472 GLN cc_start: 0.4025 (tp40) cc_final: 0.3032 (tm130) REVERT: H 479 LEU cc_start: 0.5143 (tt) cc_final: 0.4797 (mt) REVERT: H 490 GLU cc_start: 0.5792 (tp30) cc_final: 0.5441 (tp30) REVERT: H 521 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.4673 (m-10) REVERT: H 528 LYS cc_start: 0.2392 (mtpp) cc_final: 0.1993 (mttt) REVERT: H 531 GLN cc_start: 0.3415 (mt0) cc_final: 0.2928 (mp10) REVERT: A 31 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8432 (mptt) REVERT: A 403 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: A 566 MET cc_start: 0.8316 (tpp) cc_final: 0.8044 (mmt) REVERT: A 629 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8055 (mmp) REVERT: A 643 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7994 (t70) REVERT: A 662 GLN cc_start: 0.6658 (mm-40) cc_final: 0.5958 (mm-40) REVERT: A 848 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7986 (mp-120) REVERT: A 859 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7384 (pm20) REVERT: A 991 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8342 (t0) REVERT: D 588 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7943 (mtm-85) REVERT: D 661 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: E 86 MET cc_start: 0.8083 (mmt) cc_final: 0.7586 (mmp) REVERT: E 105 MET cc_start: 0.5168 (pmm) cc_final: 0.3248 (tpp) REVERT: E 119 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7457 (tm-30) REVERT: E 148 SER cc_start: 0.8585 (p) cc_final: 0.8310 (m) REVERT: F 66 ASN cc_start: 0.7733 (p0) cc_final: 0.7492 (p0) REVERT: F 72 GLU cc_start: 0.8467 (pt0) cc_final: 0.8145 (pp20) outliers start: 39 outliers final: 25 residues processed: 217 average time/residue: 0.6288 time to fit residues: 153.3483 Evaluate side-chains 225 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 521 PHE Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 428 VAL 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 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 522 GLN Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 661 GLU Chi-restraints excluded: chain E residue 92 SER 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 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 Chi-restraints excluded: chain G residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 196 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 467 GLN ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 865 HIS F 81 ASN F 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.167980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112417 restraints weight = 23916.446| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.08 r_work: 0.3050 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 19449 Z= 0.156 Angle : 0.732 13.318 27008 Z= 0.332 Chirality : 0.063 0.643 3113 Planarity : 0.003 0.031 2835 Dihedral : 17.046 179.263 3989 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 2.23 % Allowed : 15.18 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1823 helix: 2.09 (0.19), residues: 789 sheet: 0.22 (0.32), residues: 259 loop : -0.49 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 49 TYR 0.014 0.002 TYR A 490 PHE 0.019 0.002 PHE H 525 TRP 0.016 0.002 TRP A 496 HIS 0.004 0.001 HIS A 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (19445) covalent geometry : angle 0.72930 / 0.33 (27002) hydrogen bonds : bond 0.05069 / 3.65 ( 799) hydrogen bonds : angle 4.12001 / 2.87 ( 2292) metal coordination : bond 0.00705 / 0.35 ( 4) metal coordination : angle 4.33325 / 2.29 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7710.21 seconds wall clock time: 131 minutes 54.47 seconds (7914.47 seconds total)