Starting phenix.real_space_refine on Sat Sep 12 21:34:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lmb_23439/09_2026/7lmb_23439.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lmb_23439/09_2026/7lmb_23439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lmb_23439/09_2026/7lmb_23439.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lmb_23439/09_2026/7lmb_23439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lmb_23439/09_2026/7lmb_23439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lmb_23439/09_2026/7lmb_23439.map" model { file = "/net/cci-nas-00/data/ceres_data/7lmb_23439/09_2026/7lmb_23439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lmb_23439/09_2026/7lmb_23439.cif" } resolution = 3.8 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 162 5.49 5 S 65 5.16 5 C 11247 2.51 5 N 3115 2.21 5 O 3908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 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: 18498 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3189 Classifications: {'RNAv2': 151} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 18, 'rna3p_pur': 64, 'rna3p_pyr': 60} Link IDs: {'rna2p': 26, 'rna3p': 124} Chain breaks: 1 Chain: "C" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain breaks: 1 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1367 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 7, 'GLN:plan1': 3, 'TYR:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8542 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 22, 'TRANS': 989} Chain breaks: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "E" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1188 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 4, 'TRANS': 142} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 885 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 Chain: "G" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1542 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 1, 'TRANS': 182} Chain: "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 13842 SG CYS D 572 72.985 72.349 83.189 1.00 61.65 S ATOM 13863 SG CYS D 575 74.480 73.378 86.248 1.00 63.38 S Time building chain proxies: 3.46, per 1000 atoms: 0.19 Number of scatterers: 18498 At special positions: 0 Unit cell: (148.24, 160.48, 118.32, 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 162 15.00 O 3908 8.00 N 3115 7.00 C 11247 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: 1.54 Conformation dependent library (CDL) restraints added in 536.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 900 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 575 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 572 " 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3562 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 19 sheets defined 47.3% alpha, 16.7% beta 43 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'H' and resid 115 through 131 removed outlier: 3.784A pdb=" N CYS H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 138 removed outlier: 4.021A pdb=" N HIS H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 147 Processing helix chain 'H' and resid 155 through 160 removed outlier: 3.700A pdb=" N LEU H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 155 through 160' Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.530A pdb=" N GLN H 166 " --> pdb=" O ASN H 162 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE H 167 " --> pdb=" O LYS H 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 162 through 167' Processing helix chain 'H' and resid 203 through 215 Processing helix chain 'H' and resid 391 through 401 removed outlier: 4.185A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 480 removed outlier: 4.828A pdb=" N GLN H 477 " --> pdb=" O ARG H 473 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS H 478 " --> pdb=" O LEU H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 531 Processing helix chain 'A' and resid 19 through 26 removed outlier: 3.890A pdb=" N VAL A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 134 through 144 Processing helix chain 'A' and resid 144 through 155 removed outlier: 4.645A pdb=" N TYR A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.878A pdb=" N GLN A 228 " --> pdb=" O GLN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.562A pdb=" N ARG A 304 " --> pdb=" O CYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.845A pdb=" N PHE A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 356 through 368 Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.160A pdb=" N ASN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.573A pdb=" N PHE A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 3.676A pdb=" N TYR A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 467 removed outlier: 3.640A pdb=" N TYR A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 4.689A 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 508 removed outlier: 3.532A pdb=" N GLU A 508 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 560 through 577 removed outlier: 5.556A pdb=" N ASP