Starting phenix.real_space_refine (version: dev) on Tue Dec 13 01:08:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/12_2022/7ckm_30388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/12_2022/7ckm_30388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/12_2022/7ckm_30388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/12_2022/7ckm_30388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/12_2022/7ckm_30388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/12_2022/7ckm_30388.pdb" } resolution = 3.37 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 2": "OD1" <-> "OD2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A ASP 119": "OD1" <-> "OD2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ASP 354": "OD1" <-> "OD2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ARG 376": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A ARG 455": "NH1" <-> "NH2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 691": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 766": "OD1" <-> "OD2" Residue "A ASP 769": "OD1" <-> "OD2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A ASP 863": "OD1" <-> "OD2" Residue "A ASP 866": "OD1" <-> "OD2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A ASP 973": "OD1" <-> "OD2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A ARG 1129": "NH1" <-> "NH2" Residue "A TYR 1132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1135": "OD1" <-> "OD2" Residue "A GLU 1146": "OE1" <-> "OE2" Residue "A ASP 1147": "OD1" <-> "OD2" Residue "A GLU 1168": "OE1" <-> "OE2" Residue "A ARG 1169": "NH1" <-> "NH2" Residue "A ASP 1188": "OD1" <-> "OD2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "A GLU 1237": "OE1" <-> "OE2" Residue "A GLU 1268": "OE1" <-> "OE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1300": "OD1" <-> "OD2" Residue "A ASP 1315": "OD1" <-> "OD2" Residue "A ASP 1319": "OD1" <-> "OD2" Residue "A TYR 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1330": "OD1" <-> "OD2" Residue "A PHE 1386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1417": "OE1" <-> "OE2" Residue "A ARG 1438": "NH1" <-> "NH2" Residue "A ARG 1473": "NH1" <-> "NH2" Residue "A ARG 1479": "NH1" <-> "NH2" Residue "A PHE 1485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1487": "OD1" <-> "OD2" Residue "A ASP 1488": "OD1" <-> "OD2" Residue "A GLU 1490": "OE1" <-> "OE2" Residue "A GLU 1513": "OE1" <-> "OE2" Residue "A GLU 1540": "OE1" <-> "OE2" Residue "A ARG 1543": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1631": "NH1" <-> "NH2" Residue "A TYR 1644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1725": "NH1" <-> "NH2" Residue "A ASP 1729": "OD1" <-> "OD2" Residue "A ARG 1742": "NH1" <-> "NH2" Residue "A ASP 1749": "OD1" <-> "OD2" Residue "A GLU 1750": "OE1" <-> "OE2" Residue "A PHE 1755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1758": "OD1" <-> "OD2" Residue "A ARG 1769": "NH1" <-> "NH2" Residue "A ASP 1774": "OD1" <-> "OD2" Residue "A ARG 1796": "NH1" <-> "NH2" Residue "B TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 70": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 13114 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1603, 12702 Classifications: {'peptide': 1603} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 47, 'TRANS': 1555} Chain breaks: 16 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 284 51.305 69.871 26.726 1.00 33.30 S ATOM 2195 SG CYS A 287 54.815 70.105 24.870 1.00 35.01 S ATOM 3474 SG CYS A 470 51.367 70.972 22.964 1.00 81.64 S ATOM 11406 SG CYS A1650 41.739 16.812 43.377 1.00 82.16 S ATOM 11419 SG CYS A1652 38.652 16.222 44.857 1.00 81.31 S ATOM 11438 SG CYS A1655 40.724 20.132 43.603 1.00 64.80 S ATOM 11510 SG CYS A1664 40.880 17.040 46.700 1.00 55.65 S ATOM 12763 SG CYS B 39 23.850 80.360 54.941 1.00 42.32 S ATOM 12784 SG CYS B 42 26.136 82.388 53.549 1.00 34.63 S ATOM 12918 SG CYS B 58 23.069 83.737 54.842 1.00 57.08 S ATOM 12943 SG CYS B 61 22.984 81.129 51.433 1.00 56.47 S ATOM 12866 SG CYS B 52 16.451 73.693 57.557 1.00 73.10 S ATOM 13033 SG CYS B 72 18.354 72.080 55.250 1.00 57.48 S ATOM 13057 SG CYS B 75 18.227 70.906 58.418 1.00 46.83 S Time building chain proxies: 8.26, per 1000 atoms: 0.63 Number of scatterers: 13114 At special positions: 0 Unit cell: (122.04, 114.48, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Mn 1 24.99 S 94 16.00 O 2452 8.00 N 2205 7.00 C 8358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.04 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.32 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1650 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1652 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1655 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1664 " pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 52 " Number of angles added : 18 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3152 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 10 sheets defined 52.