Starting phenix.real_space_refine (version: dev) on Fri Apr 8 12:45:01 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/04_2022/7ast_11904.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/04_2022/7ast_11904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/04_2022/7ast_11904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/04_2022/7ast_11904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/04_2022/7ast_11904.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ast_11904/04_2022/7ast_11904.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "M TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 34518 Number of models: 1 Model: "" Number of chains: 17 Chain: "N" Number of atoms: 9385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1238, 9385 Classifications: {'peptide': 1238} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 49, 'CIS': 26, 'TRANS': 1159, 'PCIS': 3} Chain breaks: 8 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 316 Unresolved non-hydrogen angles: 402 Unresolved non-hydrogen dihedrals: 248 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 155 Chain: "A" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 288 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "B" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "C" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 972 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 117} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "F" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 794 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2635 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 17, 'TRANS': 311} Chain: "I" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1008 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1442 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'CIS': 1, 'TRANS': 168} Chain breaks: 1 Chain: "K" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1119 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'CIS': 1, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 620 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain breaks: 1 Chain: "M" Number of atoms: 8811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8811 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 51, 'TRANS': 1061, 'PCIS': 1} Chain: "Z" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 518 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain breaks: 2 Chain: "X" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'CIS': 5, 'TRANS': 425} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Y" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 180 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 4, 'TRANS': 31} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 18.36, per 1000 atoms: 0.53 Number of scatterers: 34518 At special positions: 0 Unit cell: (187.44, 146.97, 164.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 236 16.00 O 6421 8.00 N 6002 7.00 C 21859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS N 69 " - pdb=" SG CYS N 79 " distance=2.03 Simple disulfide: pdb=" SG CYS N 92 " - pdb=" SG CYS N 317 " distance=2.03 Simple disulfide: pdb=" SG CYS N 109 " - pdb=" SG CYS N 159 " distance=2.03 Simple disulfide: pdb=" SG CYS N 960 " - pdb=" SG CYS N 961 " distance=2.04 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 25 " distance=2.05 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 28 " distance=2.02 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 45 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 36 " distance=2.03 Simple disulfide: pdb=" SG CYS M1083 " - pdb=" SG CYS M1095 " distance=2.03 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: 13.85 Conformation dependent library (CDL) restraints added in 4.8 seconds 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8266 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 36 sheets defined 34.0% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'N' and resid 24 through 31 removed outlier: 4.368A pdb=" N GLN N 31 " --> pdb=" O GLU N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 105 Processing helix chain 'N' and resid 121 through 130 removed outlier: 4.396A pdb=" N PHE N 125 " --> pdb=" O GLU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 147 removed outlier: 4.293A pdb=" N ARG N 140 " --> pdb=" O TYR N 136 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS N 145 " --> pdb=" O GLY N 141 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE N 146 " --> pdb=" O LEU N 142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER N 147 " --> pdb=" O LYS N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 228 removed outlier: 3.920A pdb=" N VAL N 223 " --> pdb=" O ASN N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 285 removed outlier: 4.137A pdb=" N LEU N 283 " --> pdb=" O THR N 280 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 291 removed outlier: 3.636A pdb=" N ASP N 291 " --> pdb=" O ILE N 287 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 318 Processing helix chain 'N' and resid 400 through 409 removed outlier: 4.061A pdb=" N LEU N 407 " --> pdb=" O PHE N 403 " (cutoff:3.500A) Processing helix chain 'N' and resid 469 through 473 removed outlier: 3.775A pdb=" N ILE N 473 " --> pdb=" O LYS N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 489 through 493 removed outlier: 4.111A pdb=" N CYS N 493 " --> pdb=" O GLU N 490 " (cutoff:3.500A) Processing helix chain 'N' and resid 515 through 521 Processing helix chain 'N' and resid 544 through 554 Processing helix chain 'N' and resid 565 through 570 removed outlier: 3.696A pdb=" N ALA N 569 " --> pdb=" O GLN N 566 " (cutoff:3.500A) Processing helix chain 'N' and resid 597 through 602 removed outlier: 3.673A pdb=" N PHE N 601 " --> pdb=" O GLY N 597 " (cutoff:3.500A) Processing helix chain 'N' and resid 