Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 06:42:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/04_2023/7oti_13060.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/04_2023/7oti_13060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/04_2023/7oti_13060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/04_2023/7oti_13060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/04_2023/7oti_13060.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/04_2023/7oti_13060.pdb" } resolution = 4.2 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= 0.007 sd= 0.210 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 5895 2.51 5 N 1552 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 237": "OD1" <-> "OD2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ASP 450": "OD1" <-> "OD2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A ASP 490": "OD1" <-> "OD2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ASP 551": "OD1" <-> "OD2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 802": "OD1" <-> "OD2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 887": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A ARG 908": "NH1" <-> "NH2" Residue "A GLU 909": "OE1" <-> "OE2" Residue "A PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 990": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A ASP 1015": "OD1" <-> "OD2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A PHE 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1080": "OE1" <-> "OE2" Residue "A PHE 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1084": "OD1" <-> "OD2" Residue "A GLU 1115": "OE1" <-> "OE2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A ASP 1167": "OD1" <-> "OD2" Residue "A GLU 1205": "OE1" <-> "OE2" Residue "A GLU 1219": "OE1" <-> "OE2" Residue "A GLU 1249": "OE1" <-> "OE2" Residue "A PHE 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9171 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9171 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 29, 'TRANS': 1152} Chain breaks: 1 Time building chain proxies: 5.14, per 1000 atoms: 0.56 Number of scatterers: 9171 At special positions: 0 Unit cell: (120.988, 109.515, 112.644, 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 38 16.00 O 1686 8.00 N 1552 7.00 C 5895 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.8 seconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 68.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 3.881A pdb=" N PHE A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 40 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 86 removed outlier: 3.727A pdb=" N LEU A 48 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 3.533A pdb=" N THR A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 77 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 134 removed outlier: 4.158A pdb=" N ARG A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE A 100 " --> pdb=" O LYS A 96 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 111 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 122 " --> pdb=" O GLY A 118 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 removed outlier: 5.425A pdb=" N HIS A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 removed outlier: 3.793A pdb=" N ASP A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 181 removed outlier: 4.108A pdb=" N ASP A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 4.149A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 256 removed outlier: 3.877A pdb=" N THR A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 4.162A pdb=" N LYS A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LYS A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 263 Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.827A pdb=" N GLU A 269 " --> pdb=" O GLN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 315 removed outlier: 3.995A pdb=" N ASN A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 277 " --> pdb=" O TYR A 273 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 363 removed outlier: 3.771A pdb=" N PHE A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 3.847A pdb=" N GLY A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 436 removed outlier: 4.156A pdb=" N VAL A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 503 Processing helix chain 'A' and resid 505 through 511 removed outlier: 3.532A pdb=" N ILE A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 Processing helix chain 'A' and resid 528 through 542 removed outlier: 3.811A pdb=" N ILE A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 573 removed outlier: 4.079A pdb=" N LYS A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 590 removed outlier: 3.710A pdb=" N VAL A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.637A pdb=" N ARG A 613 " --> pdb=" O ASP A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 694 through 699 removed outlier: 3.619A pdb=" N LEU A 699 " --> pdb=" O ARG A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.649A pdb=" N GLU