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.751A pdb=" N GLU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.700A pdb=" N GLY A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 28 " --> pdb=" O HIS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 57 removed outlier: 4.035A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 removed outlier: 4.412A pdb=" N ASN A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 125 removed outlier: 4.347A pdb=" N SER A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 removed outlier: 3.763A pdb=" N LYS A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 removed outlier: 4.206A pdb=" N ARG A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.733A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 232 through 248 removed outlier: 3.844A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.886A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 338 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 346 through 365 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.520A pdb=" N CYS A 417 " --> pdb=" O TRP A 413 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.736A pdb=" N LEU A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 501 Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.561A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 578 " --> pdb=" O PRO A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 578' Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 605 through 623 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.665A pdb=" N GLN A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 removed outlier: 3.926A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 712 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.824A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 Processing helix chain 'A' and resid 863 through 872 removed outlier: 3.586A pdb=" N TYR A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 895 Processing helix chain 'A' and resid 898 through 921 Processing helix chain 'A' and resid 963 through 968 removed outlier: 4.429A pdb=" N VAL A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS A 968 " --> pdb=" O LEU A 964 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 963 through 968' Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.541A pdb=" N LEU A 975 " --> pdb=" O PRO A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.871A pdb=" N VAL A 979 " --> pdb=" O PRO A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 989 removed outlier: 4.158A pdb=" N ASP A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.756A pdb=" N ASP A1021 " --> pdb=" O SER A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1035 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 3.823A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 removed outlier: 3.660A pdb=" N HIS A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1249 Processing helix chain 'A' and resid 1264 through 1275 removed outlier: 4.679A pdb=" N GLN A1275 " --> pdb=" O HIS A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 3.749A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1429 removed outlier: 3.914A pdb=" N ASN A1429 " --> pdb=" O GLN A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1450 removed outlier: 3.624A pdb=" N SER A1450 " --> pdb=" O LEU A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1485 removed outlier: 3.744A pdb=" N PHE A1485 " --> pdb=" O ILE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1507 Processing helix chain 'A' and resid 1513 through 1520 removed outlier: 3.771A pdb=" N ASN A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 3.677A pdb=" N LEU A1545 " --> pdb=" O VAL A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.839A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1625 Processing helix chain 'A' and resid 1639 through 1645 removed outlier: 3.602A pdb=" N VAL A1643 " --> pdb=" O TYR A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1669 removed outlier: 3.800A pdb=" N ASN A1669 " --> pdb=" O ASN A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.827A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1699 removed outlier: 3.822A pdb=" N PHE A1698 " --> pdb=" O GLU A1695 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A1699 " --> pdb=" O TRP A1696 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1695 through 1699' Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1744 through 1750 Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 3.977A pdb=" N SER A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1778 through 1783 removed outlier: 3.678A pdb=" N MET A1782 " --> pdb=" O ALA A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 removed outlier: 3.758A pdb=" N LEU A1793 " --> pdb=" O ILE A1789 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.771A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 6.032A pdb=" N LEU A 559 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU A 567 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1129 through 1132 removed outlier: 3.833A pdb=" N LEU A1119 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1379 through 1381 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AA9, first strand: chain 'A' and resid 1716 through 1719 Processing sheet with id=AB1, first strand: chain 'B' and resid 50 through 51 605 hydrogen bonds defined for protein. 