651 through 656 Processing helix chain 'N' and resid 679 through 687 Processing helix chain 'N' and resid 690 through 694 Processing helix chain 'N' and resid 710 through 734 removed outlier: 4.339A pdb=" N LEU N 716 " --> pdb=" O ALA N 712 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASN N 732 " --> pdb=" O ILE N 728 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR N 733 " --> pdb=" O GLU N 729 " (cutoff:3.500A) Processing helix chain 'N' and resid 744 through 748 removed outlier: 3.622A pdb=" N THR N 747 " --> pdb=" O ALA N 744 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU N 748 " --> pdb=" O GLU N 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 744 through 748' Processing helix chain 'N' and resid 749 through 768 Processing helix chain 'N' and resid 777 through 781 Processing helix chain 'N' and resid 859 through 879 removed outlier: 5.244A pdb=" N THR N 865 " --> pdb=" O THR N 861 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA N 866 " --> pdb=" O ALA N 862 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU N 867 " --> pdb=" O VAL N 863 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY N 869 " --> pdb=" O THR N 865 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR N 870 " --> pdb=" O ALA N 866 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG N 873 " --> pdb=" O GLY N 869 " (cutoff:3.500A) Processing helix chain 'N' and resid 908 through 912 removed outlier: 3.771A pdb=" N ALA N 911 " --> pdb=" O ASP N 908 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET N 912 " --> pdb=" O PRO N 909 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 908 through 912' Processing helix chain 'N' and resid 914 through 915 No H-bonds generated for 'chain 'N' and resid 914 through 915' Processing helix chain 'N' and resid 919 through 921 No H-bonds generated for 'chain 'N' and resid 919 through 921' Processing helix chain 'N' and resid 922 through 930 removed outlier: 3.601A pdb=" N ASP N 926 " --> pdb=" O LYS N 922 " (cutoff:3.500A) Processing helix chain 'N' and resid 942 through 957 Processing helix chain 'N' and resid 967 through 992 removed outlier: 4.108A pdb=" N PHE N 972 " --> pdb=" O GLU N 968 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE N 973 " --> pdb=" O ILE N 969 " (cutoff:3.500A) Processing helix chain 'N' and resid 1001 through 1005 removed outlier: 4.067A pdb=" N ARG N1005 " --> pdb=" O GLN N1002 " (cutoff:3.500A) Processing helix chain 'N' and resid 1007 through 1025 Processing helix chain 'N' and resid 1033 through 1043 Processing helix chain 'N' and resid 1044 through 1046 No H-bonds generated for 'chain 'N' and resid 1044 through 1046' Processing helix chain 'N' and resid 1068 through 1076 removed outlier: 3.711A pdb=" N GLU N1072 " --> pdb=" O PRO N1068 " (cutoff:3.500A) Processing helix chain 'N' and resid 1094 through 1106 removed outlier: 4.399A pdb=" N VAL N1101 " --> pdb=" O TYR N1097 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU N1106 " --> pdb=" O LYS N1102 " (cutoff:3.500A) Processing helix chain 'N' and resid 1135 through 1142 removed outlier: 3.847A pdb=" N LEU N1139 " --> pdb=" O GLU N1135 " (cutoff:3.500A) Processing helix chain 'N' and resid 1145 through 1155 Processing helix chain 'N' and resid 1188 through 1194 Processing helix chain 'N' and resid 1242 through 1246 Processing helix chain 'N' and resid 1250 through 1258 removed outlier: 3.643A pdb=" N LYS N1256 " --> pdb=" O TYR N1252 " (cutoff:3.500A) Processing helix chain 'N' and resid 1259 through 1271 Processing helix chain 'N' and resid 1283 through 1295 removed outlier: 3.659A pdb=" N VAL N1287 " --> pdb=" O ASP N1283 " (cutoff:3.500A) Processing helix chain 'N' and resid 1315 through 1320 removed outlier: 3.869A pdb=" N ALA N1319 " --> pdb=" O VAL N1315 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER N1320 " --> pdb=" O LEU N1316 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 1315 through 1320' Processing helix chain 'N' and resid 1325 through 1334 removed outlier: 4.205A pdb=" N PHE N1329 " --> pdb=" O ALA N1325 " (cutoff:3.500A) Processing helix chain 'N' and resid 1343 through 1350 removed outlier: 4.202A pdb=" N ILE N1347 " --> pdb=" O VAL N1343 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE N1348 " --> pdb=" O SER N1344 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.888A pdb=" N ARG B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 62 removed outlier: 4.412A pdb=" N LYS B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 76 removed outlier: 4.034A pdb=" N CYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 22 removed outlier: 5.078A pdb=" N TYR F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 Processing helix chain 'F' and resid 36 through 45 Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'F' and resid 111 through 121 Processing helix chain 'F' and resid 152 through 163 Processing helix chain 'F' and resid 178 through 183 removed outlier: 4.060A pdb=" N PHE F 183 " --> pdb=" O VAL F 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 61 removed outlier: 3.514A pdb=" N GLY G 52 " --> pdb=" O ASP G 48 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 116 removed outlier: 3.581A pdb=" N ALA G 116 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 49 removed outlier: 3.545A pdb=" N PHE H 45 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS H 47 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN H 48 " --> pdb=" O ARG H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.593A pdb=" N ALA H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 112 Processing helix chain 'H' and resid 158 through 163 Processing helix chain 'H' and resid 222 through 226 Processing helix chain 'H' and resid 247 through 250 removed outlier: 3.777A pdb=" N ALA H 250 " --> pdb=" O GLY H 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 