A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.953A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 4.078A pdb=" N SER A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.529A pdb=" N GLN A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 749 " --> pdb=" O ARG A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 793 removed outlier: 4.248A pdb=" N LYS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 838 removed outlier: 3.652A pdb=" N THR A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ALA A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU A 829 " --> pdb=" O THR A 825 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 removed outlier: 3.815A pdb=" N ILE A 843 " --> pdb=" O LEU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 889 Proline residue: A 862 - end of helix removed outlier: 4.117A pdb=" N LYS A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 899 through 905 removed outlier: 3.830A pdb=" N VAL A 903 " --> pdb=" O PHE A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 920 removed outlier: 4.155A pdb=" N GLN A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 918 " --> pdb=" O THR A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 955 removed outlier: 3.929A pdb=" N MET A 945 " --> pdb=" O THR A 941 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.740A pdb=" N GLN A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1010 removed outlier: 3.716A pdb=" N VAL A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER A 989 " --> pdb=" O GLY A 985 " (cutoff:3.500A) Proline residue: A 992 - end of helix removed outlier: 3.613A pdb=" N THR A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS A1003 " --> pdb=" O VAL A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1027 Processing helix chain 'A' and resid 1042 through 1046 Processing helix chain 'A' and resid 1071 through 1080 removed outlier: 4.459A pdb=" N LEU A1078 " --> pdb=" O THR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1100 Processing helix chain 'A' and resid 1101 through 1106 Processing helix chain 'A' and resid 1122 through 1128 removed outlier: 3.939A pdb=" N ALA A1128 " --> pdb=" O ALA A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1148 Processing helix chain 'A' and resid 1151 through 1156 Processing helix chain 'A' and resid 1159 through 1163 Processing helix chain 'A' and resid 1173 through 1187 Processing helix chain 'A' and resid 1204 through 1215 Processing helix chain 'A' and resid 1229 through 1235 removed outlier: 3.756A pdb=" N ILE A1233 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1257 Processing helix chain 'A' and resid 1261 through 1269 removed outlier: 5.395A pdb=" N VAL A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 409 removed outlier: 3.890A pdb=" N GLY A 408 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 393 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 393 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP A 444 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.409A pdb=" N ALA A 420 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 597 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL A 422 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 604 " --> pdb=" O GLY A 596 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP A 598 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 466 through 468 Processing sheet with id=AA4, first strand: chain 'A' and resid 1049 through 1055 removed outlier: 6.264A pdb=" N GLN A1050 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL A1037 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU A1052 " --> pdb=" O GLY A1035 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A1036 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA A1087 " --> pdb=" O VAL A1036 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1192 through 1195 removed outlier: 6.573A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN A1060 " --> pdb=" O CYS A1223 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL A1225 " --> pdb=" O GLN A1060 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A1062 " --> pdb=" O VAL A1225 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A1061 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL A1240 " --> pdb=" O THR A1061 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A1063 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE A1242 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL A1065 " --> pdb=" O ILE A1242 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A1249 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN A1243 " --> pdb=" O VAL A1247 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL A1247 " --> pdb=" O GLN A1243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1120 through 1121 removed outlier: 4.239A pdb=" N GLY A1166 " --> pdb=" O CYS A1121 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1524 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: 3.22 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1817 1.33 - 1.45: 2112 1.45 - 1.58: 5341 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 