1752 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: 4.56 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4235 1.35 - 1.46: 2978 1.46 - 1.58: 5996 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 13341 Sorted by residual: bond pdb=" N ILE B 50 " pdb=" CA ILE B 50 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" N LYS B 40 " pdb=" CA LYS B 40 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.28e-02 6.10e+03 8.40e+00 bond pdb=" N LEU B 57 " pdb=" CA LEU B 57 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.85e+00 bond pdb=" N CYS B 58 " pdb=" CA CYS B 58 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.31e-02 5.83e+03 7.66e+00 bond pdb=" N ARG B 60 " pdb=" CA ARG B 60 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.28e-02 6.10e+03 6.86e+00 ... (remaining 13336 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.87: 286 106.87 - 113.67: 7523 113.67 - 120.47: 5232 120.47 - 127.26: 4850 127.26 - 134.06: 110 Bond angle restraints: 18001 Sorted by residual: angle pdb=" N ILE A1654 " pdb=" CA ILE A1654 " pdb=" C ILE A1654 " ideal model delta sigma weight residual 113.71 108.31 5.40 9.50e-01 1.11e+00 3.23e+01 angle pdb=" C LYS B 40 " pdb=" CA LYS B 40 " pdb=" CB LYS B 40 " ideal model delta sigma weight residual 109.83 115.39 -5.56 9.90e-01 1.02e+00 3.15e+01 angle pdb=" CA CYS B 39 " pdb=" C CYS B 39 " pdb=" O CYS B 39 " ideal model delta sigma weight residual 120.63 116.18 4.45 1.08e+00 8.57e-01 1.70e+01 angle pdb=" N CYS B 41 " pdb=" CA CYS B 41 " pdb=" C CYS B 41 " ideal model delta sigma weight residual 113.88 108.87 5.01 1.23e+00 6.61e-01 1.66e+01 angle pdb=" O CYS B 39 " pdb=" C CYS B 39 " pdb=" N LYS B 40 " ideal model delta sigma weight residual 122.12 126.03 -3.91 1.06e+00 8.90e-01 1.36e+01 ... (remaining 17996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7375 17.97 - 35.95: 572 35.95 - 53.92: 127 53.92 - 71.89: 22 71.89 - 89.87: 13 Dihedral angle restraints: 8109 sinusoidal: 3274 harmonic: 4835 Sorted by residual: dihedral pdb=" CA THR A1753 " pdb=" C THR A1753 " pdb=" N PRO A1754 " pdb=" CA PRO A1754 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" C LYS B 40 " pdb=" N LYS B 40 " pdb=" CA LYS B 40 " pdb=" CB LYS B 40 " ideal model delta harmonic sigma weight residual -122.60 -133.40 10.80 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" N LYS B 40 " pdb=" C LYS B 40 " pdb=" CA LYS B 40 " pdb=" CB LYS B 40 " ideal model delta harmonic sigma weight residual 122.80 133.35 -10.55 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 8106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1897 0.069 - 0.138: 169 0.138 - 0.207: 6 0.207 - 0.275: 0 0.275 - 0.344: 1 Chirality restraints: 2073 Sorted by residual: chirality pdb=" CA LYS B 40 " pdb=" N LYS B 40 " pdb=" C LYS B 40 " pdb=" CB LYS B 40 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ILE B 50 " pdb=" N ILE B 50 " pdb=" C ILE B 50 " pdb=" CB ILE B 50 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CB VAL A1465 " pdb=" CA VAL A1465 " pdb=" CG1 VAL A1465 " pdb=" CG2 VAL A1465 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 2070 not shown) Planarity restraints: 2274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A1393 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO A1394 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 39 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C CYS B 39 " 0.029 2.00e-02 2.50e+03 pdb=" O CYS B 39 " -0.011 2.00e-02 2.50e+03 pdb=" N LYS B 40 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 737 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO A 738 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " 0.022 5.00e-02 4.00e+02 ... (remaining 2271 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2992 2.78 - 3.31: 12415 3.31 - 3.84: 19912 3.84 - 4.37: 22789 4.37 - 4.90: 40391 Nonbonded interactions: 98499 Sorted by model distance: nonbonded pdb=" O VAL A 27 " pdb=" OG SER A 31 " model vdw 2.250 2.440 nonbonded pdb=" OD2 ASP A1173 " pdb=" OH TYR A1325 " model vdw 2.277 2.440 nonbonded pdb=" O THR A1377 " pdb=" OG1 THR A1377 " model vdw 2.284 2.440 nonbonded pdb=" ND2 ASN A 788 " pdb=" OE1 GLU A1209 " model vdw 2.300 2.520 nonbonded pdb=" O ASN A 412 " pdb=" ND2 ASN A 416 " model vdw 2.303 2.520 ... (remaining 98494 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 Zn 4 6.06 5 S 94 5.16 5 C 