Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 12 06:55:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgh_34739/07_2023/8hgh_34739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgh_34739/07_2023/8hgh_34739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgh_34739/07_2023/8hgh_34739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgh_34739/07_2023/8hgh_34739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgh_34739/07_2023/8hgh_34739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgh_34739/07_2023/8hgh_34739.pdb" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 228 5.16 5 C 15968 2.51 5 N 4430 2.21 5 O 4884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1498": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 25512 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1462, 11420 Classifications: {'peptide': 1462} Link IDs: {'PTRANS': 95, 'TRANS': 1366} Chain breaks: 5 Chain: "B" Number of atoms: 11420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1462, 11420 Classifications: {'peptide': 1462} Link IDs: {'PTRANS': 95, 'TRANS': 1366} Chain breaks: 5 Chain: "C" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1335 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1335 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 2, 'TRANS': 168} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.45, per 1000 atoms: 0.45 Number of scatterers: 25512 At special positions: 0 Unit cell: (194.12, 155.085, 139.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 228 16.00 O 4884 8.00 N 4430 7.00 C 15968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=85, symmetry=0 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS G 120 " distance=2.03 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 695 " - pdb=" SG CYS A 701 " distance=2.03 Simple disulfide: pdb=" SG CYS A 867 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 891 " distance=2.03 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A 910 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A 990 " distance=2.03 Simple disulfide: pdb=" SG CYS A 971 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS A1135 " - pdb=" SG CYS A1189 " distance=2.03 Simple disulfide: pdb=" SG CYS A1147 " - pdb=" SG CYS A1158 " distance=2.03 Simple disulfide: pdb=" SG CYS A1162 " - pdb=" SG CYS A1200 " distance=2.03 Simple disulfide: pdb=" SG CYS A1205 " - pdb=" SG CYS A1249 " distance=2.03 Simple disulfide: pdb=" SG CYS A1220 " - pdb=" SG CYS A1230 " distance=2.03 Simple disulfide: pdb=" SG CYS A1234 " - pdb=" SG CYS A1262 " distance=2.03 Simple disulfide: pdb=" SG CYS A1266 " - pdb=" SG CYS A1319 " distance=2.03 Simple disulfide: pdb=" SG CYS A1282 " - pdb=" SG CYS A1293 " distance=2.03 Simple disulfide: pdb=" SG CYS A1297 " - pdb=" SG CYS A1330 " distance=2.03 Simple disulfide: pdb=" SG CYS A1335 " - pdb=" SG CYS A1378 " distance=2.03 Simple disulfide: pdb=" SG CYS A1348 " - pdb=" SG CYS A1358 " distance=2.03 Simple disulfide: pdb=" SG CYS A1412 " - pdb=" SG CYS A1422 " distance=2.03 Simple disulfide: pdb=" SG CYS A1426 " - pdb=" SG CYS A1474 " distance=2.03 Simple disulfide: pdb=" SG CYS A1478 " - pdb=" SG CYS A1496 " distance=2.03 Simple disulfide: pdb=" SG CYS A1487 " - pdb=" SG CYS A1503 " distance=2.03 Simple disulfide: pdb=" SG CYS A1504 " - pdb=" SG CYS A1528 " distance=2.03 Simple disulfide: pdb=" SG CYS A1520 " - pdb=" SG CYS A1526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 247 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 652 " - pdb=" SG CYS C 120 " distance=2.03 Simple disulfide: pdb=" SG CYS B 673 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 695 " - pdb=" SG CYS B 701 " distance=2.03 Simple disulfide: pdb=" SG CYS B 867 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 880 " - pdb=" SG CYS B 891 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B 910 " distance=2.03 Simple disulfide: pdb=" SG CYS B 919 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B 956 " - pdb=" SG CYS B 990 " distance=2.03 Simple disulfide: pdb=" SG CYS B 971 " - pdb=" SG CYS B1059 " distance=2.03 Simple disulfide: pdb=" SG CYS B1135 " - pdb=" SG CYS B1189 " distance=2.03 Simple disulfide: pdb=" SG CYS B1147 " - pdb=" SG CYS B1158 " distance=2.03 Simple disulfide: pdb=" SG CYS B1162 " - pdb=" SG CYS B1200 " distance=2.03 Simple disulfide: pdb=" SG CYS B1205 " - pdb=" SG CYS B1249 " distance=2.03 Simple disulfide: pdb=" SG CYS B1220 " - pdb=" SG CYS B1230 " distance=2.03 Simple disulfide: pdb=" SG CYS B1234 " - pdb=" SG CYS B1262 " distance=2.03 Simple disulfide: pdb=" SG CYS B1266 " - pdb=" SG CYS B1319 " distance=2.03 Simple disulfide: pdb=" SG CYS B1282 " - pdb=" SG CYS B1293 " distance=2.03 Simple disulfide: pdb=" SG CYS B1297 " - pdb=" SG CYS B1330 " distance=2.03 Simple disulfide: pdb=" SG