247 through 250' Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 286 through 290 removed outlier: 3.971A pdb=" N ASN H 290 " --> pdb=" O ILE H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 334 removed outlier: 3.524A pdb=" N MET H 330 " --> pdb=" O ILE H 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 28 removed outlier: 3.527A pdb=" N LYS I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 40 through 56 removed outlier: 3.830A pdb=" N THR I 44 " --> pdb=" O GLN I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 72 Processing helix chain 'I' and resid 73 through 77 removed outlier: 3.786A pdb=" N LYS I 77 " --> pdb=" O LYS I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 90 removed outlier: 3.698A pdb=" N LYS I 83 " --> pdb=" O THR I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 99 removed outlier: 4.155A pdb=" N ILE I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN I 98 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 124 removed outlier: 3.715A pdb=" N LEU I 116 " --> pdb=" O GLN I 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 18 removed outlier: 3.733A pdb=" N GLN J 17 " --> pdb=" O PRO J 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE J 18 " --> pdb=" O PRO J 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 14 through 18' Processing helix chain 'J' and resid 22 through 33 removed outlier: 4.080A pdb=" N LYS J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 70 removed outlier: 4.210A pdb=" N CYS K 70 " --> pdb=" O PRO K 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 67 through 70' Processing helix chain 'K' and resid 71 through 78 removed outlier: 4.060A pdb=" N ILE K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.774A pdb=" N SER K 112 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 336 removed outlier: 3.887A pdb=" N GLY L 335 " --> pdb=" O ARG L 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 28 removed outlier: 3.520A pdb=" N TRP M 27 " --> pdb=" O VAL M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 34 Processing helix chain 'M' and resid 41 through 53 Processing helix chain 'M' and resid 53 through 60 Processing helix chain 'M' and resid 235 through 243 Processing helix chain 'M' and resid 247 through 256 removed outlier: 3.601A pdb=" N ILE M 251 " --> pdb=" O SER M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 258 through 276 removed outlier: 3.636A pdb=" N MET M 262 " --> pdb=" O GLU M 258 " (cutoff:3.500A) Proline residue: M 267 - end of helix Processing helix chain 'M' and resid 284 through 289 Processing helix chain 'M' and resid 292 through 300 removed outlier: 3.556A pdb=" N MET M 296 " --> pdb=" O ARG M 293 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLY M 298 " --> pdb=" O ARG M 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 314 Processing helix chain 'M' and resid 315 through 320 Processing helix chain 'M' and resid 328 through 339 Processing helix chain 'M' and resid 364 through 391 Processing helix chain 'M' and resid 410 through 422 Processing helix chain 'M' and resid 445 through 452 removed outlier: 3.658A pdb=" N MET M 452 " --> pdb=" O ALA M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 472 through 476 removed outlier: 3.990A pdb=" N GLN M 475 " --> pdb=" O GLN M 472 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP M 476 " --> pdb=" O PRO M 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 472 through 476' Processing helix chain 'M' and resid 508 through 519 removed outlier: 5.103A pdb=" N LEU M 514 " --> pdb=" O PRO M 510 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY M 519 " --> pdb=" O ALA M 515 " (cutoff:3.500A) Processing helix chain 'M' and resid 522 through 526 Processing helix chain 'M' and resid 551 through 564 removed outlier: 4.677A pdb=" N ASN M 557 " --> pdb=" O LYS M 553 " (cutoff:3.500A) Processing helix chain 'M' and resid 610 through 615 Processing helix chain 'M' and resid 635 through 641 Processing helix chain 'M' and resid 660 through 664 removed outlier: 4.073A pdb=" N THR M 663 " --> pdb=" O GLU M 660 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU M 664 " --> pdb=" O PRO M 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 660 through 664' Processing helix chain 'M' and resid 679 through 693 removed outlier: 3.657A pdb=" N ASN M 683 " --> pdb=" O GLN M 679 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS M 691 " --> pdb=" O CYS M 687 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN M 692 " --> pdb=" O ALA M 688 " (cutoff:3.500A) Processing helix chain 'M' and resid 700 through 704 Processing helix chain 'M' and resid 722 through 728 removed outlier: 3.516A pdb=" N GLU M 726 " --> pdb=" O THR M 722 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU M 727 " --> pdb=" O LYS M 723 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE M 728 " --> pdb=" O THR M 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 722 through 728' Processing helix chain 'M' and resid 912 through 916 Processing helix chain 'M' and resid 944 through 954 removed outlier: 3.983A pdb=" N LYS M 950 " --> pdb=" O LEU M 946 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU M 954 " --> pdb=" O LYS M 950 " (cutoff:3.500A) Processing helix chain 'M' and resid 968 through 979 removed outlier: 3.976A pdb=" N VAL M 972 " --> pdb=" O LYS M 968 " (cutoff:3.500A) Processing helix chain 'M' and resid 1048 through 1057 Processing helix chain 'M' and resid 1060 through 1070 Processing helix chain 'M' and resid 1107 through 1120 removed outlier: 3.885A pdb=" N LYS M1111 " --> pdb=" O PRO M1107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER M1119 " --> pdb=" O GLN M1115 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET M1120 " --> pdb=" O GLU M1116 " (cutoff:3.500A) Processing helix chain 'Z' and resid 177 through 189 removed