A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 removed outlier: 3.676A pdb=" N ILE A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 794 removed outlier: 4.080A pdb=" N SER A 783 " --> pdb=" O GLY A 779 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 804 removed outlier: 4.253A pdb=" N LYS A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N GLN A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 removed outlier: 3.579A pdb=" N ALA A 827 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 removed outlier: 3.794A pdb=" N GLN A 848 " --> pdb=" O PHE A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 Processing helix chain 'A' and resid 911 through 926 removed outlier: 3.987A pdb=" N LYS A 917 " --> pdb=" O LYS A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.648A pdb=" N MET A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 972 through 980 removed outlier: 4.736A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1009 removed outlier: 4.013A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A1009 " --> pdb=" O CYS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1038 removed outlier: 3.754A pdb=" N LYS A1018 " --> pdb=" O ASN A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1075 removed outlier: 3.894A pdb=" N LEU A1050 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1094 removed outlier: 3.846A pdb=" N ASN A1094 " --> pdb=" O PHE A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 4.354A pdb=" N THR A1102 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1109 removed outlier: 4.342A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 526 removed outlier: 3.793A pdb=" N ILE D 520 " --> pdb=" O SER D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 615 Processing helix chain 'D' and resid 622 through 634 removed outlier: 3.561A pdb=" N GLY D 634 " --> pdb=" O CYS D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 679 through 696 removed outlier: 3.667A pdb=" N LYS D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 110 through 123 removed outlier: 4.205A pdb=" N TYR E 116 " --> pdb=" O PHE E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 175 removed outlier: 3.871A pdb=" N SER E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLY E 173 " --> pdb=" O GLN E 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 22 removed outlier: 3.874A pdb=" N ALA F 19 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG F 22 " --> pdb=" O MET F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 114 through 119 removed outlier: 3.902A pdb=" N PHE F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 114 through 119' Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 9 through 29 removed outlier: 4.032A pdb=" N LYS G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 87 through 94 removed outlier: 3.952A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 156 removed outlier: 3.516A pdb=" N ILE G 155 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 161 Processing helix chain 'G' and resid 162 through 184 Processing sheet with id=AA1, first strand: chain 'H' and resid 153 through 154 Processing sheet with id=AA2, first strand: chain 'H' and resid 407 through 411 Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.724A pdb=" N ALA A 170 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 159 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 168 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 10.239A 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 34 removed outlier: 3.724A pdb=" N ALA A 170 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 159 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A 168 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN A 733 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N ALA A 170 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 112 through 115 Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA7, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AA8, first strand: chain 'A' and resid 532 through 535 Processing sheet with id=AA9, first strand: chain 'A' and resid 613 through 615 Processing sheet with id=AB1, first strand: chain 'D' and resid 532 through 537 removed outlier: 6.398A pdb=" N ILE D 652 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE D 675 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU D 654 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 669 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR D 670 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D 541 " --> pdb=" O ALA D 649 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 649 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AB3, first strand: chain 'D' and resid 661 through 662 Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 33 Processing sheet with id=AB5, first strand: chain 'E' and resid 31 through 33 removed outlier: 5.886A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL E 98 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE E 85 " --> pdb=" O ILE E 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 58 through 59 