CYS B1335 " - pdb=" SG CYS B1378 " distance=2.03 Simple disulfide: pdb=" SG CYS B1348 " - pdb=" SG CYS B1358 " distance=2.03 Simple disulfide: pdb=" SG CYS B1412 " - pdb=" SG CYS B1422 " distance=2.03 Simple disulfide: pdb=" SG CYS B1426 " - pdb=" SG CYS B1474 " distance=2.03 Simple disulfide: pdb=" SG CYS B1478 " - pdb=" SG CYS B1496 " distance=2.03 Simple disulfide: pdb=" SG CYS B1487 " - pdb=" SG CYS B1503 " distance=2.03 Simple disulfide: pdb=" SG CYS B1504 " - pdb=" SG CYS B1528 " distance=2.03 Simple disulfide: pdb=" SG CYS B1520 " - pdb=" SG CYS B1526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 125 " distance=2.03 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 197 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 211 " - pdb=" SG CYS G 211 " distance=2.03 Simple disulfide: pdb=" SG CYS G 56 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 85 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 125 " distance=2.03 Simple disulfide: pdb=" SG CYS G 109 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 146 " - pdb=" SG CYS G 181 " distance=2.03 Simple disulfide: pdb=" SG CYS G 197 " - pdb=" SG CYS G 205 " 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: 8.92 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 486 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 482 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 492 " pdb=" ZN B1601 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 482 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 486 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 492 " 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6092 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 44 sheets defined 17.7% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.503A pdb=" N GLN A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.624A pdb=" N HIS A 215 " --> pdb=" O ASN A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.517A pdb=" N ALA A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.651A pdb=" N LEU A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 307 Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.529A pdb=" N ARG A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 removed outlier: 4.235A pdb=" N GLY A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 341' Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.683A pdb=" N GLY A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 4.181A pdb=" N THR A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 418 through 426 Processing helix chain 'A' and resid 473 through 477 removed outlier: 4.053A pdb=" N THR A 477 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 488 Processing helix chain 'A' and resid 569 through 582 removed outlier: 4.151A pdb=" N ALA A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 Processing helix chain 'A' and resid 873 through 877 removed outlier: 3.513A pdb=" N GLY A 877 " --> pdb=" O LYS A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1001 removed outlier: 3.505A pdb=" N GLN A1001 " --> pdb=" O SER A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1110 removed outlier: 3.747A pdb=" N LEU A1109 " --> pdb=" O ASP A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1284 removed outlier: 3.620A pdb=" N ARG A1283 " --> pdb=" O ALA A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1496 through 1501 removed outlier: 4.245A pdb=" N GLY A1500 " --> pdb=" O CYS A1496 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A1501 " --> pdb=" O ASN A1497 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1496 through 1501' Processing helix chain 'A' and resid 1504 through 1508 removed outlier: 3.632A pdb=" N VAL A1508 " --> pdb=" O THR A1505 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 212 through 216 removed outlier: 4.430A pdb=" N ALA B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 216' Processing helix chain 'B' and resid 250 through 253 removed outlier: 3.561A pdb=" N ASP B 253 " --> pdb=" O THR B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 254 through 259 removed outlier: 3.501A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.647A pdb=" N LEU B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 307 removed outlier: 3.513A pdb=" N HIS B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 336 through 341 removed outlier: 4.002A pdb=" N GLY B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 400 through 405 removed outlier: 4.068A pdb=" N THR B 404 " --> pdb=" O ASN B 400 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 405' Processing helix chain 'B' and resid 418 through 426 Processing helix chain 'B' and resid 478 through 487 removed outlier: 3.544A pdb=" N GLU B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.712A pdb=" N MET B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 