8358 2.51 5 N 2205 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.410 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: 3.970 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.110 Process input model: 39.930 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.003 0.039 13341 Z= 0.203 Angle : 0.581 9.424 18001 Z= 0.331 Chirality : 0.041 0.344 2073 Planarity : 0.004 0.043 2274 Dihedral : 14.022 89.867 4951 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.19), residues: 1616 helix: -0.54 (0.17), residues: 805 sheet: -1.61 (0.44), residues: 121 loop : -3.86 (0.18), residues: 690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 270 time to evaluate : 1.615 Fit side-chains outliers start: 53 outliers final: 35 residues processed: 312 average time/residue: 0.2773 time to fit residues: 121.3459 Evaluate side-chains 238 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1178 time to fit residues: 10.0240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 0.3980 chunk 95 optimal weight: 0.1980 chunk 148 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 431 HIS A 628 ASN A 647 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1013 ASN A1124 GLN A1128 ASN A1308 GLN A1414 GLN A1429 ASN A1542 ASN A1611 GLN A1783 ASN B 48 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 13341 Z= 0.157 Angle : 0.551 9.033 18001 Z= 0.282 Chirality : 0.040 0.198 2073 Planarity : 0.004 0.040 2274 Dihedral : 4.086 21.673 1755 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer Outliers : 2.62 % 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: -1.78 (0.20), residues: 1616 helix: 0.48 (0.18), residues: 831 sheet: -1.13 (0.46), residues: 121 loop : -3.51 (0.20), residues: 664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 226 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 14 residues processed: 256 average time/residue: 0.2535 time to fit residues: 94.5554 Evaluate side-chains 213 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 1.523 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1185 time to fit residues: 5.2683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 0.1980 chunk 161 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 0.0270 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1743 ASN A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 13341 Z= 0.151 Angle : 0.540 9.916 18001 Z= 0.274 Chirality : 0.039 0.169 2073 Planarity : 0.004 0.054 2274 Dihedral : 4.111 38.813 1755 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.21), residues: 1616 helix: 0.95 (0.18), residues: 832 sheet: -1.13 (0.46), residues: 128 loop : -3.39 (0.20), residues: 656 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 232 average time/residue: 0.2602 time to fit residues: 87.5679 Evaluate side-chains 206 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.585 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1192 time to fit residues: 5.8407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 HIS B 38 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 13341 Z= 0.344 Angle : 0.628 8.979 18001 Z= 0.321 Chirality : 0.043 0.167 2073 Planarity : 0.004 0.053 2274 Dihedral : 4.383 22.732 1755 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer Outliers : 2.82 % 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: -1.28 (0.21), residues: 1616 helix: 0.95 (0.18), residues: 825 sheet: -0.86 (0.47), residues: 126 loop : -3.35 (0.20), residues: 665 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 200 time to evaluate : 1.727 Fit side-chains outliers start: 42 outliers final: 25 residues processed: 233 average time/residue: 0.2654 time to fit residues: 89.6306 Evaluate side-chains 209 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 1.576 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1240 time to fit residues: 8.0064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 800 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 13341 Z= 0.258 Angle : 0.601 13.654 18001 Z= 0.305 Chirality : 0.042 0.164 2073 Planarity : 0.004 0.051 2274 Dihedral : 4.411 23.032 1755 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer Outliers : 2.28 % 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 (0.21), residues: 1616 helix: 1.12 (0.18), residues: 824 sheet: -0.78 (0.47), residues: 126 loop : -3.29 (0.21), residues: 666 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 202 time to evaluate : 1.636 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 224 average time/residue: 0.2663 time to fit residues: 86.4872 Evaluate side-chains 206 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1485 time to fit residues: 7.3366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 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 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 ASN A1414 GLN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13341 Z= 0.175 