removed outlier: 3.800A pdb=" N PHE E 64 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.809A pdb=" N HIS F 53 " --> pdb=" O PHE F 45 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS F 24 " --> pdb=" O VAL F 77 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.866A pdb=" N ILE G 114 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG G 49 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR G 112 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER G 51 " --> pdb=" O TRP G 110 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TRP G 110 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 15.980A pdb=" N LYS G 80 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 13.061A pdb=" N LEU G 125 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N ILE G 82 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ILE G 127 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN G 84 " --> pdb=" O ILE G 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.866A pdb=" N ILE G 114 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG G 49 " --> pdb=" O TYR G 112 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR G 112 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER G 51 " --> pdb=" O TRP G 110 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TRP G 110 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 15.980A pdb=" N LYS G 80 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 13.061A pdb=" N LEU G 125 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N ILE G 82 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N ILE G 127 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN G 84 " --> pdb=" O ILE G 127 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.995A pdb=" N SER G 103 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE G 106 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N CYS G 132 " --> pdb=" O ILE G 106 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 105 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 4.12 Time building geometry restraints manager: 2.09 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: 4796 1.33 - 1.45: 4335 1.45 - 1.57: 9620 1.57 - 1.69: 320 1.69 - 1.81: 97 Bond restraints: 19168 Sorted by residual: bond pdb=" C3' DT C 8 " pdb=" C2' DT C 8 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.26e+00 bond pdb=" CA ASN A 465 " pdb=" C ASN A 465 " ideal model delta sigma weight residual 1.522 1.481 0.040 1.72e-02 3.38e+03 5.47e+00 bond pdb=" C1' DT C 8 " pdb=" N1 DT C 8 " ideal model delta sigma weight residual 1.468 1.499 -0.031 1.40e-02 5.10e+03 4.83e+00 bond pdb=" C3' DT C 20 " pdb=" C2' DT C 20 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.80e+00 bond pdb=" C1' DT C 20 " pdb=" N1 DT C 20 " ideal model delta sigma weight residual 1.468 1.497 -0.029 1.40e-02 5.10e+03 4.39e+00 ... (remaining 19163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 24882 1.40 - 2.79: 1339 2.79 - 4.19: 271 4.19 - 5.58: 75 5.58 - 6.98: 9 Bond angle restraints: 26576 Sorted by residual: angle pdb=" N LYS A 657 " pdb=" CA LYS A 657 " pdb=" C LYS A 657 " ideal model delta sigma weight residual 113.18 118.56 -5.38 1.21e+00 6.83e-01 1.97e+01 angle pdb=" N3 DT C 15 " pdb=" C4 DT C 15 " pdb=" O4 DT C 15 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C 8 " pdb=" C4 DT C 8 " pdb=" O4 DT C 8 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.65e+01 angle pdb=" N3 DT C 14 " pdb=" C4 DT C 14 " pdb=" O4 DT C 14 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.60e+01 ... (remaining 26571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 10694 35.54 - 71.08: 520 71.08 - 106.61: 49 106.61 - 142.15: 0 142.15 - 177.69: 3 Dihedral angle restraints: 11266 sinusoidal: 5788 harmonic: 5478 Sorted by residual: dihedral pdb=" C4' U B 157 " pdb=" C3' U B 157 " pdb=" C2' U B 157 " pdb=" C1' U B 157 " ideal model delta sinusoidal sigma weight residual 36.34 -38.51 74.86 1 3.10e+00 1.04e-01 7.38e+02 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 -37.40 73.75 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' U B 87 " pdb=" C3' U B 87 " pdb=" C2' U B 87 " pdb=" C1' U B 87 " ideal model delta sinusoidal sigma weight residual 36.34 -37.34 73.69 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 11263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2478 0.065 - 0.129: 350 0.129 - 0.194: 38 0.194 - 0.258: 152 0.258 - 0.323: 47 Chirality restraints: 3065 Sorted by residual: 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 -2.50 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C3' U B 157 " pdb=" C4' U B 157 " pdb=" O3' U B 157 " pdb=" C2' U B 157 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3' U B 138 " pdb=" C4' U B 138 " pdb=" O3' U B 138 " pdb=" C2' U B 138 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3062 not shown) Planarity restraints: 2809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG C 17 " 0.015 2.00e-02 2.50e+03 1.54e-02 7.10e+00 pdb=" N9 DG C 17 " -0.012 2.00e-02 2.50e+03 pdb=" C8 DG C 17 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG C 17 