579 " --> pdb=" O MET B 575 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP B 580 " --> pdb=" O HIS B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 820 removed outlier: 3.526A pdb=" N SER B 820 " --> pdb=" O MET B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 removed outlier: 3.530A pdb=" N GLN B 876 " --> pdb=" O GLN B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1001 Processing helix chain 'B' and resid 1279 through 1284 removed outlier: 3.635A pdb=" N ARG B1283 " --> pdb=" O ALA B1280 " (cutoff:3.500A) Processing helix chain 'B' and resid 1493 through 1495 No H-bonds generated for 'chain 'B' and resid 1493 through 1495' Processing helix chain 'B' and resid 1496 through 1502 Processing helix chain 'B' and resid 1504 through 1508 removed outlier: 3.630A pdb=" N VAL B1508 " --> pdb=" O THR B1505 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 4.100A pdb=" N LEU C 47 " --> pdb=" O ARG C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 60 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.631A pdb=" N LYS C 94 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 117 Processing helix chain 'C' and resid 124 through 142 removed outlier: 3.691A pdb=" N LYS C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.953A pdb=" N ILE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 182 removed outlier: 3.628A pdb=" N GLY C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 200 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'G' and resid 49 through 60 removed outlier: 3.868A pdb=" N ILE G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 95 Processing helix chain 'G' and resid 96 through 117 Processing helix chain 'G' and resid 124 through 142 removed outlier: 3.720A pdb=" N LYS G 142 " --> pdb=" O GLU G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 152 Processing helix chain 'G' and resid 152 through 159 removed outlier: 4.076A pdb=" N ILE G 156 " --> pdb=" O ASN G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 179 Processing helix chain 'G' and resid 182 through 200 Processing helix chain 'G' and resid 202 through 207 removed outlier: 3.506A pdb=" N SER G 206 " --> pdb=" O GLY G 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 140 removed outlier: 6.765A pdb=" N LEU A 130 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 139 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET A 128 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP A 44 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 175 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG A 46 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE A 173 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 140 removed outlier: 6.765A pdb=" N LEU A 130 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR A 139 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N MET A 128 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP A 44 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS A 175 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG A 46 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE A 173 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N HIS A 175 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 10.391A pdb=" N ARG A 15 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS A 227 " --> pdb=" O TYR A 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 105 removed outlier: 3.641A pdb=" N THR A 103 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 94 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP A 73 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY A 59 " --> pdb=" O TRP A 73 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 75 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 160 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 315 removed outlier: 6.005A pdb=" N LYS A 271 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU A 314 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 273 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU A 318 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL A 277 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 320 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN A 279 " --> pdb=" O VAL A 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 6.005A pdb=" N LYS A 271 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU A 314 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 273 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N PHE A 437 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N LEU A 280 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN A 434 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A 466 " --> pdb=" O ASN A 434 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE A 436 