Starting phenix.real_space_refine on Thu Mar 14 15:42:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/03_2024/7oti_13060.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/03_2024/7oti_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_13060/03_2024/7oti_13060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/03_2024/7oti_13060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/03_2024/7oti_13060.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oti_13060/03_2024/7oti_13060.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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-dev-5265/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: 5.25, per 1000 atoms: 0.57 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: 3.66 Conformation dependent library (CDL) restraints added in 1.7 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: 1.05 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: 3.27 Time building geometry restraints manager: 3.96 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: 0.450 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: 2.840 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.680 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- 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 % Allowed : 9.63 % Favored : 85.66 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.130 0.023 TRP A 132 HIS 0.027 0.005 HIS A1003 PHE 0.069 0.013 PHE A 979 TYR 0.189 0.029 TYR A 359 ARG 0.024 0.003 ARG A1164 *********************** 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 : 0.999 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: A 64 LEU cc_start: 0.7039 (mt) cc_final: 0.6543 (mm) REVERT: A 108 THR cc_start: 0.1207 (m) cc_final: 0.0797 (m) REVERT: A 175 VAL cc_start: 0.3434 (m) cc_final: 0.2806 (m) REVERT: A 202 ILE cc_start: 0.6083 (mp) cc_final: 0.5833 (tp) REVERT: A 512 LEU cc_start: -0.0350 (mt) cc_final: -0.0670 (mt) REVERT: A 542 VAL cc_start: -0.1632 (OUTLIER) cc_final: -0.2003 (p) REVERT: A 574 GLU cc_start: -0.1997 (OUTLIER) cc_final: -0.3300 (mm-30) REVERT: A 721 GLN cc_start: 0.5273 (mm-40) cc_final: 0.5044 (mm-40) REVERT: A 926 ASN cc_start: 0.3776 (t0) cc_final: 0.3178 (t0) REVERT: A 941 THR cc_start: 0.5614 (m) cc_final: 0.5199 (m) REVERT: A 978 VAL cc_start: 0.6526 (t) cc_final: 0.6311 (t) REVERT: A 1078 LEU cc_start: 0.1434 (mt) cc_final: 0.0882 (mp) REVERT: A 1139 GLU cc_start: 0.4120 (mp0) cc_final: 0.2274 (pp20) outliers start: 46 outliers final: 5 residues processed: 302 average time/residue: 0.2597 time to fit residues: 102.1292 Evaluate side-chains 162 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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: 3.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 107 optimal weight: 0.2980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3037 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9339 Z= 0.245 Angle : 0.812 10.683 12626 Z= 0.440 Chirality : 0.046 0.191 1456 Planarity : 0.005 0.048 1605 Dihedral : 7.066 42.201 1267 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.22 % Favored : 92.28 % Rotamer: Outliers : 0.72 % Allowed : 5.23 % Favored : 94.06 % 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: -1.99 (0.23), residues: 1178 helix: -0.54 (0.18), residues: 751 sheet: -2.61 (0.56), residues: 58 loop : -2.57 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 694 HIS 0.007 0.002 HIS A1253 PHE 0.041 0.003 PHE A 196 TYR 0.020 0.002 TYR A1263 ARG 0.005 0.001 ARG A 785 *********************** 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 208 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ILE cc_start: 0.5683 (mm) cc_final: 0.3894 (mm) REVERT: A 186 ILE cc_start: 0.5481 (pt) cc_final: 0.4628 (pt) REVERT: A 812 THR cc_start: 0.6733 (p) cc_final: 0.6330 (p) REVERT: A 897 ILE cc_start: 0.5234 (pt) cc_final: 0.4717 (pt) REVERT: A 1026 MET cc_start: 0.1738 (mpp) cc_final: 0.1305 (mpp) outliers start: 7 outliers final: 2 residues processed: 207 average time/residue: 0.2442 time to fit residues: 67.6610 Evaluate side-chains 132 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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: 0.0050 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 29 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 95 optimal weight: 0.0170 chunk 106 optimal weight: 0.0070 chunk 36 optimal weight: 0.0470 chunk 86 optimal weight: 0.9990 overall best weight: 0.0748 ------------------------------------------------------------------------------- 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN A 292 ASN A 437 GLN ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN A1020 GLN A1234 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3015 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9339 Z= 