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG C 17 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG C 17 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG C 17 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG C 17 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DG C 17 " -0.041 2.00e-02 2.50e+03 pdb=" N2 DG C 17 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DG C 17 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG C 17 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 536 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.09e+00 pdb=" N PRO A 537 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 537 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 537 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 656 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ASN A 656 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN A 656 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 657 " -0.011 2.00e-02 2.50e+03 ... (remaining 2806 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 914 2.71 - 3.26: 18684 3.26 - 3.80: 29429 3.80 - 4.35: 36553 4.35 - 4.90: 58013 Nonbonded interactions: 143593 Sorted by model distance: nonbonded pdb=" N CYS D 575 " pdb="ZN ZN D 900 " model vdw 2.160 2.310 nonbonded pdb=" OG SER A 823 " pdb=" OD1 ASN A 826 " model vdw 2.198 3.040 nonbonded pdb=" OP1 A B 136 " pdb=" OG SER A 972 " model vdw 2.202 3.040 nonbonded pdb=" OE1 GLN A1008 " pdb=" OH TYR A1025 " model vdw 2.206 3.040 nonbonded pdb=" O PHE A 525 " pdb=" NZ LYS A 555 " model vdw 2.213 3.120 ... (remaining 143588 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.140 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 19170 Z= 0.216 Angle : 0.760 6.977 26576 Z= 0.398 Chirality : 0.075 0.323 3065 Planarity : 0.004 0.051 2809 Dihedral : 18.729 177.688 7704 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.17), residues: 1809 helix: -1.80 (0.16), residues: 731 sheet: -2.61 (0.30), residues: 242 loop : -3.01 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.021 0.002 TYR G 26 PHE 0.022 0.002 PHE D 662 TRP 0.023 0.003 TRP A 604 HIS 0.006 0.001 HIS A 949 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (19168) covalent geometry : angle 0.76043 / 0.40 (26576) hydrogen bonds : bond 0.13051 / 6.60 ( 806) hydrogen bonds : angle 6.45986 / 2.54 ( 2272) metal coordination : bond 0.20586 / 10.29 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 PHE cc_start: 0.4481 (t80) cc_final: 0.4007 (t80) REVERT: F 21 PHE cc_start: 0.7468 (m-10) cc_final: 0.7124 (m-10) REVERT: F 120 ASP cc_start: 0.5892 (p0) cc_final: 0.5201 (p0) REVERT: G 130 MET cc_start: 0.7285 (mtm) cc_final: 0.7051 (mtm) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.1310 time to fit residues: 68.0464 Evaluate side-chains 198 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 388 GLN H 468 ASN H 484 ASN H 485 ASN A 12 GLN A 320 ASN A 324 ASN A 349 GLN A 364 ASN A 440 GLN A 444 GLN A 482 HIS A 733 ASN A 747 ASN A 748 HIS A 756 ASN A 826 ASN A 835 GLN A 841 ASN A 872 ASN A 901 GLN A 904 ASN A 918 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN D 629 ASN D 633 ASN D 635 GLN E 151 ASN F 53 HIS G 34 GLN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.149898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.120226 restraints weight = 35764.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.119781 restraints weight = 39002.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120886 restraints weight = 40616.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.121127 restraints weight = 28682.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.121698 restraints weight = 25553.261| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19170 Z= 0.205 Angle : 1.185 22.573 26576 Z= 0.499 Chirality : 0.107 1.328 3065 Planarity : 0.004 0.049 2809 Dihedral : 16.895 171.216 3881 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.64 % Allowed : 12.66 % Favored : 85.71 % 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: -2.19 (0.19), residues: 1809 helix: -0.21 (0.18), residues: 731 sheet: -2.00 (0.32), residues: 239 loop : -2.43 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 158 TYR 0.031 0.001 TYR G 26 PHE 0.036 0.002 PHE H 524 TRP 0.022 0.002 TRP A 604 HIS 0.009 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (19168) covalent geometry : angle 1.18493 / 0.50 (26576) hydrogen bonds : bond 0.05285 / 2.71 ( 806) hydrogen bonds : angle 5.03070 / 1.98 ( 2272) metal coordination : bond 0.00819 / 0.41 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 231 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 497 ASP cc_start: 0.6586 (t0) cc_final: 0.5950 (m-30) REVERT: A 285 ILE cc_start: 0.7633 (mt) cc_final: 0.7354 (mm) REVERT: A 508 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: A 578 MET cc_start: 0.7401 (mtp) cc_final: 0.6810 (mmp) REVERT: A 991 ASP cc_start: 0.7175 (t0) cc_final: 0.6726 (m-30) REVERT: F 59 TYR cc_start: 0.4866 (t80) cc_final: 0.3627 (t80) REVERT: F 78 LEU cc_start: 0.7632 (mt) cc_final: 0.7408 (mp) REVERT: F 89 THR cc_start: 0.5591 (m) cc_final: 0.4342 (m) REVERT: F 120 ASP cc_start: 0.6402 (p0) cc_final: 0.5646 (p0) REVERT: G 133 ILE cc_start: 0.8635 (tt) cc_final: 0.8414 (tt) outliers start: 27 outliers final: 12 residues processed: 249 average time/residue: 0.1259 time to fit residues: 49.0091 Evaluate side-chains 211 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain F residue 85 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 110 optimal weight: 0.5980 chunk 165 optimal weight: 0.4980 chunk 143 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 440 GLN E 114 GLN F 53 HIS F 107 HIS G 84 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.150453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.120530 restraints weight = 35887.