Starting phenix.real_space_refine (version: dev) on Mon Feb 20 13:01:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgi_31970/02_2023/7vgi_31970_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgi_31970/02_2023/7vgi_31970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgi_31970/02_2023/7vgi_31970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgi_31970/02_2023/7vgi_31970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgi_31970/02_2023/7vgi_31970_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgi_31970/02_2023/7vgi_31970_updated.pdb" } resolution = 3.36 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 327": "NH1" <-> "NH2" Residue "B ARG 330": "NH1" <-> "NH2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "B TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 602": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 631": "NH1" <-> "NH2" Residue "B GLU 662": "OE1" <-> "OE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "B GLU 747": "OE1" <-> "OE2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 760": "OD1" <-> "OD2" Residue "B GLU 788": "OE1" <-> "OE2" Residue "B ARG 797": "NH1" <-> "NH2" Residue "B ARG 832": "NH1" <-> "NH2" Residue "B GLU 843": "OE1" <-> "OE2" Residue "B ARG 882": "NH1" <-> "NH2" Residue "B GLU 914": "OE1" <-> "OE2" Residue "B PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 930": "NH1" <-> "NH2" Residue "B ARG 941": "NH1" <-> "NH2" Residue "B ARG 946": "NH1" <-> "NH2" Residue "B ARG 952": "NH1" <-> "NH2" Residue "B PHE 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1009": "OD1" <-> "OD2" Residue "B ARG 1032": "NH1" <-> "NH2" Residue "B GLU 1174": "OE1" <-> "OE2" Residue "B ARG 1182": "NH1" <-> "NH2" Residue "B ARG 1206": "NH1" <-> "NH2" Residue "B ARG 1225": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12174 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2662 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 25, 'TRANS': 305} Chain: "B" Number of atoms: 9416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 9416 Classifications: {'peptide': 1162} Link IDs: {'PTRANS': 31, 'TRANS': 1130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.74, per 1000 atoms: 0.55 Number of scatterers: 12174 At special positions: 0 Unit cell: (107.06, 116.15, 163.62, 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) S 58 16.00 P 1 15.00 Mg 1 11.99 O 2235 8.00 N 2051 7.00 C 7828 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 104 " 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 Links applied ALPHA1-4 " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 401 " - " ASN A 294 " " NAG A 402 " - " ASN A 107 " " NAG C 1 " - " ASN B 368 " " NAG D 1 " - " ASN A 180 " Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 1.9 seconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 9 sheets defined 33.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 47 through 50 No H-bonds generated for 'chain 'A' and resid 47 through 50' Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.921A pdb=" N GLY A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.780A pdb=" N PHE A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 removed outlier: 4.081A pdb=" N LYS A 93 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 94 " --> pdb=" O CYS A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 94' Processing helix chain 'A' and resid 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 155 through 160 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 173 through 177 removed outlier: 4.019A pdb=" N SER A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 223 through 226 No H-bonds generated for 'chain 'A' and resid 223 through 226' Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.593A pdb=" N TRP A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.551A pdb=" N ILE A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 340 No H-bonds generated for 'chain 'A' and resid 337 through 340' Processing helix chain 'A' and resid 347 through 350 No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 119 through 130 removed outlier: 3.571A pdb=" N LEU B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 172 removed outlier: 3.555A pdb=" N THR B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS B 171 " --> pdb=" O HIS B 167 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 246 through 249 No H-bonds generated for 'chain 'B' and resid 246 through 249' Processing helix chain 'B' and resid 253 through 256 No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 336 through 363 removed outlier: 3.879A pdb=" N VAL B 341 " --> pdb=" O MET B 337 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 357 " --> pdb=" O ALA B 353 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 398 removed outlier: 3.792A pdb=" N PHE B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N THR B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 411 through 414 No H-bonds generated for 'chain 'B' and resid 411 through 414' Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 442 through 447 removed outlier: 3.793A pdb=" N GLY B 446 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 removed outlier: 3.762A pdb=" N GLN B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 removed outlier: 3.829A pdb=" N GLN B 526 " --> pdb=" O PRO B 522 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE B 527 " --> pdb=" O GLU B 523 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 532 " --> pdb=" O PHE B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 565 removed outlier: 3.532A pdb=" N ALA B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 