Starting phenix.real_space_refine on Wed Nov 15 20:51:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/11_2023/7ckm_30388.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/11_2023/7ckm_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_30388/11_2023/7ckm_30388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/11_2023/7ckm_30388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/11_2023/7ckm_30388.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckm_30388/11_2023/7ckm_30388.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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. 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-1.21rc1-5144/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: 7.07, per 1000 atoms: 0.54 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: 5.07 Conformation dependent library (CDL) restraints added in 2.4 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: 1.75 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: 4.60 Time building geometry restraints manager: 5.42 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 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: 0.590 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: 3.530 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.890 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.56 % Allowed : 10.60 % Favored : 85.84 % 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 : 1.617 Fit side-chains outliers start: 53 outliers final: 35 residues processed: 312 average time/residue: 0.2988 time to fit residues: 129.4532 Evaluate side-chains 238 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 203 time to evaluate : 1.541 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1218 time to fit residues: 10.0333 ------------------------------------------------------------------------------- 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: 0.7889 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 21.670 1755 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.62 % Allowed : 16.38 % Favored : 81.01 % 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 : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 14 residues processed: 256 average time/residue: 0.2638 time to fit residues: 98.2090 Evaluate side-chains 213 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 199 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1234 time to fit residues: 5.1807 ------------------------------------------------------------------------------- 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: 10.0000 chunk 46 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 0.5980 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: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 644 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** A1743 ASN A1783 ASN B 38 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13341 Z= 0.194 Angle : 0.563 10.266 18001 Z= 0.286 Chirality : 0.040 0.172 2073 Planarity : 0.004 0.056 2274 Dihedral : 4.211 38.277 1755 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.48 % Allowed : 19.33 % Favored : 78.19 % 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: -1.38 (0.21), residues: 1616 helix: 0.89 (0.18), residues: 831 sheet: -1.10 (0.46), residues: 128 loop : -3.43 (0.20), residues: 657 *********************** 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: 37 poor density : 208 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 20 residues processed: 232 average time/residue: 0.2771 time to fit residues: 92.0508 Evaluate side-chains 209 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1519 time to fit residues: 7.7112 ------------------------------------------------------------------------------- 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: 2.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 158 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 A1711 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: 0.7931 moved from start: 0.1734 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= 0.194 Angle : 0.556 10.265 18001 Z= 0.283 Chirality : 0.040 0.163 2073 Planarity : 0.004 0.050 2274 Dihedral : 4.174 22.134 1755 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.62 % Allowed : 20.27 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1616 helix: 1.10 (0.18), residues: 833 sheet: -0.93 (0.47), residues: 128 loop : -3.30 (0.21), residues: 655 *********************** 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 241 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 231 average time/residue: 0.2693 time to fit residues: 90.4662 Evaluate side-chains 204 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1207 time to fit residues: 6.3808 ------------------------------------------------------------------------------- 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: 7.9990 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A 704 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1711 ASN A1726 GLN A1743 ASN A1783 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13341 Z= 0.323 Angle : 0.636 9.167 18001 Z= 0.326 Chirality : 0.043 0.164 2073 Planarity : 0.004 0.047 2274 Dihedral : 4.562 23.235 1755 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 2.62 % Allowed : 20.81 % Favored : 76.58 % 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: -1.14 (0.21), residues: 1616 helix: 1.06 (0.18), residues: 831 sheet: -0.68 (0.49), residues: 125 loop : -3.34 (0.20), residues: 660 *********************** 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 242 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 1.653 Fit side-chains outliers start: 39 outliers final: 22 residues processed: 231 average time/residue: 0.2835 time to fit residues: 93.9173 Evaluate side-chains 213 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1295 time to fit residues: 7.5185 ------------------------------------------------------------------------------- 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: 0.3980 chunk 142 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 901 GLN 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: 0.7975 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13341 Z= 0.230 Angle : 0.597 14.417 18001 Z= 0.304 Chirality : 0.041 0.164 2073 Planarity : 0.004 