outlier: 3.565A pdb=" N GLN Z 183 " --> pdb=" O VAL Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 222 Processing helix chain 'Z' and resid 231 through 244 removed outlier: 4.431A pdb=" N LEU Z 242 " --> pdb=" O ILE Z 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 17 Processing helix chain 'X' and resid 18 through 32 removed outlier: 3.671A pdb=" N GLU X 22 " --> pdb=" O GLY X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 44 Processing helix chain 'X' and resid 46 through 60 Processing helix chain 'X' and resid 78 through 84 Processing helix chain 'X' and resid 86 through 99 removed outlier: 4.554A pdb=" N ARG X 90 " --> pdb=" O LEU X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 112 Processing helix chain 'X' and resid 117 through 130 Processing helix chain 'X' and resid 140 through 154 removed outlier: 3.888A pdb=" N VAL X 144 " --> pdb=" O ASP X 140 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 259 removed outlier: 3.533A pdb=" N PHE X 242 " --> pdb=" O ASN X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 272 removed outlier: 3.525A pdb=" N SER X 264 " --> pdb=" O ASP X 260 " (cutoff:3.500A) Processing helix chain 'X' and resid 289 through 296 Processing helix chain 'X' and resid 304 through 317 Processing helix chain 'X' and resid 337 through 357 Processing helix chain 'X' and resid 359 through 370 removed outlier: 3.506A pdb=" N ALA X 363 " --> pdb=" O GLY X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 379 through 385 removed outlier: 4.196A pdb=" N PHE X 383 " --> pdb=" O GLN X 379 " (cutoff:3.500A) Processing helix chain 'X' and resid 387 through 402 Processing helix chain 'X' and resid 427 through 456 Processing helix chain 'X' and resid 460 through 477 removed outlier: 3.791A pdb=" N ALA X 476 " --> pdb=" O ALA X 472 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR X 477 " --> pdb=" O SER X 473 " (cutoff:3.500A) Processing helix chain 'X' and resid 480 through 491 removed outlier: 3.921A pdb=" N LEU X 484 " --> pdb=" O GLU X 480 " (cutoff:3.500A) Processing helix chain 'X' and resid 492 through 530 Processing helix chain 'Y' and resid 3 through 20 removed outlier: 4.224A pdb=" N UNK Y 11 " --> pdb=" O UNK Y 7 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N UNK Y 14 " --> pdb=" O UNK Y 10 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N UNK Y 20 " --> pdb=" O UNK Y 16 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 17 through 18 removed outlier: 4.022A pdb=" N HIS N 17 " --> pdb=" O LYS M1127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 164 through 166 removed outlier: 4.079A pdb=" N THR N 165 " --> pdb=" O HIS N 176 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS N 176 " --> pdb=" O THR N 165 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'N' and resid 462 through 463 removed outlier: 4.057A pdb=" N ASN N 506 " --> pdb=" O ASN N 463 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 558 through 559 Processing sheet with id=AA5, first strand: chain 'N' and resid 1215 through 1216 Processing sheet with id=AA6, first strand: chain 'A' and resid 4 through 5 removed outlier: 3.605A pdb=" N ASN A 10 " --> pdb=" O CYS A 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 19 Processing sheet with id=AA8, first strand: chain 'C' and resid 54 through 56 removed outlier: 3.777A pdb=" N PHE C 55 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL H 92 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU H 142 " --> pdb=" O LEU H 210 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU H 138 " --> pdb=" O CYS H 214 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN H 139 " --> pdb=" O ILE H 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AB1, first strand: chain 'E' and resid 105 through 108 Processing sheet with id=AB2, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 151 removed outlier: 4.108A pdb=" N VAL F 190 " --> pdb=" O MET F 151 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 40 through 44 removed outlier: 3.667A pdb=" N VAL G 40 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 84 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN G 85 " --> pdb=" O GLU G 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 60 through 66 removed outlier: 4.164A pdb=" N MET H 65 " --> pdb=" O TYR H 306 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 2 through 3 removed outlier: 3.547A pdb=" N GLU I 2 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET J 7 " --> pdb=" O PHE J 72 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE J 72 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 99 through 100 Processing sheet with id=AB8, first strand: chain 'J' and resid 106 through 107 removed outlier: 7.210A pdb=" N ASP J 106 " --> pdb=" O LEU J 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 129 through 131 removed outlier: 3.860A pdb=" N HIS J 138 " --> pdb=" O TYR J 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 124 through 125 Processing sheet with id=AC2, first strand: chain 'K' and resid 28 through 29 removed outlier: 3.787A pdb=" N ARG K 136 " --> pdb=" O CYS K 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 208 through 209 Processing sheet with id=AC4, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AC5, first strand: chain 'M' and resid 183 through 184 removed outlier: 3.813A pdb=" N GLN M 183 " --> pdb=" O ARG M 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 191 through 193 removed outlier: 3.723A pdb=" N VAL M 199 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA M 198 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER M 202 " --> pdb=" O ARG M 213 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG M 213 " --> pdb=" O SER M 202 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR M 214 " --> pdb=" O ARG M 226 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR M 224 " --> pdb=" O MET M 216 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 423 through 424 removed outlier: 4.192A pdb=" N ARG M 433 " --> pdb=" O TRP M 424 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 454 through 456 Processing sheet with id=AC9, first strand: chain 'M' and resid 540 through 541 removed outlier: 5.532A pdb=" N PHE M 540 " --> pdb=" O ILE M 585 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 630 through 633 removed outlier: 3.696A pdb=" N ARG M 594 " --> pdb=" O LEU M 633 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 720 through 721 Processing sheet with id=AD3, first strand: chain 'M' and resid 927 through 929 removed outlier: 8.569A pdb=" N ILE M 927 " --> pdb=" O ASN M 738 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR M 740 " --> pdb=" O ILE M 927 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N MET M 929 " --> pdb=" O THR M 740 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA M 742 " --> pdb=" O MET M 929 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 754 through 755 Processing sheet with id=AD5, first strand: chain 'M' and resid 865 through 870 removed outlier: 6.139A pdb=" N LEU M 884 " --> pdb=" O GLU M 867 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL M 869 " --> pdb=" O LYS M 882 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS M 882 " --> pdb=" O VAL M 869 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 986 through 987 Processing sheet with id=AD7, first strand: chain 'M' and resid 1075 through 1077 removed outlier: 3.619A pdb=" N PHE M1075 " --> pdb=" O ILE M1106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 34 through 35 Processing sheet with id=AD9, first strand: chain 'X' and resid 157 through 159 962 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.83 Time building geometry restraints manager: 14.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.62: 34734 1.62 - 2.03: 384 2.03 - 2.44: 0 2.44 - 2.85: 0 2.85 - 3.25: 2 Bond restraints: 35120 Sorted by residual: bond pdb=" CB ARG N 29 " pdb=" CG ARG N 29 " ideal model delta sigma weight residual 1.520 3.254 -1.734 3.00e-02 1.11e+03 3.34e+03 bond pdb=" CD LYS D 146 " pdb=" CE LYS D 146 " ideal model delta sigma weight residual 1.520 3.094 -1.574 3.00e-02 1.11e+03 2.75e+03 bond pdb=" CD1 PHE D 88 " pdb=" CE1 PHE D 88 " ideal model delta sigma weight residual 1.382 1.989 -0.607 3.00e-02 1.11e+03 4.10e+02 bond pdb=" CD2 PHE D 88 " pdb=" CE2 PHE D 88 " ideal model delta sigma weight residual 1.382 1.988 -0.606 3.00e-02 1.11e+03 4.07e+02 bond pdb=" CD2 TYR N 85 " pdb=" CE2 TYR N 85 " ideal model delta sigma weight residual 1.382 1.987 -0.605 3.00e-02 1.11e+03 4.07e+02 ... (remaining 35115 not shown) Histogram of bond angle deviations from ideal: 96.75 - 106.24: 985 106.24 - 115.73: 21986 115.73 - 125.22: 23898 125.22 - 134.72: 526 134.72 - 144.21: 4 Bond angle restraints: 47399 Sorted by residual: angle pdb=" CG LYS D 146 " pdb=" CD LYS D 146 " pdb=" CE LYS D 146 " ideal model delta sigma weight residual 111.30 141.41 -30.11 2.30e+00 1.89e-01 1.71e+02 angle pdb=" CA ARG N 29 " pdb=" CB ARG N 29 " pdb=" CG ARG N 29 " ideal model delta sigma weight residual 114.10 134.80 -20.70 2.00e+00 2.50e-01 1.07e+02 angle pdb=" CB ARG N 29 " pdb=" CG ARG N 29 " pdb=" CD ARG N 29 " ideal model delta sigma weight residual 111.30 134.41 -23.11 2.30e+00 1.89e-01 1.01e+02 angle pdb=" N PRO N 612 " pdb=" CA PRO N 612 " pdb=" CB PRO N 612 " ideal model delta sigma weight residual 103.25 111.90 -8.65 1.05e+00 9.07e-01 6.79e+01 angle pdb=" N PRO N1123 " pdb=" CA PRO N1123 " pdb=" CB PRO N1123 " ideal model delta sigma weight residual 103.34 110.40 -7.06 9.30e-01 1.16e+00 5.77e+01 ... (remaining 47394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 18779 17.78 - 35.56: 2303 35.56 - 53.35: 380 53.35 - 71.13: 49 71.13 - 88.91: 26 Dihedral angle restraints: 21537 sinusoidal: 8755 harmonic: 12782 Sorted by residual: dihedral pdb=" CA ASN N1277 " pdb=" C ASN N1277 " pdb=" N HIS N1278 " pdb=" CA HIS N1278 " ideal model delta harmonic sigma weight residual -180.00 -123.50 -56.50 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA CYS N 960 " pdb=" C CYS N 960 " pdb=" N CYS N 961 " pdb=" CA CYS N 961 " ideal model delta harmonic sigma weight residual -180.00 -124.91 -55.09 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA SER N 776 " pdb=" C SER N 776 " pdb=" N PRO N 777 " pdb=" CA PRO N 777 " ideal model delta harmonic sigma weight residual -180.00 -127.57 -52.43 0 5.00e+00 4.00e-02 1.10e+02 ... (remaining 21534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4414 0.070 - 0.140: 863 0.140 - 0.210: 87 0.210 - 0.280: 18 0.280 - 0.350: 3 Chirality restraints: 5385 Sorted by residual: chirality pdb=" CG LEU M 546 " pdb=" CB LEU M 546 " pdb=" CD1 LEU M 546 " pdb=" CD2 LEU M 546 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CA LEU M 498 " pdb=" N LEU M 498 " pdb=" C LEU M 498 " pdb=" CB LEU M 498 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CA PRO N1162 " pdb=" N PRO N1162 " pdb=" C PRO N1162 " pdb=" CB PRO N1162 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 5382 not shown) Planarity restraints: 6096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG M 594 " 0.086 5.00e-02 4.00e+02 1.33e-01 2.84e+01 pdb=" N PRO M 595 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO M 595 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO M 595 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 203 " 0.061 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO K 204 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO K 204 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO K 204 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 52 " 0.054 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO F 53 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO F 53 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO F 53 " 0.046 5.00e-02 4.00e+02 ... (remaining 6093 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 485 2.51 - 3.11: 28028 3.11 - 3.71: 54757 3.71 - 4.30: 78257 4.30 - 4.90: 122470 Nonbonded interactions: 283997 Sorted by model distance: nonbonded pdb=" SD MET N1275 " pdb=" CE MET N1280 " model vdw 1.913 3.820 nonbonded pdb=" OG1 THR B 9 " pdb=" O CYS M 924 " model vdw 1.962 2.440 nonbonded pdb=" OG SER N 817 " pdb=" O ALA N 830 " model vdw 2.041 2.440 nonbonded pdb=" O ALA H 39 " pdb=" NH2 ARG H 44 " model vdw 2.061 2.520 nonbonded pdb=" OE2 GLU M 726 " pdb=" OH TYR M 960 " model vdw 2.096 2.440 ... (remaining 283992 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 236 5.16 5 C 21859 2.51 5 N 6002 2.21 5 O 6421 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.110 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: 0.040 Extract box with map and model: 13.270 Check model and map are aligned: 0.490 Convert atoms to be neutral: 0.290 Process input model: 82.310 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4614 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 : 0.016 1.734 35120 Z= 1.104 Angle : 1.100 30.109 47399 Z= 0.590 Chirality : 0.056 0.350 5385 Planarity : 0.007 0.133 6096 Dihedral : 15.357 88.910 13241 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 32.60 Ramachandran Plot: Outliers : 0.61 % Allowed : 20.78 % Favored : 78.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.72 % Twisted Proline : 3.30 % Twisted General : 1.25 % 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: -4.78 (0.11), residues: 4297 helix: -1.63 (0.13), residues: 1334 sheet: -4.22 (0.27), residues: 231 loop : -4.19 (0.10), residues: 2732 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 4.393 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 0.5394 time to fit residues: 547.1784 Evaluate side-chains 357 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 4.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 0.5980 chunk 327 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 chunk 338 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 392 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 ASN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1277 ASN ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 169 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 GLN K 29 GLN M 79 ASN M 208 HIS ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN ** M 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 423 ASN M 475 GLN M 535 ASN M 642 ASN ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 738 ASN ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 806 HIS ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 913 GLN M1034 GLN ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4712 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 1.727 35120 Z= 1.082 Angle : 0.987 25.691 47399 Z= 0.492 Chirality : 0.050 0.269 5385 Planarity : 0.007 0.122 6096 Dihedral : 8.609 53.528 4758 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.51 % Allowed : 18.22 % Favored : 81.27 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.89 % 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: -4.34 (0.11), residues: 4297 helix: -1.32 (0.13), residues: 1347 sheet: -3.82 (0.27), residues: 254 loop : -3.89 (0.10), residues: 2696 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 406 time to evaluate : 3.908 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 31 residues processed: 445 average time/residue: 0.4832 time to fit residues: 341.9385 Evaluate side-chains 362 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 331 time to evaluate : 4.220 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3582 time to fit residues: 25.5467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 218 optimal weight: 50.0000 chunk 121 optimal weight: 9.9990 chunk 326 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 393 optimal weight: 5.9990 chunk 424 optimal weight: 5.9990 chunk 350 optimal weight: 0.0770 chunk 389 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 315 optimal weight: 0.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 ASN ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 157 HIS N 182 ASN ** N 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 802 GLN ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN K 110 ASN ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 423 ASN M 552 HIS ** M 676 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 806 HIS ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 445 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5015 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.017 1.731 35120 Z= 1.142 Angle : 1.071 23.132 47399 Z= 0.537 Chirality : 0.053 0.288 5385 Planarity : 0.008 0.119 6096 Dihedral : 8.671 52.452 4758 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 33.53 Ramachandran Plot: Outliers : 0.51 % Allowed : 19.92 % Favored : 79.57 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.77 % Twisted Proline : 1.10 % Twisted General : 0.92 % 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: -4.36 (0.11), residues: 4297 helix: -1.33 (0.13), residues: 1371 sheet: -3.77 (0.27), residues: 280 loop : -3.92 (0.10), residues: 2646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 359 time to evaluate : 4.233 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 53 residues processed: 456 average time/residue: 0.4753 time to fit residues: 353.9758 Evaluate side-chains 362 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 309 time to evaluate : 4.053 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 53 outliers final: 1 residues processed: 53 average time/residue: 0.3394 time to fit residues: 38.5549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 