565 " --> pdb=" O ALA B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 622 through 625 No H-bonds generated for 'chain 'B' and resid 622 through 625' Processing helix chain 'B' and resid 638 through 648 Processing helix chain 'B' and resid 665 through 677 removed outlier: 3.624A pdb=" N LYS B 672 " --> pdb=" O GLU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 715 through 723 removed outlier: 3.663A pdb=" N LYS B 720 " --> pdb=" O GLU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 745 Processing helix chain 'B' and resid 758 through 764 removed outlier: 3.629A pdb=" N ASN B 762 " --> pdb=" O GLY B 758 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 769 No H-bonds generated for 'chain 'B' and resid 766 through 769' Processing helix chain 'B' and resid 803 through 809 removed outlier: 3.554A pdb=" N GLU B 808 " --> pdb=" O SER B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 859 removed outlier: 3.685A pdb=" N GLU B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU B 859 " --> pdb=" O ASP B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 880 removed outlier: 4.134A pdb=" N ALA B 874 " --> pdb=" O PRO B 870 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 875 " --> pdb=" O LYS B 871 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 880 " --> pdb=" O VAL B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 903 removed outlier: 3.726A pdb=" N VAL B 898 " --> pdb=" O ALA B 895 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 899 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 902 " --> pdb=" O ASN B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 937 removed outlier: 3.719A pdb=" N GLN B 933 " --> pdb=" O ARG B 930 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 935 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B 937 " --> pdb=" O ARG B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 957 removed outlier: 3.620A pdb=" N ARG B 952 " --> pdb=" O CYS B 948 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 956 " --> pdb=" O ARG B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 962 No H-bonds generated for 'chain 'B' and resid 959 through 962' Processing helix chain 'B' and resid 964 through 971 removed outlier: 4.294A pdb=" N PHE B 970 " --> pdb=" O PHE B 966 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE B 971 " --> pdb=" O TRP B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1001 Processing helix chain 'B' and resid 1011 through 1014 No H-bonds generated for 'chain 'B' and resid 1011 through 1014' Processing helix chain 'B' and resid 1016 through 1022 removed outlier: 3.565A pdb=" N VAL B1021 " --> pdb=" O LEU B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1038 No H-bonds generated for 'chain 'B' and resid 1035 through 1038' Processing helix chain 'B' and resid 1043 through 1055 removed outlier: 3.837A pdb=" N PHE B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) Proline residue: B1051 - end of helix Processing helix chain 'B' and resid 1069 through 1084 removed outlier: 3.509A pdb=" N VAL B1074 " --> pdb=" O GLN B1070 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B1076 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B1077 " --> pdb=" O ALA B1073 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B1082 " --> pdb=" O SER B1078 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B1083 " --> pdb=" O ALA B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1114 Processing helix chain 'B' and resid 1136 through 1139 No H-bonds generated for 'chain 'B' and resid 1136 through 1139' Processing helix chain 'B' and resid 1145 through 1158 removed outlier: 4.175A pdb=" N ILE B1150 " --> pdb=" O TRP B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1166 removed outlier: 3.512A pdb=" N LEU B1166 " --> pdb=" O ALA B1162 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1162 through 1166' Processing helix chain 'B' and resid 1174 through 1180 removed outlier: 3.934A pdb=" N ILE B1178 " --> pdb=" O GLU B1174 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN B1179 " --> pdb=" O SER B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1223 Processing sheet with id= A, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.760A pdb=" N ARG A 307 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 118 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR A 122 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU A 272 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU A 124 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG A 270 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 104 through 110 removed outlier: 3.777A pdb=" N GLY A 289 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 182 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 200 through 203 removed outlier: 3.762A pdb=" N SER B 216 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 309 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEU B 214 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 237 through 241 removed outlier: 4.039A pdb=" N TYR B 225 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 277 through 279 removed outlier: 4.508A pdb=" N GLY B 277 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 906 through 909 removed outlier: 6.504A pdb=" N TYR B 450 " --> pdb=" O LEU B 889 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE B 891 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE B 452 " --> pdb=" O ILE B 891 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 727 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER B 453 