Angle : 0.559 11.799 18001 Z= 0.285 Chirality : 0.040 0.164 2073 Planarity : 0.004 0.045 2274 Dihedral : 4.238 21.916 1755 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer Outliers : 1.74 % 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: -0.79 (0.21), residues: 1616 helix: 1.36 (0.18), residues: 823 sheet: -0.54 (0.49), residues: 119 loop : -3.12 (0.21), residues: 674 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 1.496 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 17 residues processed: 226 average time/residue: 0.2683 time to fit residues: 89.3369 Evaluate side-chains 205 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1308 time to fit residues: 6.3704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1711 ASN A1743 ASN A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13341 Z= 0.189 Angle : 0.571 10.558 18001 Z= 0.290 Chirality : 0.040 0.163 2073 Planarity : 0.004 0.050 2274 Dihedral : 4.195 21.297 1755 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer Outliers : 1.28 % 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: -0.67 (0.21), residues: 1616 helix: 1.48 (0.18), residues: 823 sheet: -0.54 (0.50), residues: 121 loop : -3.09 (0.21), residues: 672 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 1.472 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 204 average time/residue: 0.2767 time to fit residues: 81.5678 Evaluate side-chains 198 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 188 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1217 time to fit residues: 4.5411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN A1743 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 13341 Z= 0.305 Angle : 0.632 9.402 18001 Z= 0.323 Chirality : 0.043 0.163 2073 Planarity : 0.004 0.058 2274 Dihedral : 4.496 22.548 1755 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer Outliers : 1.21 % 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: -0.82 (0.21), residues: 1616 helix: 1.33 (0.18), residues: 824 sheet: -0.47 (0.50), residues: 121 loop : -3.15 (0.21), residues: 671 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 1.728 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 210 average time/residue: 0.2796 time to fit residues: 84.1867 Evaluate side-chains 194 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1286 time to fit residues: 4.1790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 0.3980 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 13341 Z= 0.184 Angle : 0.574 9.525 18001 Z= 0.293 Chirality : 0.040 0.166 2073 Planarity : 0.004 0.071 2274 Dihedral : 4.323 21.053 1755 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer Outliers : 0.40 % 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: -0.63 (0.21), residues: 1616 helix: 1.51 (0.18), residues: 821 sheet: -0.70 (0.50), residues: 118 loop : -3.00 (0.21), residues: 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 1.663 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 198 average time/residue: 0.2707 time to fit residues: 77.6081 Evaluate side-chains 191 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1211 time to fit residues: 2.9942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13341 Z= 0.186 Angle : 0.583 9.212 18001 Z= 0.298 Chirality : 0.040 0.166 2073 Planarity : 0.004 0.074 2274 Dihedral : 4.259 21.413 1755 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer Outliers : 0.27 % 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: -0.56 (0.21), residues: 1616 helix: 1.56 (0.18), residues: 822 sheet: -0.71 (0.50), residues: 116 loop : -2.95 (0.22), residues: 678 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 1.807 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 191 average time/residue: 0.2814 time to fit residues: 77.8610 Evaluate side-chains 190 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1320 time to fit residues: 2.9855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 119 optimal weight: 0.0050 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 133 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.169223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.129853 restraints weight = 16871.242| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.75 r_work: 0.3168 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 13341 Z= 0.148 Angle : 0.554 10.775 18001 Z= 0.282 Chirality : 0.040 0.230 2073 Planarity : 0.004 0.072 2274 Dihedral : 4.074 20.826 1755 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 0.20 % 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: -0.38 (0.22), residues: 1616 helix: 1.75 (0.18), residues: 821 sheet: -0.72 (0.49), residues: 116 loop : -2.89 (0.22), residues: 679 =============================================================================== Job complete usr+sys time: 2688.66 seconds wall clock time: 49 minutes 42.96 seconds (2982.96 seconds total)