388 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 394 optimal weight: 8.9990 chunk 417 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 373 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 HIS ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 GLN H 268 GLN ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 ASN ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 913 GLN ** M 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5032 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 1.726 35120 Z= 1.116 Angle : 1.003 24.120 47399 Z= 0.501 Chirality : 0.051 0.285 5385 Planarity : 0.007 0.149 6096 Dihedral : 8.404 52.339 4758 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 32.14 Ramachandran Plot: Outliers : 0.47 % Allowed : 18.62 % Favored : 80.92 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.77 % 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: -4.20 (0.12), residues: 4297 helix: -1.18 (0.14), residues: 1371 sheet: -3.80 (0.26), residues: 289 loop : -3.81 (0.11), residues: 2637 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 334 time to evaluate : 4.703 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 52 residues processed: 439 average time/residue: 0.4666 time to fit residues: 336.0035 Evaluate side-chains 343 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 291 time to evaluate : 4.137 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.3245 time to fit residues: 37.1975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 347 optimal weight: 2.9990 chunk 237 optimal weight: 50.0000 chunk 6 optimal weight: 8.9990 chunk 310 optimal weight: 0.8980 chunk 172 optimal weight: 40.0000 chunk 356 optimal weight: 0.9990 chunk 288 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 213 optimal weight: 0.5980 chunk 374 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 927 ASN ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 913 GLN ** M 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1021 HIS ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5032 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 1.728 35120 Z= 1.219 Angle : 1.231 106.100 47399 Z= 0.554 Chirality : 0.051 0.415 5385 Planarity : 0.007 0.129 6096 Dihedral : 8.366 52.324 4758 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 33.18 Ramachandran Plot: Outliers : 0.44 % Allowed : 19.64 % Favored : 79.92 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.70 % 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: -4.17 (0.12), residues: 4297 helix: -1.12 (0.14), residues: 1366 sheet: -3.74 (0.26), residues: 274 loop : -3.82 (0.11), residues: 2657 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 308 time to evaluate : 4.480 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 28 residues processed: 362 average time/residue: 0.4856 time to fit residues: 291.4886 Evaluate side-chains 320 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 292 time to evaluate : 4.138 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3414 time to fit residues: 23.3153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 140 optimal weight: 0.4980 chunk 376 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 245 optimal weight: 40.0000 chunk 103 optimal weight: 30.0000 chunk 417 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 138 optimal weight: 0.9990 chunk 219 optimal weight: 50.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 693 ASN ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 358 GLN ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 183 GLN ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4973 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.017 1.730 35120 Z= 1.182 Angle : 1.079 106.100 47399 Z= 0.500 Chirality : 0.049 0.329 5385 Planarity : 0.006 0.098 6096 Dihedral : 8.154 52.192 4758 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 30.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 18.34 % Favored : 81.20 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.65 % Twisted General : 0.55 % 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: -4.04 (0.12), residues: 4297 helix: -1.02 (0.14), residues: 1370 sheet: -3.64 (0.27), residues: 259 loop : -3.76 (0.11), residues: 2668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 322 time to evaluate : 3.979 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 35 residues processed: 383 average time/residue: 0.4796 time to fit residues: 304.1841 Evaluate side-chains 326 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 291 time to evaluate : 4.379 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3427 time to fit residues: 28.4885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 5.9990 chunk 47 optimal weight: 0.0770 chunk 238 optimal weight: 30.0000 chunk 305 optimal weight: 30.0000 chunk 236 optimal weight: 0.3980 chunk 351 optimal weight: 0.7980 chunk 233 optimal weight: 40.0000 chunk 416 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 chunk 253 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1026 GLN ** N1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4985 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 1.730 35120 Z= 1.202 Angle : 1.100 73.866 47399 Z= 0.524 Chirality : 0.050 0.414 5385 Planarity : 0.007 0.122 6096 Dihedral : 8.133 52.197 4758 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 33.25 Ramachandran Plot: Outliers : 0.54 % Allowed : 18.62 % Favored : 80.85 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.55 % 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: -4.05 (0.12), residues: 4297 helix: -1.04 (0.14), residues: 1371 sheet: -3.62 (0.27), residues: 254 loop : -3.76 (0.11), residues: 2672 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 296 time to evaluate : 4.226 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 