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP B 729 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 863 " --> pdb=" O VAL B 730 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 799 " --> pdb=" O ILE B 864 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS B 866 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 801 " --> pdb=" O CYS B 866 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 469 through 471 removed outlier: 3.689A pdb=" N CYS B 469 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 474 " --> pdb=" O ILE B 471 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 538 through 541 removed outlier: 3.511A pdb=" N ASP B 540 " --> pdb=" O ASN B 547 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 547 " --> pdb=" O ASP B 540 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 568 through 572 removed outlier: 3.513A pdb=" N ALA B 568 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR B 578 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG B 572 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 606 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 593 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER B 604 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 654 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B 702 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR B 658 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU B 700 " --> pdb=" O TYR B 658 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3855 1.34 - 1.46: 2473 1.46 - 1.58: 6038 1.58 - 1.70: 0 1.70 - 1.81: 90 Bond restraints: 12456 Sorted by residual: bond pdb=" N ILE B 661 " pdb=" CA ILE B 661 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.59e+00 bond pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.43e+00 bond pdb=" C LEU A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 1.331 1.352 -0.020 7.90e-03 1.60e+04 6.70e+00 bond pdb=" N MET B 834 " pdb=" CA MET B 834 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.38e-02 5.25e+03 6.67e+00 bond pdb=" N LYS B 67 " pdb=" CA LYS B 67 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.64e+00 ... (remaining 12451 not shown) Histogram of bond angle deviations from ideal: 96.80 - 104.26: 164 104.26 - 111.71: 5514 111.71 - 119.16: 4505 119.16 - 126.61: 6509 126.61 - 134.07: 176 Bond angle restraints: 16868 Sorted by residual: angle pdb=" N VAL B 410 " pdb=" CA VAL B 410 " pdb=" C VAL B 410 " ideal model delta sigma weight residual 112.96 107.39 5.57 1.00e+00 1.00e+00 3.11e+01 angle pdb=" C2 NAG C 1 " pdb=" N2 NAG C 1 " pdb=" C7 NAG C 1 " ideal model delta sigma weight residual 123.12 129.20 -6.08 1.28e+00 6.08e-01 2.24e+01 angle pdb=" N ILE A 253 " pdb=" CA ILE A 253 " pdb=" C ILE A 253 " ideal model delta sigma weight residual 112.29 108.42 3.87 9.40e-01 1.13e+00 1.70e+01 angle pdb=" N ILE A 53 " pdb=" CA ILE A 53 " pdb=" C ILE A 53 " ideal model delta sigma weight residual 113.39 108.26 5.13 1.47e+00 4.63e-01 1.22e+01 angle pdb=" C ARG B 835 " pdb=" N THR B 836 " pdb=" CA THR B 836 " ideal model delta sigma weight residual 121.54 114.90 6.64 1.91e+00 2.74e-01 1.21e+01 ... (remaining 16863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.95: 6820 21.95 - 43.89: 527 43.89 - 65.84: 51 65.84 - 87.79: 17 87.79 - 109.74: 3 Dihedral angle restraints: 7418 sinusoidal: 3041 harmonic: 4377 Sorted by residual: dihedral pdb=" CA GLN B 787 " pdb=" C GLN B 787 " pdb=" N GLU B 788 " pdb=" CA GLU B 788 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" C1 NAG A 401 " pdb=" C2 NAG A 401 " pdb=" C3 NAG A 401 " pdb=" C4 NAG A 401 " ideal model delta sinusoidal sigma weight residual -50.00 59.74 -109.74 1 2.00e+01 2.50e-03 3.21e+01 dihedral pdb=" CA THR B 398 " pdb=" C THR B 398 " pdb=" N MET B 399 " pdb=" CA MET B 399 " ideal model delta harmonic sigma weight residual 180.00 153.40 26.60 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 7415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1814 0.107 - 0.213: 63 0.213 - 0.320: 1 0.320 - 0.427: 0 0.427 - 0.534: 1 Chirality restraints: 1879 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN B 368 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.12e+00 chirality pdb=" CB ILE B 136 " pdb=" CA ILE B 136 " pdb=" CG1 ILE B 136 " pdb=" CG2 ILE B 136 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2 NAG C 1 " pdb=" C1 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" N2 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1876 not shown) Planarity restraints: 2140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 659 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.16e+00 pdb=" C LYS B 659 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS B 659 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU B 660 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 246 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO A 247 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1191 " -0.027 2.00e-02 2.50e+03 1.57e-02 6.19e+00 pdb=" CG TRP B1191 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B1191 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B1191 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1191 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1191 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B1191 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1191 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1191 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B1191 " -0.003 2.00e-02 2.50e+03 ... (remaining 2137 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 137 2.61 - 3.18: 10447 