Starting phenix.real_space_refine on Sat Feb 17 11:18:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmb_23439/02_2024/7lmb_23439.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmb_23439/02_2024/7lmb_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmb_23439/02_2024/7lmb_23439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmb_23439/02_2024/7lmb_23439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmb_23439/02_2024/7lmb_23439.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lmb_23439/02_2024/7lmb_23439.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 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 Residue "H ARG 465": "NH1" <-> "NH2" Residue "H GLU 471": "OE1" <-> "OE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A GLU 517": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A ARG 766": "NH1" <-> "NH2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A GLU 801": "OE1" <-> "OE2" Residue "A GLU 873": "OE1" <-> "OE2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A GLU 998": "OE1" <-> "OE2" Residue "A TYR 1006": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1055": "NH1" <-> "NH2" Residue "A ARG 1058": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D ARG 554": "NH1" <-> "NH2" Residue "D ARG 588": "NH1" <-> "NH2" Residue "D GLU 632": "OE1" <-> "OE2" Residue "D GLU 676": "OE1" <-> "OE2" Residue "D GLU 692": "OE1" <-> "OE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G ARG 131": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'RNA': 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: {'GLN:plan1': 3, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8542 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 22, 'TRANS': 989} Chain breaks: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "E" Number of atoms: 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: 10.14, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 7.92 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 5.98 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: 8.10 Time building geometry restraints manager: 8.51 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=" 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=" CB VAL A 119 " pdb=" CG2 VAL A 119 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.83e+00 bond pdb=" O5' C B 49 " pdb=" C5' C B 49 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.66e+00 bond pdb=" CB CYS A1001 " pdb=" SG CYS A1001 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.53e+00 bond pdb=" CB ILE A 478 " pdb=" CG2 ILE A 478 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.47e+00 ... (remaining 19163 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.26: 1079 106.26 - 113.19: 10358 113.19 - 120.12: 7089 120.12 - 127.05: 7643 127.05 - 133.98: 407 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=" CA ASN A 465 " pdb=" C ASN A 465 " pdb=" N LYS A 466 " ideal model delta sigma weight residual 118.59 124.16 -5.57 1.63e+00 3.76e-01 1.17e+01 angle pdb=" N GLY D 596 " pdb=" CA GLY D 596 " pdb=" C GLY D 596 " ideal model delta sigma weight residual 110.73 117.21 -6.48 1.90e+00 2.77e-01 1.16e+01 angle pdb=" CA TYR G 26 " pdb=" CB TYR G 26 " pdb=" CG TYR G 26 " ideal model delta sigma weight residual 113.90 119.18 -5.28 1.80e+00 3.09e-01 8.61e+00 angle pdb=" C PHE G 25 " pdb=" N TYR G 26 " pdb=" CA TYR G 26 " ideal model delta sigma weight residual 122.31 116.81 5.50 2.00e+00 2.50e-01 7.55e+00 ... (remaining 26571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 11115 35.73 - 71.45: 531 71.45 - 107.18: 61 107.18 - 142.91: 1 142.91 - 178.63: 8 Dihedral angle restraints: 11716 sinusoidal: 6238 harmonic: 5478 Sorted by residual: dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 200.00 53.91 146.09 1 1.50e+01 4.44e-03 7.81e+01 dihedral pdb=" O4' C B 43 " pdb=" C1' C B 43 " pdb=" N1 C B 43 " pdb=" C2 C B 43 " ideal model delta sinusoidal sigma weight residual -160.00 -26.18 -133.82 1 1.50e+01 4.44e-03 7.22e+01 dihedral pdb=" O4' U B 41 " pdb=" C1' U B 41 " pdb=" N1 U B 41 " pdb=" C2 U B 41 " ideal model delta sinusoidal sigma weight residual -128.00 50.63 -178.63 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 11713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2334 0.047 - 0.094: 604 0.094 - 0.141: 112 0.141 - 0.188: 14 0.188 - 0.234: 1 Chirality restraints: 3065 Sorted by residual: chirality pdb=" CA LYS A 657 " pdb=" N LYS A 657 " pdb=" C LYS A 657 " pdb=" CB LYS A 657 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C3' C B 49 " pdb=" C4' C B 49 " pdb=" O3' C B 49 " pdb=" C2' C B 49 " both_signs ideal model delta sigma weight residual False -2.48 -2.64 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CB ILE H 464 " pdb=" CA ILE H 464 " pdb=" CG1 ILE H 464 " pdb=" CG2 ILE H 464 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.51e-01 ... (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 2.440 nonbonded pdb=" OP1 A B 136 " pdb=" OG SER A 972 " model vdw 2.202 2.440 nonbonded pdb=" OE1 GLN A1008 " pdb=" OH TYR A1025 " model vdw 2.206 2.440 nonbonded pdb=" O PHE A 525 " pdb=" NZ LYS A 555 " model vdw 2.213 2.520 ... (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 ========== 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.370 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 57.700 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.004 0.045 19168 Z= 0.259 Angle : 0.634 6.849 26576 Z= 0.358 Chirality : 0.043 0.234 3065 Planarity : 0.004 0.051 2809 Dihedral : 19.411 178.633 8154 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.003 TRP A 604 HIS 0.006 0.001 HIS A 949 PHE 0.022 0.002 PHE D 662 TYR 0.021 0.002 TYR G 26 ARG 0.003 0.000 ARG A 237 *********************** 