9339 Sorted by residual: bond pdb=" CA PRO A 740 " pdb=" C PRO A 740 " ideal model delta sigma weight residual 1.517 1.549 -0.032 9.30e-03 1.16e+04 1.18e+01 bond pdb=" CA PRO A 689 " pdb=" C PRO A 689 " ideal model delta sigma weight residual 1.517 1.548 -0.031 9.30e-03 1.16e+04 1.13e+01 bond pdb=" CZ ARG A1229 " pdb=" NH2 ARG A1229 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.96e+00 bond pdb=" CZ ARG A 783 " pdb=" NH2 ARG A 783 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.51e+00 bond pdb=" CZ ARG A1218 " pdb=" NH2 ARG A1218 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.46e+00 ... (remaining 9334 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.33: 214 106.33 - 113.66: 4588 113.66 - 121.00: 5005 121.00 - 128.34: 2750 128.34 - 135.68: 69 Bond angle restraints: 12626 Sorted by residual: angle pdb=" N PRO A 689 " pdb=" CA PRO A 689 " pdb=" C PRO A 689 " ideal model delta sigma weight residual 110.70 122.42 -11.72 1.22e+00 6.72e-01 9.23e+01 angle pdb=" CA PHE A 979 " pdb=" CB PHE A 979 " pdb=" CG PHE A 979 " ideal model delta sigma weight residual 113.80 122.00 -8.20 1.00e+00 1.00e+00 6.72e+01 angle pdb=" N PRO A 740 " pdb=" CA PRO A 740 " pdb=" C PRO A 740 " ideal model delta sigma weight residual 110.70 119.98 -9.28 1.22e+00 6.72e-01 5.78e+01 angle pdb=" CA ASP A 558 " pdb=" CB ASP A 558 " pdb=" CG ASP A 558 " ideal model delta sigma weight residual 112.60 119.77 -7.17 1.00e+00 1.00e+00 5.14e+01 angle pdb=" CA PHE A 39 " pdb=" CB PHE A 39 " pdb=" CG PHE A 39 " ideal model delta sigma weight residual 113.80 119.83 -6.03 1.00e+00 1.00e+00 3.64e+01 ... (remaining 12621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 5040 19.50 - 38.99: 389 38.99 - 58.49: 93 58.49 - 77.98: 28 77.98 - 97.48: 18 Dihedral angle restraints: 5568 sinusoidal: 2178 harmonic: 3390 Sorted by residual: dihedral pdb=" CA VAL A 474 " pdb=" C VAL A 474 " pdb=" N LEU A 475 " pdb=" CA LEU A 475 " ideal model delta harmonic sigma weight residual 180.00 142.13 37.87 0 5.00e+00 4.00e-02 5.74e+01 dihedral pdb=" CA ILE A 384 " pdb=" C ILE A 384 " pdb=" N GLN A 385 " pdb=" CA GLN A 385 " ideal model delta harmonic sigma weight residual 180.00 143.38 36.62 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA LEU A1092 " pdb=" C LEU A1092 " pdb=" N ASP A1093 " pdb=" CA ASP A1093 " ideal model delta harmonic sigma weight residual 180.00 143.68 36.32 0 5.00e+00 4.00e-02 5.28e+01 ... (remaining 5565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1079 0.108 - 0.215: 310 0.215 - 0.323: 50 0.323 - 0.430: 13 0.430 - 0.538: 4 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CA THR A1204 " pdb=" N THR A1204 " pdb=" C THR A1204 " pdb=" CB THR A1204 " both_signs ideal model delta sigma weight residual False 2.53 1.99 0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" CA ASP A 517 " pdb=" N ASP A 517 " pdb=" C ASP A 517 " pdb=" CB ASP A 517 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA LYS A1010 " pdb=" N LYS A1010 " pdb=" C LYS A1010 " pdb=" CB LYS A1010 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.82e+00 ... (remaining 1453 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 359 " 0.188 2.00e-02 2.50e+03 1.12e-01 2.50e+02 pdb=" CG TYR A 359 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 359 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 359 " -0.093 2.00e-02 2.50e+03 pdb=" CE1 TYR A 359 " -0.086 2.00e-02 2.50e+03 pdb=" CE2 TYR A 359 " -0.072 2.00e-02 2.50e+03 pdb=" CZ TYR A 359 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 359 " 0.189 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1083 " -0.186 2.00e-02 2.50e+03 1.07e-01 2.31e+02 pdb=" CG TYR A1083 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A1083 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR A1083 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A1083 " 0.065 2.00e-02 2.50e+03 pdb=" CE2 TYR A1083 " 0.077 2.00e-02 2.50e+03 pdb=" CZ TYR A1083 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A1083 " -0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 243 " -0.187 2.00e-02 2.50e+03 9.75e-02 1.90e+02 pdb=" CG TYR A 243 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR A 243 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 243 " 0.090 2.00e-02 2.50e+03 pdb=" CE1 TYR A 243 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR A 243 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 243 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 243 " -0.131 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4404 2.99 - 3.46: 10662 3.46 - 3.94: 15991 3.94 - 4.42: 17608 4.42 - 4.90: 27951 Nonbonded interactions: 76616 Sorted by model distance: nonbonded pdb=" OD1 ASP A 687 " pdb=" OG SER A1000 " model vdw 2.507 2.440 nonbonded pdb=" OG SER A1173 " pdb=" OD2 ASP A1203 " model vdw 2.525 2.440 nonbonded pdb=" OG SER A 88 " pdb=" OD2 ASP A 95 " model vdw 2.531 2.440 nonbonded pdb=" OD2 ASP A 802 " pdb=" OG1 THR A1042 " model vdw 2.536 2.440 nonbonded pdb=" OE2 GLU A 155 " pdb=" OG SER A 375 " model vdw 2.538 2.440 ... (remaining 76611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.170 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.630 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2534 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 : 0.014 0.041 9339 Z= 0.922 Angle : 1.994 11.720 12626 Z= 1.325 Chirality : 0.104 0.538 1456 Planarity : 0.018 0.181 1605 Dihedral : 16.952 97.478 3394 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 1.36 % Allowed : 10.78 % Favored : 87.86 % Rotamer Outliers : 4.71 % Cbeta Deviations : 1.