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 331 Processing sheet with id=AA7, first strand: chain 'A' and resid 600 through 604 removed outlier: 5.334A pdb=" N VAL A 601 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU A 612 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 609 " --> pdb=" O ASP A 830 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 830 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 633 through 634 removed outlier: 3.825A pdb=" N ILE A 638 " --> pdb=" O LEU A 634 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU A 639 " --> pdb=" O SER A 791 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 641 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU A 783 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP A 719 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 787 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR A 717 " --> pdb=" O ALA A 787 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 789 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER A 715 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER A 791 " --> pdb=" O PRO A 713 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 645 through 647 removed outlier: 5.963A pdb=" N TYR A 771 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 736 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 805 through 810 Processing sheet with id=AB2, first strand: chain 'A' and resid 902 through 903 Processing sheet with id=AB3, first strand: chain 'A' and resid 940 through 943 removed outlier: 3.621A pdb=" N ALA A1018 " --> pdb=" O ARG A1099 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 948 through 949 removed outlier: 7.773A pdb=" N GLN A1080 " --> pdb=" O PHE A1010 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 948 through 949 removed outlier: 7.773A pdb=" N GLN A1080 " --> pdb=" O PHE A1010 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1069 through 1071 removed outlier: 3.547A pdb=" N HIS A1070 " --> pdb=" O HIS B1070 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS B1070 " --> pdb=" O HIS A1070 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1143 through 1144 removed outlier: 3.716A pdb=" N SER A1161 " --> pdb=" O SER A1144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1166 through 1172 Processing sheet with id=AB9, first strand: chain 'A' and resid 1216 through 1219 removed outlier: 3.772A pdb=" N SER A1231 " --> pdb=" O SER A1219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1265 through 1266 Processing sheet with id=AC2, first strand: chain 'A' and resid 1275 through 1277 Processing sheet with id=AC3, first strand: chain 'A' and resid 1301 through 1302 Processing sheet with id=AC4, first strand: chain 'A' and resid 1409 through 1410 removed outlier: 3.554A pdb=" N SER A1425 " --> pdb=" O LYS A1409 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1431 through 1435 Processing sheet with id=AC6, first strand: chain 'B' and resid 135 through 140 removed outlier: 6.899A pdb=" N LEU B 130 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B 139 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET B 128 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 44 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS B 175 " --> pdb=" O TRP B 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 135 through 140 removed outlier: 6.899A pdb=" N LEU B 130 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B 139 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET B 128 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS B 227 " --> pdb=" O TYR B 18 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.964A pdb=" N TRP B 73 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLY B 59 " --> pdb=" O TRP B 73 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL B 75 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 160 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 321 removed outlier: 3.792A pdb=" N VAL B 277 " --> pdb=" O ASP B 316 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE B 437 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU B 280 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 329 through 331 Processing sheet with id=AD2, first strand: chain 'B' and resid 600 through 604 removed outlier: 7.051A pdb=" N THR B 610 " --> pdb=" O LEU B 602 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 609 " --> pdb=" O ASP B 830 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP B 830 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 640 through 642 removed outlier: 3.621A pdb=" N GLN B 641 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU B 783 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP B 719 " --> pdb=" O ASP B 785 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA B 787 " --> pdb=" O THR