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 fitting. rotamer outliers: 1 poor density : 335 time to evaluate : 2.003 Fit side-chains revert: symmetry clash 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: 0.7122 (m-10) REVERT: F 120 ASP cc_start: 0.5892 (p0) cc_final: 0.5206 (p0) REVERT: G 130 MET cc_start: 0.7285 (mtm) cc_final: 0.7052 (mtm) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.3032 time to fit residues: 153.8352 Evaluate side-chains 198 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 388 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 484 ASN H 485 ASN ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 320 ASN A 324 ASN A 349 GLN A 440 GLN A 482 HIS A 574 ASN A 590 ASN A 733 ASN A 747 ASN A 748 HIS A 756 ASN 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 577 GLN D 629 ASN D 633 ASN D 635 GLN E 159 HIS F 53 HIS F 107 HIS G 34 GLN ** G 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19168 Z= 0.179 Angle : 0.564 7.867 26576 Z= 0.300 Chirality : 0.040 0.154 3065 Planarity : 0.004 0.043 2809 Dihedral : 20.152 179.012 4331 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.30 % Allowed : 12.05 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1809 helix: -0.07 (0.18), residues: 746 sheet: -2.05 (0.32), residues: 239 loop : -2.43 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 604 HIS 0.005 0.001 HIS F 53 PHE 0.029 0.002 PHE H 524 TYR 0.028 0.001 TYR G 26 ARG 0.005 0.000 ARG E 158 *********************** 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 276 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 238 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 473 ARG cc_start: 0.5852 (tpp-160) cc_final: 0.5592 (ptp-170) REVERT: A 1100 ILE cc_start: 0.6540 (OUTLIER) cc_final: 0.6298 (tp) REVERT: F 120 ASP cc_start: 0.6103 (p0) cc_final: 0.5267 (p0) outliers start: 38 outliers final: 19 residues processed: 263 average time/residue: 0.2938 time to fit residues: 120.3354 Evaluate side-chains 222 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 202 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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 33 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 12 GLN A 636 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN F 53 HIS G 84 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19168 Z= 0.254 Angle : 0.592 8.559 26576 Z= 0.314 Chirality : 0.041 0.153 3065 Planarity : 0.004 0.044 2809 Dihedral : 20.098 178.743 4331 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.30 % Allowed : 14.84 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.19), residues: 1809 helix: 0.40 (0.19), residues: 747 sheet: -2.11 (0.31), residues: 253 loop : -2.22 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 604 HIS 0.006 0.001 HIS A 949 PHE 0.056 0.002 PHE H 524 TYR 0.026 0.002 TYR G 26 ARG 0.005 0.000 ARG A 573 *********************** 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 246 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 208 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 TYR cc_start: 0.8732 (m-80) cc_final: 0.8451 (m-80) REVERT: A 575 LEU cc_start: 0.7882 (tp) cc_final: 0.7635 (tt) REVERT: D 586 MET cc_start: 0.7622 (ppp) cc_final: 0.7410 (ppp) REVERT: F 120 ASP cc_start: 0.5879 (p0) cc_final: 0.4913 (p0) outliers start: 38 outliers final: 30 residues processed: 228 average time/residue: 0.3184 time to fit residues: 113.5113 Evaluate side-chains 216 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 1.845 ------------------------------------------------------------------------------- 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 33 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 61 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 420 LEU Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 HIS Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain D residue 691 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 10 ILE 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 176 optimal weight: 10.0000 chunk 134 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 477 GLN ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 GLN A 129 GLN E 101 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19168 Z= 0.170 Angle : 0.536 9.272 26576 Z= 0.283 Chirality : 0.039 0.150 3065 Planarity : 0.003 0.043 2809 Dihedral : 19.975 179.065 4331 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.24 % Allowed : 15.93 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1809 helix: 0.91 (0.19), residues: 750 sheet: -1.86 (0.30), residues: 261 loop : -1.96 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 604 HIS 0.006 0.001 HIS F 53 PHE 0.061 0.001 PHE H 524 TYR 0.024 0.001 TYR G 26 ARG 0.002 0.000 ARG A 446 *********************** 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 258 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 TYR cc_start: 0.8616 (m-80) cc_final: 0.8367 (m-80) REVERT: A 228 GLN cc_start: 0.8264 (mm110) cc_final: 0.8025 (tt0) REVERT: F 20 GLN cc_start: 0.7176 (pp30) cc_final: 0.6949 (pp30) outliers start: 37 outliers final: 27 residues processed: 243 average time/residue: 0.2886 time to fit residues: 109.4825 Evaluate side-chains 220 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 193 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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 19 ASP Chi-restraints excluded: chain A residue 21 LEU 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 420 LEU Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1108 SER 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 78 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 0.3980 chunk 78 