3.18 - 3.75: 16967 3.75 - 4.33: 25650 4.33 - 4.90: 41687 Nonbonded interactions: 94888 Sorted by model distance: nonbonded pdb=" OD2 PHD B 454 " pdb="MG MG B1401 " model vdw 2.032 2.170 nonbonded pdb=" OE2 GLU B 829 " pdb=" N THR B 836 " model vdw 2.083 2.520 nonbonded pdb=" O LEU B 279 " pdb=" OG SER B 285 " model vdw 2.138 2.440 nonbonded pdb=" O PRO A 287 " pdb=" OH TYR A 291 " model vdw 2.174 2.440 nonbonded pdb=" OG SER B 416 " pdb=" OD1 ASN B 442 " model vdw 2.216 2.440 ... (remaining 94883 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 P 1 5.49 5 Mg 1 5.21 5 S 58 5.16 5 C 7828 2.51 5 N 2051 2.21 5 O 2235 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.110 Check model and map are aligned: 0.170 Process input model: 33.900 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 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 : 0.005 0.044 12456 Z= 0.335 Angle : 0.740 8.743 16868 Z= 0.419 Chirality : 0.049 0.534 1879 Planarity : 0.004 0.069 2136 Dihedral : 15.161 109.736 4595 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.46 % Favored : 89.34 % Rotamer Outliers : 0.38 % 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: -4.39 (0.18), residues: 1482 helix: -3.53 (0.16), residues: 556 sheet: -0.92 (0.40), residues: 168 loop : -2.91 (0.20), residues: 758 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.532 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 1 residues processed: 133 average time/residue: 0.2505 time to fit residues: 48.7625 Evaluate side-chains 113 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.442 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1200 time to fit residues: 2.2313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 0.0040 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 HIS B 913 GLN ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 12456 Z= 0.180 Angle : 0.602 7.165 16868 Z= 0.323 Chirality : 0.045 0.538 1879 Planarity : 0.004 0.048 2136 Dihedral : 7.021 108.455 1687 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer Outliers : 0.61 % 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: -3.57 (0.20), residues: 1482 helix: -2.41 (0.20), residues: 539 sheet: -0.39 (0.41), residues: 163 loop : -2.85 (0.20), residues: 780 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.535 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 7 residues processed: 123 average time/residue: 0.2592 time to fit residues: 47.1883 Evaluate side-chains 115 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.583 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.1307 time to fit residues: 3.6407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 0.3980 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 120 optimal weight: 0.2980 chunk 134 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 GLN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 12456 Z= 0.166 Angle : 0.557 6.834 16868 Z= 0.296 Chirality : 0.044 0.505 1879 Planarity : 0.004 0.047 2136 Dihedral : 6.753 106.862 1687 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer Outliers : 0.38 % 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: -3.12 (0.20), residues: 1482 helix: -1.84 (0.22), residues: 543 sheet: -0.16 (0.42), residues: 163 loop : -2.74 (0.20), residues: 776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 1.528 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 2 residues processed: 128 average time/residue: 0.2511 time to fit residues: 48.3583 Evaluate side-chains 118 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.489 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.3593 time to fit residues: 2.8518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 575 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 12456 Z= 0.267 Angle : 0.587 7.935 16868 Z= 0.310 Chirality : 0.046 0.483 1879 Planarity : 0.004 0.048 2136 Dihedral : 6.812 106.313 1687 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer Outliers : 1.14 % 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: -3.02 (0.21), residues: 1482 helix: -1.65 (0.22), residues: 553 sheet: -0.23 (0.42), residues: 165 loop : -2.75 (0.20), residues: 764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.591 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 15 outliers final: 8 residues processed: 122 average time/residue: 0.2399 time to fit residues: 44.7758 Evaluate side-chains 115 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.648 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1274 time to fit residues: 4.1303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 2 optimal weight: 0.0270 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 HIS ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1085 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 12456 Z= 0.264 Angle : 0.591 9.758 16868 Z= 0.310 Chirality : 0.046 0.479 1879 Planarity : 0.004 0.047 2136 Dihedral : 6.803 105.262 1687 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer Outliers : 0.76 % 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: -2.89 (0.21), residues: 1482 helix: -1.47 (0.22), residues: 548 sheet: -0.24 (0.42), residues: 165 loop : -2.71 (0.20), residues: 769 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.560 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 10 outliers final: 4 residues processed: 121 average time/residue: 0.2486 time to fit residues: 45.8454 Evaluate side-chains 113 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 1.499 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1553 time to fit residues: 