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.20), residues: 1178 helix: -1.84 (0.16), residues: 743 sheet: -3.47 (0.59), residues: 43 loop : -3.14 (0.27), residues: 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 267 time to evaluate : 1.034 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 outliers start: 46 outliers final: 5 residues processed: 302 average time/residue: 0.2634 time to fit residues: 103.4889 Evaluate side-chains 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2173 time to fit residues: 2.9578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN A 424 ASN A 437 GLN A 504 ASN A 608 HIS A 820 GLN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2953 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9339 Z= 0.234 Angle : 0.805 10.499 12626 Z= 0.436 Chirality : 0.046 0.200 1456 Planarity : 0.005 0.049 1605 Dihedral : 7.028 41.225 1267 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.22 % Favored : 92.28 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.23), residues: 1178 helix: -0.47 (0.18), residues: 750 sheet: -2.75 (0.54), residues: 57 loop : -2.52 (0.30), residues: 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 203 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 208 average time/residue: 0.2554 time to fit residues: 70.6324 Evaluate side-chains 129 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0806 time to fit residues: 1.5224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN A 437 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN ** A 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN A1020 GLN A1234 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3119 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9339 Z= 0.204 Angle : 0.743 9.480 12626 Z= 0.400 Chirality : 0.044 0.155 1456 Planarity : 0.005 0.052 1605 Dihedral : 6.310 34.128 1267 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.22 % Favored : 92.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.24), residues: 1178 helix: -0.09 (0.19), residues: 742 sheet: -2.29 (0.60), residues: 58 loop : -2.31 (0.30), residues: 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.032 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 outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2427 time to fit residues: 59.0409 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.1980 chunk 80 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3213 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9339 Z= 0.195 Angle : 0.716 9.966 12626 Z= 0.382 Chirality : 0.044 0.161 1456 Planarity : 0.005 0.054 1605 Dihedral : 5.969 34.631 1267 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.30 % Favored : 92.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1178 helix: 0.09 (0.19), residues: 734 sheet: -1.81 (0.61), residues: 61 loop : -2.16 (0.30), residues: 383 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.200 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 outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2442 time to fit residues: 60.7901 Evaluate side-chains 132 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.1980 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 0.0030 overall best weight: 2.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 394 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3533 moved from start: 0.7407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 9339 Z= 0.235 Angle : 0.777 10.400 12626 Z= 0.414 Chirality : 0.046 0.244 1456 Planarity : 0.005 0.055 1605 Dihedral : 5.978 34.707 1267 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.98 % Favored : 91.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.23), residues: 1178 helix: -0.17 (0.18), residues: 755 sheet: -1.88 (0.64), residues: 56 loop : -2.33 (0.30), residues: 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.022 Fit side-chains 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: 170 average time/residue: 0.2430 time to fit residues: 56.2443 Evaluate side-chains 124 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.0010 chunk 22 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 HIS ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 452 GLN A 926 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3577 moved from start: 0.7939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9339 Z= 0.211 Angle : 0.753 10.598 12626 Z= 0.400 Chirality : 0.044 0.163 1456 Planarity : 0.005 0.047 1605 Dihedral : 5.762 34.490 1267 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.96 % Favored : 92.