0.209 Angle : 0.746 8.562 12626 Z= 0.403 Chirality : 0.044 0.162 1456 Planarity : 0.005 0.050 1605 Dihedral : 6.390 35.498 1267 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.05 % Favored : 92.44 % Rotamer: Outliers : 0.10 % Allowed : 3.79 % Favored : 96.11 % 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: -1.50 (0.24), residues: 1178 helix: -0.15 (0.19), residues: 735 sheet: -2.36 (0.57), residues: 58 loop : -2.32 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 799 HIS 0.008 0.001 HIS A1191 PHE 0.037 0.002 PHE A 148 TYR 0.030 0.002 TYR A 41 ARG 0.012 0.001 ARG A 463 *********************** 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 183 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.782 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: A 99 MET cc_start: 0.3166 (mmm) cc_final: 0.2002 (mpp) REVERT: A 131 PHE cc_start: 0.2824 (t80) cc_final: 0.2612 (t80) REVERT: A 152 MET cc_start: 0.2949 (ptt) cc_final: 0.2209 (ptt) REVERT: A 461 TYR cc_start: 0.3286 (t80) cc_final: 0.3068 (t80) REVERT: A 845 ILE cc_start: 0.3078 (mm) cc_final: 0.2708 (mm) REVERT: A 897 ILE cc_start: 0.4743 (pt) cc_final: 0.4431 (pt) REVERT: A 904 VAL cc_start: 0.5383 (t) cc_final: 0.5070 (t) REVERT: A 1026 MET cc_start: 0.0956 (mpp) cc_final: -0.0339 (ppp) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2465 time to fit residues: 60.1578 Evaluate side-chains 131 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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: 0.0000 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 overall best weight: 0.9790 ------------------------------------------------------------------------------- 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 ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 GLN ** 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** ** A1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3154 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9339 Z= 0.187 Angle : 0.702 10.192 12626 Z= 0.374 Chirality : 0.043 0.157 1456 Planarity : 0.005 0.050 1605 Dihedral : 5.975 34.198 1267 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.05 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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: 0.02 (0.19), residues: 739 sheet: -2.00 (0.58), residues: 66 loop : -2.28 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 799 HIS 0.007 0.001 HIS A1191 PHE 0.034 0.002 PHE A 196 TYR 0.021 0.002 TYR A 243 ARG 0.004 0.000 ARG A 138 *********************** 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 178 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.981 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: A 99 MET cc_start: 0.3092 (mmm) cc_final: 0.1989 (mpp) REVERT: A 152 MET cc_start: 0.3097 (ptt) cc_final: 0.2563 (ptm) REVERT: A 788 VAL cc_start: 0.6588 (m) cc_final: 0.5675 (m) REVERT: A 845 ILE cc_start: 0.3270 (mm) cc_final: 0.2959 (mm) REVERT: A 891 LYS cc_start: 0.7090 (mmmt) cc_final: 0.6685 (mmmt) REVERT: A 897 ILE cc_start: 0.4975 (pt) cc_final: 0.4478 (pt) REVERT: A 904 VAL cc_start: 0.5422 (t) cc_final: 0.5013 (t) REVERT: A 1026 MET cc_start: 0.0848 (mpp) cc_final: -0.0681 (ppp) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2412 time to fit residues: 59.0009 Evaluate side-chains 130 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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: 8.9990 chunk 64 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 149 HIS A 153 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3741 moved from start: 0.7712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 9339 Z= 0.325 Angle : 0.881 9.081 12626 Z= 0.470 Chirality : 0.049 0.215 1456 Planarity : 0.007 0.091 1605 Dihedral : 6.461 36.532 1267 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 27.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.49 % Favored : 91.00 % Rotamer: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.47 % 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: -2.02 (0.23), residues: 1178 helix: -0.56 (0.18), residues: 755 sheet: -2.33 (0.63), residues: 53 loop : -2.66 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 158 HIS 0.014 0.003 HIS A1253 PHE 0.035 0.003 PHE A 196 TYR 0.028 0.003 TYR A1263 ARG 0.017 0.002 ARG A 828 *********************** 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 175 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 174 time to evaluate : 1.016 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: A 99 MET cc_start: 0.2841 (mmm) cc_final: 0.2149 (mpp) REVERT: A 152 MET cc_start: 0.2981 (ptt) cc_final: 0.2708 (ptm) REVERT: A 186 ILE cc_start: 0.5309 (pt) cc_final: 0.4374 (pt) REVERT: A 812 THR cc_start: 0.7270 (p) cc_final: 0.6952 (p) REVERT: A 845 ILE cc_start: 0.3863 (mm) cc_final: 0.3550 (mm) REVERT: A 904 VAL cc_start: 0.5539 (t) cc_final: 0.5252 (t) REVERT: A 937 THR cc_start: 0.6374 (p) cc_final: 0.6100 (p) REVERT: A 1026 MET cc_start: 0.1725 (mpp) cc_final: -0.0400 (ppp) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.2455 time to fit residues: 57.2478 Evaluate side-chains 127 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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: 10.0000 chunk 102 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 154 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3561 moved from start: 0.7957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9339 Z= 0.199 Angle : 0.757 11.156 12626 Z= 0.394 Chirality : 0.045 0.266 1456 Planarity : 0.005 0.047 1605 Dihedral : 5.894 32.939 1267 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.56 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: -1.51 (0.24), residues: 1178 helix: -0.22 (0.18), residues: 750 sheet: -2.37 (0.68), residues: 48 loop : -2.29 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 694 HIS 0.007 0.001 HIS A1253 PHE 0.042 0.002 PHE A 979 TYR 0.022 0.002 TYR A 112 ARG 0.008 0.001 ARG A1229 *********************** 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 161 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.998 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: A 152 MET cc_start: 0.2676 (ptt) cc_final: 0.1823 (ptp) REVERT: A 186 ILE cc_start: 0.5653 (pt) cc_final: 0.4393 (pt) REVERT: A 788 VAL cc_start: 0.6608 (m) cc_final: 0.6376 (m) REVERT: A 845 ILE cc_start: 0.3537 (mm) cc_final: 0.3184 (mm) REVERT: A 904 VAL cc_start: 0.5476 (t) cc_final: 0.5104 (t) REVERT: A 1014 ILE cc_start: 0.4643 (pt) cc_final: 0.4442 (pt) REVERT: A 1026 MET cc_start: 0.1148 (mpp) cc_final: -0.0962 (ppp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.2352 time to fit residues: 51.5877 Evaluate side-chains 116 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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: 8.9990 chunk 12 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN ** A 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3547 moved from start: 0.8275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9339 Z= 0.200 Angle : 0.712 9.786 12626 Z= 0.373 Chirality : 0.044 0.202 1456 Planarity : 0.005 0.045 1605 Dihedral : 5.615 32.961 1267 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.64 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -1.31 (0.24), residues: 1178 helix: -0.08 (0.18), residues: 743 sheet: -1.97 (0.66), residues: 56 loop : -2.15 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 694 HIS 0.006 0.001 HIS A1253 PHE 0.030 0.002 PHE A 196 TYR 0.021 0.002 TYR A 359 ARG 0.008 0.001 ARG A 258 *********************** 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 156 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.075 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: A 50 MET cc_start: 0.2791 (tmm) cc_final: 0.2500 (tmm) REVERT: A 152 MET cc_start: 0.3037 (ptt) cc_final: 0.2174 (ptp) REVERT: A 186 ILE cc_start: 0.5033 (pt) cc_final: 0.4825 (pt) REVERT: A 845 ILE cc_start: 0.3292 (mm) cc_final: 0.3048 (mm) REVERT: A 904 VAL cc_start: 0.5377 (t) cc_final: 0.4909 (t) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2500 time to fit residues: 52.8104 Evaluate side-chains 128 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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: 0.9980 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 162 HIS ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 GLN A 926 ASN A1020 GLN A1149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3515 moved from start: 0.8579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9339 Z= 0.184 Angle : 0.708 9.879 12626 Z= 0.370 Chirality : 0.043 0.167 1456 Planarity : 0.004 0.045 1605 Dihedral : 5.496 30.703 1267 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.88 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: -1.23 (0.24), residues: 1178 helix: 0.01 (0.19), residues: 734 sheet: -1.51 (0.67), residues: 58 loop : -2.22 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 799 HIS 0.005 0.001 HIS A1253 PHE 0.029 0.002 PHE A 78 TYR 0.016 0.002 TYR A1040 ARG 0.010 0.001 ARG A1229 *********************** 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 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.3028 (ptt) cc_final: 0.2241 (ptp) REVERT: A 186 ILE cc_start: 0.5542 (pt) cc_final: 0.5162 (pt) REVERT: A 785 ARG cc_start: 0.2566 (mtt-85) cc_final: 0.1365 (mtp85) REVERT: A 788 VAL cc_start: 0.6512 (m) cc_final: 0.6220 (m) REVERT: A 845 ILE cc_start: 0.3218 (mm) cc_final: 0.2966 (mm) REVERT: A 904 VAL cc_start: 0.5284 (t) cc_final: 0.4769 (t) REVERT: A 1014 ILE cc_start: 0.4710 (pt) cc_final: 0.4503 (pt) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2354 time to fit residues: 50.3716 Evaluate side-chains 125 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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: 0.