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120470 restraints weight = 37753.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.121280 restraints weight = 40476.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.121670 restraints weight = 28377.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.121877 restraints weight = 25272.370| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19170 Z= 0.163 Angle : 0.925 19.037 26576 Z= 0.406 Chirality : 0.078 0.883 3065 Planarity : 0.004 0.041 2809 Dihedral : 16.929 174.289 3881 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.88 % Allowed : 14.17 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.54 (0.19), residues: 1809 helix: 0.42 (0.19), residues: 748 sheet: -1.90 (0.32), residues: 251 loop : -2.13 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 812 TYR 0.031 0.001 TYR G 26 PHE 0.024 0.002 PHE F 15 TRP 0.017 0.002 TRP A 604 HIS 0.012 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (19168) covalent geometry : angle 0.92546 / 0.41 (26576) hydrogen bonds : bond 0.04898 / 2.51 ( 806) hydrogen bonds : angle 4.71810 / 1.84 ( 2272) metal coordination : bond 0.00079 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 497 ASP cc_start: 0.6302 (t0) cc_final: 0.5884 (m-30) REVERT: A 150 TYR cc_start: 0.8582 (m-80) cc_final: 0.8381 (m-80) REVERT: A 508 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: A 991 ASP cc_start: 0.7197 (t0) cc_final: 0.6741 (m-30) REVERT: A 1089 GLU cc_start: 0.5466 (tp30) cc_final: 0.4993 (tp30) REVERT: F 120 ASP cc_start: 0.6353 (p0) cc_final: 0.5649 (p0) REVERT: G 133 ILE cc_start: 0.8606 (tt) cc_final: 0.8361 (tt) outliers start: 31 outliers final: 19 residues processed: 246 average time/residue: 0.1258 time to fit residues: 49.0598 Evaluate side-chains 206 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 169 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 0.0060 chunk 150 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 134 optimal weight: 0.0970 chunk 125 optimal weight: 0.6980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN A 109 GLN E 159 HIS F 20 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.152000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.122161 restraints weight = 35885.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.122351 restraints weight = 37384.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.123279 restraints weight = 39489.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123506 restraints weight = 27374.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.123850 restraints weight = 24965.210| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19170 Z= 0.138 Angle : 0.836 15.950 26576 Z= 0.372 Chirality : 0.069 0.692 3065 Planarity : 0.003 0.042 2809 Dihedral : 16.612 175.431 3881 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.18 % Allowed : 15.14 % Favored : 82.68 % 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: -1.13 (0.20), residues: 1809 helix: 0.78 (0.19), residues: 748 sheet: -1.67 (0.32), residues: 251 loop : -1.93 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 108 TYR 0.028 0.001 TYR G 26 PHE 0.026 0.001 PHE F 21 TRP 0.014 0.001 TRP A 604 HIS 0.003 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (19168) covalent geometry : angle 0.83633 / 0.37 (26576) hydrogen bonds : bond 0.04517 / 2.32 ( 806) hydrogen bonds : angle 4.50545 / 1.75 ( 2272) metal coordination : bond 0.00026 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 497 ASP cc_start: 0.6285 (t0) cc_final: 0.5932 (m-30) REVERT: A 508 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: A 575 LEU cc_start: 0.8253 (tp) cc_final: 0.7957 (tt) REVERT: A 578 MET cc_start: 0.6984 (mtp) cc_final: 0.6558 (mmp) REVERT: A 1029 MET cc_start: 0.7744 (mtm) cc_final: 0.7215 (mtm) outliers start: 36 outliers final: 25 residues processed: 238 average time/residue: 0.1231 time to fit residues: 46.7069 Evaluate side-chains 217 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 397 LEU Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 63 optimal weight: 0.2980 chunk 15 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 162 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 109 GLN A 949 HIS F 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.151375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.120643 restraints weight = 35624.