B 717 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR B 717 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU B 789 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER B 715 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER B 791 " --> pdb=" O PRO B 713 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 645 through 647 removed outlier: 6.071A pdb=" N TYR B 771 " --> pdb=" O PHE B 707 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 805 through 810 Processing sheet with id=AD6, first strand: chain 'B' and resid 902 through 903 Processing sheet with id=AD7, first strand: chain 'B' and resid 940 through 943 removed outlier: 3.741A pdb=" N ILE B1020 " --> pdb=" O ALA B1097 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B1018 " --> pdb=" O ARG B1099 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 948 through 949 removed outlier: 7.534A pdb=" N GLN B1080 " --> pdb=" O PHE B1010 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 948 through 949 removed outlier: 7.534A pdb=" N GLN B1080 " --> pdb=" O PHE B1010 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1143 through 1144 removed outlier: 3.803A pdb=" N SER B1161 " --> pdb=" O SER B1144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1166 through 1172 Processing sheet with id=AE3, first strand: chain 'B' and resid 1216 through 1219 removed outlier: 3.658A pdb=" N SER B1231 " --> pdb=" O SER B1219 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1265 through 1266 Processing sheet with id=AE5, first strand: chain 'B' and resid 1275 through 1277 Processing sheet with id=AE6, first strand: chain 'B' and resid 1301 through 1302 Processing sheet with id=AE7, first strand: chain 'B' and resid 1408 through 1411 removed outlier: 3.890A pdb=" N ALA B1423 " --> pdb=" O GLN B1411 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1431 through 1435 667 hydrogen bonds defined for protein. 1791 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: 10.67 Time building geometry restraints manager: 9.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8172 1.34 - 1.46: 5540 1.46 - 1.58: 12174 1.58 - 1.70: 0 1.70 - 1.82: 278 Bond restraints: 26164 Sorted by residual: bond pdb=" N ILE B1066 " pdb=" CA ILE B1066 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.08e+01 bond pdb=" N ILE A1066 " pdb=" CA ILE A1066 " ideal model delta sigma weight residual 1.458 1.492 -0.034 7.70e-03 1.69e+04 1.96e+01 bond pdb=" N TYR A1466 " pdb=" CA TYR A1466 " ideal model delta sigma weight residual 1.461 1.492 -0.031 9.20e-03 1.18e+04 1.16e+01 bond pdb=" N HIS A1236 " pdb=" CA HIS A1236 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 9.02e+00 bond pdb=" N TYR B1466 " pdb=" CA TYR B1466 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.04e-02 9.25e+03 8.90e+00 ... (remaining 26159 not shown) Histogram of bond angle deviations from ideal: 100.17 - 107.00: 1043 107.00 - 113.83: 14325 113.83 - 120.66: 10149 120.66 - 127.49: 9683 127.49 - 134.32: 376 Bond angle restraints: 35576 Sorted by residual: angle pdb=" N LEU C 45 " pdb=" CA LEU C 45 " pdb=" C LEU C 45 " ideal model delta sigma weight residual 113.16 107.22 5.94 1.24e+00 6.50e-01 2.29e+01 angle pdb=" N THR C 50 " pdb=" CA THR C 50 " pdb=" C THR C 50 " ideal model delta sigma weight residual 113.20 107.71 5.49 1.21e+00 6.83e-01 2.06e+01 angle pdb=" C GLU B 442 " pdb=" N GLU B 443 " pdb=" CA GLU B 443 " ideal model delta sigma weight residual 122.61 128.77 -6.16 1.56e+00 4.11e-01 1.56e+01 angle pdb=" N MET A1518 " pdb=" CA MET A1518 " pdb=" C MET A1518 " ideal model delta sigma weight residual 113.01 108.35 4.66 1.20e+00 6.94e-01 1.51e+01 angle pdb=" C TRP B 764 " pdb=" N ASP B 765 " pdb=" CA ASP B 765 " ideal model delta sigma weight residual 122.08 127.78 -5.70 1.47e+00 4.63e-01 1.50e+01 ... (remaining 35571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 14632 17.57 - 35.14: 962 35.14 - 52.71: 225 52.71 - 70.28: 37 70.28 - 87.85: 5 Dihedral angle restraints: 15861 sinusoidal: 6411 harmonic: 9450 Sorted by residual: dihedral pdb=" CB CYS G 109 " pdb=" SG CYS G 109 " pdb=" SG CYS G 139 " pdb=" CB CYS G 139 " ideal model delta sinusoidal sigma weight residual 93.00 157.22 -64.22 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS C 109 " pdb=" SG CYS C 109 " pdb=" SG CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sinusoidal sigma weight residual 93.00 156.99 -63.99 1 1.00e+01 1.00e-02 5.39e+01 dihedral pdb=" CB CYS B 956 " pdb=" SG CYS B 956 " pdb=" SG CYS B 990 " pdb=" CB CYS B 990 " ideal model delta sinusoidal sigma weight residual 93.00 148.80 -55.80 1 1.00e+01 1.00e-02 4.20e+01 ... (remaining 15858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3269 0.065 - 0.129: 521 0.129 - 0.194: 52 0.194 - 0.259: 5 0.259 - 0.323: 3 Chirality restraints: 3850 Sorted