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.0370 chunk 32 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.7662 ------------------------------------------------------------------------------- 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 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3497 moved from start: 0.8779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9339 Z= 0.179 Angle : 0.701 10.040 12626 Z= 0.364 Chirality : 0.043 0.227 1456 Planarity : 0.004 0.048 1605 Dihedral : 5.339 30.146 1267 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.30 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -1.14 (0.24), residues: 1178 helix: 0.06 (0.19), residues: 738 sheet: -1.32 (0.69), residues: 58 loop : -2.18 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 799 HIS 0.005 0.001 HIS A1253 PHE 0.028 0.002 PHE A 78 TYR 0.018 0.002 TYR A1040 ARG 0.008 0.001 ARG A1229 *********************** 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 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.052 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: A 50 MET cc_start: 0.2659 (tmm) cc_final: 0.2283 (tmm) REVERT: A 152 MET cc_start: 0.3162 (ptt) cc_final: 0.2501 (ptm) REVERT: A 788 VAL cc_start: 0.6380 (m) cc_final: 0.5958 (m) REVERT: A 904 VAL cc_start: 0.5363 (t) cc_final: 0.4919 (t) REVERT: A 1014 ILE cc_start: 0.4722 (pt) cc_final: 0.4513 (mm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2351 time to fit residues: 50.6064 Evaluate side-chains 129 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 0.0770 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.7942 ------------------------------------------------------------------------------- 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3506 moved from start: 0.9072 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= 0.176 Angle : 0.698 9.906 12626 Z= 0.362 Chirality : 0.043 0.176 1456 Planarity : 0.004 0.048 1605 Dihedral : 5.247 29.935 1267 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.62 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1178 helix: 0.10 (0.19), residues: 736 sheet: -1.26 (0.69), residues: 58 loop : -2.17 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 799 HIS 0.004 0.001 HIS A1253 PHE 0.027 0.002 PHE A 196 TYR 0.019 0.002 TYR A 946 ARG 0.006 0.001 ARG A1229 ********************** 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 153 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.979 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: A 50 MET cc_start: 0.2778 (tmm) cc_final: 0.2388 (tmm) REVERT: A 152 MET cc_start: 0.3082 (ptt) cc_final: 0.2817 (ptm) REVERT: A 186 ILE cc_start: 0.5986 (pt) cc_final: 0.5671 (pt) REVERT: A 257 ILE cc_start: 0.5312 (mp) cc_final: 0.4996 (mp) REVERT: A 788 VAL cc_start: 0.6330 (m) cc_final: 0.5820 (m) REVERT: A 904 VAL cc_start: 0.5391 (t) cc_final: 0.5013 (t) REVERT: A 1014 ILE cc_start: 0.4622 (pt) cc_final: 0.4272 (pt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2380 time to fit residues: 49.7986 Evaluate side-chains 130 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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: 0.6980 chunk 86 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 96 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN A 452 GLN A 721 GLN A 747 ASN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN A 918 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.180286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.167312 restraints weight = 43535.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.170089 restraints weight = 30255.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.172019 restraints weight = 21903.361| |-----------------------------------------------------------------------------| r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5098 moved from start: 0.9222 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= 0.174 Angle : 0.694 9.664 12626 Z= 0.361 Chirality : 0.043 0.174 1456 Planarity : 0.004 0.049 1605 Dihedral : 5.132 28.495 1267 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.62 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1178 helix: 0.18 (0.19), residues: 733 sheet: -1.19 (0.69), residues: 58 loop : -2.14 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 799 HIS 0.003 0.001 HIS A1253 PHE 0.046 0.002 PHE A 979 TYR 0.020 0.002 TYR A 946 ARG 0.006 0.001 ARG A 828 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2047.29 seconds wall clock time: 37 minutes 43.10 seconds (2263.10 seconds total)