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.121404 restraints weight = 41245.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.122279 restraints weight = 41766.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122428 restraints weight = 26362.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.122861 restraints weight = 26031.690| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19170 Z= 0.142 Angle : 0.803 14.117 26576 Z= 0.359 Chirality : 0.064 0.692 3065 Planarity : 0.003 0.040 2809 Dihedral : 16.437 174.861 3881 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.24 % Allowed : 16.54 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.00 (0.20), residues: 1809 helix: 0.92 (0.19), residues: 754 sheet: -1.93 (0.31), residues: 255 loop : -1.77 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 158 TYR 0.027 0.001 TYR G 26 PHE 0.021 0.001 PHE F 21 TRP 0.013 0.001 TRP A 604 HIS 0.003 0.001 HIS D 584 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (19168) covalent geometry : angle 0.80341 / 0.36 (26576) hydrogen bonds : bond 0.04406 / 2.27 ( 806) hydrogen bonds : angle 4.45395 / 1.74 ( 2272) metal coordination : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 473 ARG cc_start: 0.5293 (mmt180) cc_final: 0.4729 (ptp-170) REVERT: H 497 ASP cc_start: 0.5880 (t0) cc_final: 0.5590 (m-30) REVERT: A 508 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: A 578 MET cc_start: 0.6984 (mtp) cc_final: 0.6542 (mmp) REVERT: A 991 ASP cc_start: 0.7012 (t0) cc_final: 0.6611 (m-30) REVERT: A 1029 MET cc_start: 0.7791 (mtm) cc_final: 0.7202 (mtm) REVERT: E 158 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7865 (ttp80) REVERT: F 116 SER cc_start: 0.6462 (p) cc_final: 0.6235 (p) outliers start: 37 outliers final: 30 residues processed: 220 average time/residue: 0.1202 time to fit residues: 42.2345 Evaluate side-chains 216 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 170 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 187 optimal weight: 0.0570 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 590 ASN A 636 ASN A 839 ASN A 949 HIS F 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.150929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.121537 restraints weight = 35564.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.120474 restraints weight = 40790.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121591 restraints weight = 42286.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.122394 restraints weight = 28144.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.122628 restraints weight = 26070.024| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 19170 Z= 0.146 Angle : 0.779 12.275 26576 Z= 0.350 Chirality : 0.061 0.565 3065 Planarity : 0.003 0.039 2809 Dihedral : 16.256 174.860 3881 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.54 % Allowed : 17.08 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.20), residues: 1809 helix: 1.05 (0.19), residues: 748 sheet: -1.54 (0.31), residues: 259 loop : -1.66 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 158 TYR 0.025 0.001 TYR G 26 PHE 0.019 0.001 PHE F 21 TRP 0.013 0.001 TRP A 604 HIS 0.003 0.001 HIS A 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (19168) covalent geometry : angle 0.77898 / 0.35 (26576) hydrogen bonds : bond 0.04375 / 2.26 ( 806) hydrogen bonds : angle 4.38320 / 1.71 ( 2272) metal coordination : bond 0.00095 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 484 ASN cc_start: 0.6068 (p0) cc_final: 0.5817 (p0) REVERT: A 508 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: A 560 ASN cc_start: 0.7593 (p0) cc_final: 0.7183 (p0) REVERT: A 575 LEU cc_start: 0.8256 (tp) cc_final: 0.7938 (tt) REVERT: A 578 MET cc_start: 0.7025 (mtp) cc_final: 0.6583 (mmp) REVERT: A 590 ASN cc_start: 0.8352 (m-40) cc_final: 0.8139 (m-40) REVERT: A 991 ASP cc_start: 0.7025 (t0) cc_final: 0.6552 (t0) REVERT: A 1029 MET cc_start: 0.7802 (mtm) cc_final: 0.7190 (mtm) REVERT: E 158 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7855 (ttp80) outliers start: 42 outliers final: 31 residues processed: 228 average time/residue: 0.1234 time to fit residues: 45.0338 Evaluate side-chains 220 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN A 636 ASN A 949 HIS D 584 HIS F 53 HIS F 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.150618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.120763 restraints weight = 36135.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.120304 restraints weight = 40712.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.121298 restraints weight = 41717.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.121891 restraints weight = 27925.