3.1293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 84 optimal weight: 0.0980 chunk 35 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 HIS ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.051 12456 Z= 0.378 Angle : 0.645 9.117 16868 Z= 0.339 Chirality : 0.047 0.311 1879 Planarity : 0.004 0.048 2136 Dihedral : 6.962 105.031 1687 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer Outliers : 1.07 % 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: -3.00 (0.21), residues: 1482 helix: -1.59 (0.22), residues: 555 sheet: -0.20 (0.42), residues: 165 loop : -2.79 (0.20), residues: 762 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.508 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 14 outliers final: 8 residues processed: 123 average time/residue: 0.2469 time to fit residues: 45.3931 Evaluate side-chains 114 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 1.477 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1151 time to fit residues: 3.7856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 82 optimal weight: 0.0980 chunk 105 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 545 GLN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12456 Z= 0.182 Angle : 0.556 6.989 16868 Z= 0.294 Chirality : 0.044 0.382 1879 Planarity : 0.003 0.049 2136 Dihedral : 6.720 103.835 1687 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 0.61 % 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: -2.74 (0.21), residues: 1482 helix: -1.28 (0.23), residues: 547 sheet: -0.13 (0.42), residues: 165 loop : -2.69 (0.20), residues: 770 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.516 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 8 outliers final: 6 residues processed: 114 average time/residue: 0.2548 time to fit residues: 44.2070 Evaluate side-chains 110 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.360 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1215 time to fit residues: 3.2711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 545 GLN B 547 ASN ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12456 Z= 0.176 Angle : 0.543 7.442 16868 Z= 0.286 Chirality : 0.044 0.366 1879 Planarity : 0.003 0.051 2136 Dihedral : 6.576 103.073 1687 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 0.15 % 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: -2.57 (0.21), residues: 1482 helix: -1.10 (0.23), residues: 549 sheet: -0.08 (0.42), residues: 165 loop : -2.61 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.530 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 112 average time/residue: 0.2543 time to fit residues: 43.2241 Evaluate side-chains 106 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.598 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1323 time to fit residues: 2.4633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 12456 Z= 0.197 Angle : 0.553 8.019 16868 Z= 0.290 Chirality : 0.044 0.361 1879 Planarity : 0.004 0.051 2136 Dihedral : 6.558 102.717 1687 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer Outliers : 0.38 % 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: -2.49 (0.21), residues: 1482 helix: -1.01 (0.23), residues: 550 sheet: -0.04 (0.42), residues: 165 loop : -2.58 (0.21), residues: 767 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 1.451 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 5 outliers final: 3 residues processed: 114 average time/residue: 0.2496 time to fit residues: 43.1016 Evaluate side-chains 113 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.574 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1368 time to fit residues: 2.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 12456 Z= 0.273 Angle : 0.591 7.589 16868 Z= 0.309 Chirality : 0.045 0.350 1879 Planarity : 0.004 0.064 2136 Dihedral : 6.684 102.788 1687 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer Outliers : 0.30 % 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: -2.54 (0.21), residues: 1482 helix: -1.06 (0.23), residues: 550 sheet: 0.00 (0.42), residues: 165 loop : -2.63 (0.21), residues: 767 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.627 Fit side-chains TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 2 residues processed: 109 average time/residue: 0.2538 time to fit residues: 41.6279 Evaluate side-chains 109 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 1.441 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "GLU B 692 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1227 time to fit residues: 2.3820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 121 optimal weight: 0.0970 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.0470 chunk 103 optimal weight: 0.9990 overall best weight: 0.4480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.163220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.133189 restraints weight = 14670.848| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.65 r_work: 0.3012 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 12456 Z= 0.135 Angle : 0.521 6.753 16868 Z= 0.274 Chirality : 0.043 0.375 1879 Planarity : 0.004 0.061 2136 Dihedral : 6.398 101.684 1687 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer Outliers : 0.15 % 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: -2.20 (0.22), residues: 1482 helix: -0.70 (0.24), residues: 546 sheet: 0.01 (0.42), residues: 165 loop : -2.45 (0.21), residues: 771 =============================================================================== Job complete usr+sys time: 2165.76 seconds wall clock time: 41 minutes 10.71 seconds (2470.71 seconds total)