optimal weight: 0.0980 chunk 161 optimal weight: 0.0020 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 388 GLN ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 584 HIS ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19168 Z= 0.163 Angle : 0.539 8.889 26576 Z= 0.282 Chirality : 0.039 0.183 3065 Planarity : 0.003 0.046 2809 Dihedral : 19.824 179.582 4331 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.79 % Allowed : 17.44 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1809 helix: 1.13 (0.19), residues: 756 sheet: -1.59 (0.31), residues: 270 loop : -1.82 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 604 HIS 0.003 0.001 HIS A 949 PHE 0.055 0.001 PHE H 524 TYR 0.021 0.001 TYR G 26 ARG 0.008 0.000 ARG E 158 *********************** 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 267 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 GLN cc_start: 0.8219 (mm110) cc_final: 0.7960 (tt0) REVERT: G 130 MET cc_start: 0.7238 (mtm) cc_final: 0.6965 (mtm) outliers start: 46 outliers final: 39 residues processed: 249 average time/residue: 0.2812 time to fit residues: 111.7771 Evaluate side-chains 237 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 21 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 THR 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 618 ASP Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 619 HIS Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 150 VAL 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 105 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 0.0670 chunk 189 optimal weight: 4.9990 chunk 157 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19168 Z= 0.163 Angle : 0.537 10.088 26576 Z= 0.281 Chirality : 0.039 0.155 3065 Planarity : 0.003 0.046 2809 Dihedral : 19.731 179.550 4331 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.73 % Allowed : 18.29 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1809 helix: 1.32 (0.19), residues: 754 sheet: -1.47 (0.31), residues: 270 loop : -1.68 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 604 HIS 0.002 0.001 HIS A 751 PHE 0.060 0.001 PHE H 524 TYR 0.016 0.001 TYR G 26 ARG 0.006 0.000 ARG E 158 *********************** 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 252 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.6573 (mtm) cc_final: 0.5977 (mtm) REVERT: F 116 SER cc_start: 0.6202 (p) cc_final: 0.5939 (p) outliers start: 45 outliers final: 39 residues processed: 236 average time/residue: 0.3175 time to fit residues: 118.1275 Evaluate side-chains 233 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 2.072 ------------------------------------------------------------------------------- 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 19 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 THR 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 618 ASP Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 809 LEU 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 903 ILE Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain D residue 619 HIS 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 85 CYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 40 MET 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 182 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 ASN A 949 HIS ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19168 Z= 0.187 Angle : 0.550 10.208 26576 Z= 0.287 Chirality : 0.039 0.163 3065 Planarity : 0.003 0.045 2809 Dihedral : 19.675 179.957 4331 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.21 % Allowed : 18.72 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1809 helix: 1.36 (0.19), residues: 754 sheet: -1.53 (0.30), residues: 281 loop : -1.62 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 604 HIS 0.002 0.001 HIS A 751 PHE 0.062 0.001 PHE H 524 TYR 0.015 0.001 TYR H 410 ARG 0.006 0.000 ARG E 158 *********************** 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 253 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 200 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 108 LEU cc_start: 0.8199 (mp) cc_final: 0.7995 (mt) REVERT: F 116 SER cc_start: 0.6046 (p) cc_final: 0.5763 (p) outliers start: 53 outliers final: 47 residues processed: 237 average time/residue: 0.3094 time to fit residues: 117.0293 Evaluate side-chains 241 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 194 time to evaluate : 2.092 ------------------------------------------------------------------------------- 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 498 VAL Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 61 THR 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 384 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 809 LEU 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 903 ILE Chi-restraints excluded: chain A residue 937 ASN 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 1026 SER Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 150 VAL 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 40 MET Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 133 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 0.0270 chunk 56 optimal weight: 0.0030 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 17 optimal weight: 0.0050 chunk 148 optimal weight: 0.0570 overall best weight: 0.