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.24), residues: 1178 helix: -0.13 (0.18), residues: 755 sheet: -2.14 (0.71), residues: 48 loop : -2.31 (0.31), residues: 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.134 Fit side-chains 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: 167 average time/residue: 0.2549 time to fit residues: 58.5055 Evaluate side-chains 125 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 153 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 747 ASN A 805 ASN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3883 moved from start: 0.8991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 9339 Z= 0.296 Angle : 0.856 15.360 12626 Z= 0.453 Chirality : 0.048 0.201 1456 Planarity : 0.006 0.057 1605 Dihedral : 6.263 37.089 1267 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 29.33 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.83 % Favored : 90.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.24), residues: 1178 helix: -0.38 (0.18), residues: 757 sheet: -2.27 (0.70), residues: 53 loop : -2.55 (0.31), residues: 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.026 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 outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2386 time to fit residues: 55.6538 Evaluate side-chains 119 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN A 926 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3633 moved from start: 0.9085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 9339 Z= 0.206 Angle : 0.754 14.679 12626 Z= 0.395 Chirality : 0.045 0.222 1456 Planarity : 0.005 0.054 1605 Dihedral : 5.712 32.289 1267 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.88 % Favored : 92.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.24), residues: 1178 helix: -0.11 (0.18), residues: 752 sheet: -2.25 (0.78), residues: 40 loop : -2.35 (0.32), residues: 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.970 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 outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2549 time to fit residues: 56.5022 Evaluate side-chains 125 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN A 926 ASN A1228 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3689 moved from start: 0.9396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 9339 Z= 0.201 Angle : 0.741 9.956 12626 Z= 0.392 Chirality : 0.045 0.197 1456 Planarity : 0.005 0.056 1605 Dihedral : 5.579 32.509 1267 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.72 % Favored : 91.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.24), residues: 1178 helix: -0.05 (0.19), residues: 743 sheet: -1.56 (0.73), residues: 50 loop : -2.27 (0.32), residues: 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.074 Fit side-chains 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: 163 average time/residue: 0.2539 time to fit residues: 56.1403 Evaluate side-chains 118 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3905 moved from start: 0.9868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 9339 Z= 0.266 Angle : 0.814 10.291 12626 Z= 0.432 Chirality : 0.047 0.192 1456 Planarity : 0.006 0.068 1605 Dihedral : 5.888 34.538 1267 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 27.60 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.83 % Favored : 90.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1178 helix: -0.34 (0.18), residues: 755 sheet: -1.77 (0.71), residues: 50 loop : -2.43 (0.32), residues: 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.010 Fit side-chains 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: 160 average time/residue: 0.2418 time to fit residues: 52.9506 Evaluate side-chains 113 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 0.0470 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 HIS ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 ASN A 852 GLN ** A1191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.176261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.163985 restraints weight = 43855.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.166542 restraints weight = 30227.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.168379 restraints weight = 21881.977| |-----------------------------------------------------------------------------| r_work (final): 0.4622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5283 moved from start: 0.9895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 9339 Z= 0.191 Angle : 0.751 10.130 12626 Z= 0.394 Chirality : 0.045 0.181 1456 Planarity : 0.005 0.058 1605 Dihedral : 5.563 30.607 1267 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.22 % Favored : 92.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.24), residues: 1178 helix: -0.01 (0.19), residues: 742 sheet: -1.69 (0.66), residues: 58 loop : -2.27 (0.32), residues: 378 =============================================================================== Job complete usr+sys time: 2032.14 seconds wall clock time: 37 minutes 48.31 seconds (2268.31 seconds total)