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.122107 restraints weight = 25720.377| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19170 Z= 0.151 Angle : 0.784 12.257 26576 Z= 0.355 Chirality : 0.060 0.500 3065 Planarity : 0.003 0.038 2809 Dihedral : 16.188 174.721 3881 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.30 % Allowed : 18.17 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.20), residues: 1809 helix: 1.14 (0.19), residues: 750 sheet: -1.56 (0.31), residues: 263 loop : -1.65 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 158 TYR 0.025 0.001 TYR G 26 PHE 0.016 0.001 PHE H 524 TRP 0.013 0.001 TRP A 604 HIS 0.003 0.001 HIS A 751 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (19168) covalent geometry : angle 0.78380 / 0.36 (26576) hydrogen bonds : bond 0.04404 / 2.27 ( 806) hydrogen bonds : angle 4.37694 / 1.70 ( 2272) metal coordination : bond 0.00094 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 484 ASN cc_start: 0.6198 (p0) cc_final: 0.5890 (p0) REVERT: H 497 ASP cc_start: 0.6472 (t0) cc_final: 0.5945 (m-30) REVERT: A 560 ASN cc_start: 0.7610 (p0) cc_final: 0.7193 (p0) REVERT: A 575 LEU cc_start: 0.8220 (tp) cc_final: 0.7973 (tt) REVERT: A 578 MET cc_start: 0.6874 (mtp) cc_final: 0.6438 (mmp) REVERT: A 991 ASP cc_start: 0.6990 (t0) cc_final: 0.6594 (m-30) REVERT: D 586 MET cc_start: 0.7602 (ppp) cc_final: 0.7360 (ppp) REVERT: E 86 MET cc_start: 0.7407 (mpp) cc_final: 0.7033 (mpp) REVERT: E 93 THR cc_start: 0.7800 (m) cc_final: 0.7458 (m) REVERT: E 158 ARG cc_start: 0.8131 (ttp80) cc_final: 0.7881 (ttp80) outliers start: 38 outliers final: 32 residues processed: 215 average time/residue: 0.1209 time to fit residues: 41.7712 Evaluate side-chains 217 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 464 ILE Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 19 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 109 optimal weight: 0.0000 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 297 ASN A 590 ASN A 636 ASN A 949 HIS ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.151827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.122621 restraints weight = 35629.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.122408 restraints weight = 38867.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123408 restraints weight = 41662.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.123648 restraints weight = 28002.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.124355 restraints weight = 25729.441| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19170 Z= 0.126 Angle : 0.761 11.655 26576 Z= 0.344 Chirality : 0.058 0.438 3065 Planarity : 0.003 0.047 2809 Dihedral : 16.088 174.566 3881 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.42 % Allowed : 17.87 % Favored : 79.71 % 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: -0.56 (0.20), residues: 1809 helix: 1.25 (0.19), residues: 745 sheet: -1.50 (0.31), residues: 263 loop : -1.54 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 158 TYR 0.026 0.001 TYR G 26 PHE 0.019 0.001 PHE A1060 TRP 0.013 0.001 TRP A 604 HIS 0.039 0.002 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (19168) covalent geometry : angle 0.76051 / 0.34 (26576) hydrogen bonds : bond 0.04200 / 2.16 ( 806) hydrogen bonds : angle 4.30478 / 1.67 ( 2272) metal coordination : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 484 ASN cc_start: 0.6124 (p0) cc_final: 0.5784 (p0) REVERT: A 508 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: A 560 ASN cc_start: 0.7479 (p0) cc_final: 0.7103 (p0) REVERT: A 575 LEU cc_start: 0.8273 (tp) cc_final: 0.8055 (tt) REVERT: A 578 MET cc_start: 0.6727 (mtp) cc_final: 0.6397 (mmp) REVERT: A 991 ASP cc_start: 0.6940 (t0) cc_final: 0.6609 (m-30) REVERT: D 586 MET cc_start: 0.7538 (ppp) cc_final: 0.7306 (ppp) REVERT: E 86 MET cc_start: 0.7328 (mpp) cc_final: 0.6944 (mpp) REVERT: E 93 THR cc_start: 0.7694 (m) cc_final: 0.7334 (m) REVERT: E 158 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7868 (ttp80) outliers start: 40 outliers final: 32 residues processed: 227 average time/residue: 0.1219 time to fit residues: 43.9495 Evaluate side-chains 219 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 508 GLU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 190 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 172 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 590 ASN A 926 ASN A 949 HIS ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.150741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.121062 restraints weight = 35946.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.120297 restraints weight = 40472.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.121407 restraints weight = 43060.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.121600 restraints weight = 29939.