0.049 2274 Dihedral : 4.465 22.726 1755 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.88 % Allowed : 22.35 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1616 helix: 1.19 (0.18), residues: 832 sheet: -0.47 (0.49), residues: 121 loop : -3.28 (0.20), residues: 663 *********************** 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: 28 poor density : 205 time to evaluate : 1.542 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 226 average time/residue: 0.2744 time to fit residues: 89.3972 Evaluate side-chains 204 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.500 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1310 time to fit residues: 5.9722 ------------------------------------------------------------------------------- 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: 10.0000 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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** A1296 HIS 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: 0.8005 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13341 Z= 0.298 Angle : 0.633 12.346 18001 Z= 0.323 Chirality : 0.042 0.167 2073 Planarity : 0.004 0.051 2274 Dihedral : 4.610 23.343 1755 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 1.34 % Allowed : 23.22 % Favored : 75.44 % 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: -0.98 (0.21), residues: 1616 helix: 1.18 (0.18), residues: 832 sheet: -0.35 (0.51), residues: 118 loop : -3.29 (0.20), residues: 666 *********************** 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 211 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.569 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 203 average time/residue: 0.2785 time to fit residues: 81.0959 Evaluate side-chains 197 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 1.489 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1317 time to fit residues: 5.2794 ------------------------------------------------------------------------------- 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: 0.5980 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.0170 chunk 124 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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: 0.7913 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13341 Z= 0.151 Angle : 0.567 15.033 18001 Z= 0.286 Chirality : 0.039 0.164 2073 Planarity : 0.004 0.063 2274 Dihedral : 4.299 21.474 1755 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.60 % Allowed : 24.03 % Favored : 75.37 % 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: 1.44 (0.18), residues: 833 sheet: -0.49 (0.51), residues: 114 loop : -3.01 (0.22), residues: 669 *********************** 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 213 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 204 time to evaluate : 1.463 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 209 average time/residue: 0.2859 time to fit residues: 85.7486 Evaluate side-chains 193 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 188 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1232 time to fit residues: 3.4599 ------------------------------------------------------------------------------- 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: 3.9990 chunk 151 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 0.2980 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 0.4980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7968 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13341 Z= 0.237 Angle : 0.601 14.773 18001 Z= 0.305 Chirality : 0.041 0.164 2073 Planarity : 0.004 0.068 2274 Dihedral : 4.388 21.693 1755 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 1.21 % Allowed : 23.62 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1616 helix: 1.42 (0.18), residues: 832 sheet: -0.65 (0.51), residues: 116 loop : -3.07 (0.21), residues: 668 *********************** 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 208 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.545 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 201 average time/residue: 0.2760 time to fit residues: 80.1887 Evaluate side-chains 196 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1268 time to fit residues: 4.5055 ------------------------------------------------------------------------------- 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: 1.9990 chunk 155 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** ** 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: 0.7946 moved from start: 0.2387 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= 0.196 Angle : 0.587 15.032 18001 Z= 0.298 Chirality : 0.040 0.166 2073 Planarity : 0.004 0.075 2274 Dihedral : 4.350 21.914 1755 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.34 % Allowed : 23.69 % Favored : 75.97 % 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: -0.62 (0.21), residues: 1616 helix: 1.48 (0.18), residues: 832 sheet: -0.68 (0.50), residues: 116 loop : -3.01 (0.22), residues: 668 ********************** 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 196 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 191 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 195 average time/residue: 0.2900 time to fit residues: 81.5685 Evaluate side-chains 187 residues out of total 1519 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1327 time to fit residues: 2.8409 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 0.1980 chunk 19 optimal weight: 8.9990 chunk 36 optimal weight: 0.0370 chunk 130 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127377 restraints weight = 16834.674| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.64 r_work: 0.3141 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13341 Z= 0.168 Angle : 0.579 15.122 18001 Z= 0.293 Chirality : 0.040 0.166 2073 Planarity : 0.004 0.074 2274 Dihedral : 4.232 21.026 1755 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.20 % Allowed : 24.30 % Favored : 75.50 % 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: -0.47 (0.22), residues: 1616 helix: 1.64 (0.18), residues: 826 sheet: -0.69 (0.50), residues: 116 loop : -2.92 (0.22), residues: 674 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.73 seconds wall clock time: 52 minutes 53.07 seconds (3173.07 seconds total)