332 average time/residue: 0.4717 time to fit residues: 260.6765 Evaluate side-chains 314 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 292 time to evaluate : 4.090 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3557 time to fit residues: 19.8566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 257 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 283 optimal weight: 0.5980 chunk 205 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 327 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4987 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.017 1.730 35120 Z= 1.137 Angle : 1.071 73.900 47399 Z= 0.513 Chirality : 0.050 0.384 5385 Planarity : 0.007 0.110 6096 Dihedral : 8.129 52.198 4758 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 34.02 Ramachandran Plot: Outliers : 0.47 % Allowed : 18.69 % Favored : 80.85 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.55 % 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: -4.06 (0.12), residues: 4297 helix: -1.04 (0.14), residues: 1371 sheet: -3.75 (0.26), residues: 267 loop : -3.75 (0.11), residues: 2659 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 294 time to evaluate : 4.169 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 312 average time/residue: 0.4698 time to fit residues: 242.8532 Evaluate side-chains 298 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 288 time to evaluate : 4.141 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3746 time to fit residues: 12.6375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 10.0000 chunk 398 optimal weight: 50.0000 chunk 363 optimal weight: 0.9990 chunk 388 optimal weight: 4.9990 chunk 233 optimal weight: 30.0000 chunk 169 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 350 optimal weight: 6.9990 chunk 366 optimal weight: 1.9990 chunk 386 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4994 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 1.729 35120 Z= 1.197 Angle : 1.159 86.301 47399 Z= 0.546 Chirality : 0.050 0.390 5385 Planarity : 0.006 0.107 6096 Dihedral : 8.133 52.192 4758 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 35.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 18.73 % Favored : 80.82 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.55 % 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: -4.06 (0.12), residues: 4297 helix: -1.04 (0.14), residues: 1371 sheet: -3.75 (0.26), residues: 267 loop : -3.75 (0.11), residues: 2659 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 289 time to evaluate : 4.718 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 299 average time/residue: 0.4948 time to fit residues: 244.9300 Evaluate side-chains 299 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 288 time to evaluate : 4.330 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3673 time to fit residues: 13.2674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 3.9990 chunk 410 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 285 optimal weight: 7.9990 chunk 430 optimal weight: 30.0000 chunk 396 optimal weight: 6.9990 chunk 342 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 210 optimal weight: 0.5980 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4993 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 1.729 35120 Z= 1.197 Angle : 1.159 86.301 47399 Z= 0.546 Chirality : 0.050 0.390 5385 Planarity : 0.006 0.107 6096 Dihedral : 8.133 52.192 4758 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 36.17 Ramachandran Plot: Outliers : 0.44 % Allowed : 18.73 % Favored : 80.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.55 % 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: -4.06 (0.12), residues: 4297 helix: -1.04 (0.14), residues: 1371 sheet: -3.75 (0.26), residues: 267 loop : -3.75 (0.11), residues: 2659 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8594 Ramachandran restraints generated. 4297 Oldfield, 0 Emsley, 4297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 4.253 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.4909 time to fit residues: 235.0810 Evaluate side-chains 287 residues out of total 3846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 4.560 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 0.8980 chunk 365 optimal weight: 0.7980 chunk 104 optimal weight: 40.0000 chunk 316 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 95 optimal weight: 3.9990 chunk 343 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 352 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 848 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.162354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.158869 restraints weight = 83805.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.158353 restraints weight = 146990.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.158088 restraints weight = 149581.172| |-----------------------------------------------------------------------------| r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5013 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 1.729 35120 Z= 1.197 Angle : 1.159 86.302 47399 Z= 0.546 Chirality : 0.050 0.390 5385 Planarity : 0.006 0.107 6096 Dihedral : 8.133 52.192 4758 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 36.15 Ramachandran Plot: Outliers : 0.44 % Allowed : 18.73 % Favored : 80.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.80 % Twisted Proline : 1.10 % Twisted General : 0.55 % 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: -4.06 (0.12), residues: 4297 helix: -1.04 (0.14), residues: 1371 sheet: -3.75 (0.26), residues: 267 loop : -3.75 (0.11), residues: 2659 =============================================================================== Job complete usr+sys time: 6226.46 seconds wall clock time: 116 minutes 8.88 seconds (6968.88 seconds total)