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 835 GLN A 839 ASN A 949 HIS ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19168 Z= 0.128 Angle : 0.520 10.784 26576 Z= 0.266 Chirality : 0.037 0.169 3065 Planarity : 0.003 0.044 2809 Dihedral : 19.476 178.859 4331 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.60 % Allowed : 19.44 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.20), residues: 1809 helix: 1.62 (0.20), residues: 764 sheet: -1.46 (0.30), residues: 278 loop : -1.43 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 604 HIS 0.002 0.001 HIS A 751 PHE 0.059 0.001 PHE H 524 TYR 0.011 0.001 TYR G 26 ARG 0.005 0.000 ARG E 158 *********************** 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 270 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.7684 (mtm) cc_final: 0.7227 (mtm) REVERT: D 647 ASP cc_start: 0.7648 (m-30) cc_final: 0.7428 (m-30) REVERT: F 116 SER cc_start: 0.6085 (p) cc_final: 0.5793 (p) outliers start: 43 outliers final: 37 residues processed: 257 average time/residue: 0.2985 time to fit residues: 120.6882 Evaluate side-chains 238 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 498 VAL Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 436 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 888 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 150 VAL 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 73 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 79 VAL 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 171 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 0.2980 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 138 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 0.0060 chunk 175 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS D 577 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 19168 Z= 0.142 Angle : 0.533 11.905 26576 Z= 0.272 Chirality : 0.037 0.166 3065 Planarity : 0.003 0.044 2809 Dihedral : 19.380 178.781 4331 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.30 % Allowed : 20.17 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1809 helix: 1.74 (0.20), residues: 761 sheet: -1.50 (0.30), residues: 272 loop : -1.45 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 604 HIS 0.004 0.001 HIS H 401 PHE 0.058 0.001 PHE H 524 TYR 0.016 0.001 TYR H 410 ARG 0.004 0.000 ARG E 158 *********************** 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 244 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 876 TRP cc_start: 0.7807 (t60) cc_final: 0.7488 (t60) REVERT: A 911 ASN cc_start: 0.7335 (p0) cc_final: 0.6995 (p0) REVERT: E 86 MET cc_start: 0.7299 (mpp) cc_final: 0.7065 (mpp) outliers start: 38 outliers final: 32 residues processed: 233 average time/residue: 0.2773 time to fit residues: 102.0324 Evaluate side-chains 237 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 497 ASP Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 384 ILE 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 877 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 962 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 627 VAL Chi-restraints excluded: chain D residue 641 GLN Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 163 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 ASN A 949 HIS ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19168 Z= 0.233 Angle : 0.584 11.746 26576 Z= 0.301 Chirality : 0.039 0.179 3065 Planarity : 0.003 0.051 2809 Dihedral : 19.467 178.358 4331 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.24 % Allowed : 20.59 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.20), residues: 1809 helix: 1.52 (0.19), residues: 759 sheet: -1.55 (0.30), residues: 273 loop : -1.53 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 604 HIS 0.004 0.001 HIS G 65 PHE 0.060 0.002 PHE H 524 TYR 0.016 0.001 TYR A1006 ARG 0.017 0.001 ARG G 70 ********************** 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 235 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 MET cc_start: 0.7332 (mpp) cc_final: 0.7084 (mpp) REVERT: F 116 SER cc_start: 0.6088 (p) cc_final: 0.5871 (p) REVERT: F 120 ASP cc_start: 0.5678 (p0) cc_final: 0.5021 (p0) outliers start: 37 outliers final: 32 residues processed: 223 average time/residue: 0.2665 time to fit residues: 94.3621 Evaluate side-chains 220 residues out of total 1741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 516 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 627 ASP Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 903 ILE Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 627 VAL Chi-restraints excluded: chain D residue 641 GLN Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 10 ILE Chi-restraints excluded: chain G residue 40 MET Chi-restraints excluded: chain G residue 79 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: 0.6980 chunk 165 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 482 HIS ** H 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 HIS ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 177 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 = 0.4199 r_free = 0.4199 target = 0.151104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.121368 restraints weight = 35697.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.120749 restraints weight = 40312.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.121927 restraints weight = 39192.718| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19168 Z= 0.180 Angle : 0.558 11.734 26576 Z= 0.285 Chirality : 0.038 0.177 3065 Planarity : 0.003 0.041 2809 Dihedral : 19.433 179.078 4331 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.00 % Allowed : 21.20 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1809 helix: 1.57 (0.19), residues: 758 sheet: -1.49 (0.31), residues: 262 loop : -1.48 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 604 HIS 0.002 0.001 HIS A 751 PHE 0.061 0.001 PHE H 524 TYR 0.015 0.001 TYR H 410 ARG 0.007 0.000 ARG F 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.08 seconds wall clock time: 61 minutes 21.70 seconds (3681.70 seconds total)