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.122842 restraints weight = 26157.341| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19170 Z= 0.152 Angle : 0.782 12.642 26576 Z= 0.355 Chirality : 0.058 0.475 3065 Planarity : 0.003 0.037 2809 Dihedral : 16.012 174.204 3881 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.30 % Allowed : 18.11 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1809 helix: 1.24 (0.19), residues: 745 sheet: -1.45 (0.31), residues: 258 loop : -1.53 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 158 TYR 0.023 0.001 TYR G 26 PHE 0.018 0.001 PHE H 524 TRP 0.013 0.001 TRP A 604 HIS 0.007 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (19168) covalent geometry : angle 0.78167 / 0.35 (26576) hydrogen bonds : bond 0.04309 / 2.23 ( 806) hydrogen bonds : angle 4.31442 / 1.68 ( 2272) metal coordination : bond 0.00104 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 472 GLN cc_start: 0.7021 (tp-100) cc_final: 0.6776 (tp40) REVERT: H 484 ASN cc_start: 0.6206 (p0) cc_final: 0.5841 (p0) REVERT: A 560 ASN cc_start: 0.7565 (p0) cc_final: 0.7137 (p0) REVERT: A 575 LEU cc_start: 0.8305 (tp) cc_final: 0.8083 (tt) REVERT: A 578 MET cc_start: 0.6810 (mtp) cc_final: 0.6423 (mmp) REVERT: A 991 ASP cc_start: 0.6913 (t0) cc_final: 0.6563 (m-30) REVERT: D 586 MET cc_start: 0.7676 (ppp) cc_final: 0.7465 (ppp) REVERT: E 86 MET cc_start: 0.7368 (mpp) cc_final: 0.7001 (mpp) REVERT: E 93 THR cc_start: 0.7687 (m) cc_final: 0.7362 (m) REVERT: E 158 ARG cc_start: 0.8144 (ttp80) cc_final: 0.7895 (ttp80) outliers start: 38 outliers final: 30 residues processed: 206 average time/residue: 0.1278 time to fit residues: 41.9594 Evaluate side-chains 209 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 184 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 949 HIS ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.150927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.121592 restraints weight = 35838.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.121259 restraints weight = 39338.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.122006 restraints weight = 45963.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.122683 restraints weight = 29237.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.123201 restraints weight = 26028.204| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19170 Z= 0.145 Angle : 0.773 15.447 26576 Z= 0.350 Chirality : 0.057 0.435 3065 Planarity : 0.003 0.037 2809 Dihedral : 15.946 174.298 3881 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.88 % Allowed : 18.53 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.20), residues: 1809 helix: 1.26 (0.19), residues: 746 sheet: -1.46 (0.31), residues: 258 loop : -1.50 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 158 TYR 0.022 0.001 TYR G 26 PHE 0.017 0.001 PHE H 524 TRP 0.013 0.001 TRP A 604 HIS 0.003 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (19168) covalent geometry : angle 0.77282 / 0.35 (26576) hydrogen bonds : bond 0.04268 / 2.20 ( 806) hydrogen bonds : angle 4.30241 / 1.67 ( 2272) metal coordination : bond 0.00088 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3618 Ramachandran restraints generated. 1809 Oldfield, 0 Emsley, 1809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 484 ASN cc_start: 0.6147 (p0) cc_final: 0.5768 (p0) REVERT: A 560 ASN cc_start: 0.7555 (p0) cc_final: 0.7165 (p0) REVERT: A 575 LEU cc_start: 0.8204 (tp) cc_final: 0.7948 (tt) REVERT: A 578 MET cc_start: 0.6747 (mtp) cc_final: 0.6414 (mmp) REVERT: A 879 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8332 (mmmt) REVERT: A 991 ASP cc_start: 0.7137 (t0) cc_final: 0.6732 (m-30) REVERT: E 86 MET cc_start: 0.7423 (mpp) cc_final: 0.7169 (mpp) REVERT: E 158 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8113 (ttp80) outliers start: 31 outliers final: 29 residues processed: 206 average time/residue: 0.1310 time to fit residues: 43.0319 Evaluate side-chains 209 residues out of total 1741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 984 THR Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 69 optimal weight: 0.0570 chunk 99 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 477 GLN A 12 GLN A 949 HIS ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.151577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.122341 restraints weight = 35936.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.121595 restraints weight = 41365.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.122713 restraints weight = 42045.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.123475 restraints weight = 28117.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.123737 restraints weight = 25913.985| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19170 Z= 0.133 Angle : 0.759 14.994 26576 Z= 0.344 Chirality : 0.056 0.442 3065 Planarity : 0.003 0.037 2809 Dihedral : 15.825 175.020 3881 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.94 % Allowed : 18.84 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.20), residues: 1809 helix: 1.32 (0.19), residues: 759 sheet: -1.53 (0.31), residues: 261 loop : -1.47 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 158 TYR 0.023 0.001 TYR G 26 PHE 0.016 0.001 PHE H 524 TRP 0.014 0.001 TRP A 604 HIS 0.004 0.001 HIS F 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (19168) covalent geometry : angle 0.75869 / 0.34 (26576) hydrogen bonds : bond 0.04153 / 2.14 ( 806) hydrogen bonds : angle 4.22485 / 1.64 ( 2272) metal coordination : bond 0.00081 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.15 seconds wall clock time: 43 minutes 53.14 seconds (2633.14 seconds total)