by residual: chirality pdb=" CA PHE B1516 " pdb=" N PHE B1516 " pdb=" C PHE B1516 " pdb=" CB PHE B1516 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA PHE A1516 " pdb=" N PHE A1516 " pdb=" C PHE A1516 " pdb=" CB PHE A1516 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA TRP A1465 " pdb=" N TRP A1465 " pdb=" C TRP A1465 " pdb=" CB TRP A1465 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 3847 not shown) Planarity restraints: 4690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 906 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO B 907 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 907 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 907 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 687 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 688 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 688 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 688 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 811 " -0.034 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 812 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 812 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 812 " -0.028 5.00e-02 4.00e+02 ... (remaining 4687 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7402 2.82 - 3.34: 20817 3.34 - 3.86: 41055 3.86 - 4.38: 45698 4.38 - 4.90: 79829 Nonbonded interactions: 194801 Sorted by model distance: nonbonded pdb=" OG SER B 647 " pdb=" OE1 GLU B 704 " model vdw 2.298 2.440 nonbonded pdb=" O GLY B1501 " pdb=" OG1 THR B1507 " model vdw 2.301 2.440 nonbonded pdb=" OG SER A 647 " pdb=" OE1 GLU A 704 " model vdw 2.312 2.440 nonbonded pdb=" OG1 THR B 541 " pdb=" O PHE B 544 " model vdw 2.328 2.440 nonbonded pdb=" OH TYR B1486 " pdb=" O VAL G 63 " model vdw 2.329 2.440 ... (remaining 194796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.020 Extract box with map and model: 5.830 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 66.310 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.150 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 0.040 26164 Z= 0.219 Angle : 0.618 9.926 35576 Z= 0.358 Chirality : 0.048 0.323 3850 Planarity : 0.005 0.053 4690 Dihedral : 12.046 87.854 9514 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 5.83 % Cbeta Deviations : 0.07 % 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 (0.13), residues: 3238 helix: -2.33 (0.18), residues: 511 sheet: -0.24 (0.22), residues: 614 loop : -1.20 (0.12), residues: 2113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 585 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 167 outliers final: 40 residues processed: 723 average time/residue: 0.3964 time to fit residues: 443.1324 Evaluate side-chains 272 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 3.111 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2238 time to fit residues: 20.9366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 20.0000 chunk 247 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 255 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 262 ASN A 355 HIS ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN ** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 ASN A1287 HIS ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS B 232 ASN B 285 HIS B 308 GLN B 355 HIS ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN B 781 HIS B 952 GLN B 955 GLN B1210 HIS ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1497 ASN G 98 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 26164 Z= 0.355 Angle : 0.684 9.043 35576 Z= 0.360 Chirality : 0.047 0.190 3850 Planarity : 0.006 0.054 4690 Dihedral : 4.936 31.914 3492 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.25 (0.14), residues: 3238 helix: -1.00 (0.23), residues: 477 sheet: -0.30 (0.21), residues: 625 loop : -0.96 (0.13), residues: 2136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 285 time to evaluate : 3.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 297 average time/residue: 0.3811 time to fit residues: 179.1223 Evaluate side-chains 170 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 165 time to evaluate : 2.865 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2291 time to fit residues: 6.0946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 201 optimal weight: 0.4980 chunk 81 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 320 optimal weight: 5.9990 chunk 264 optimal weight: 0.0870 chunk 294 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1491 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 HIS B1210 HIS ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN G 136 GLN G 143 HIS ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.088 26164 Z= 0.182 Angle : 0.559 9.806 35576 Z= 0.288 Chirality : 0.044 0.289 3850 Planarity : 0.004 0.047 4690 Dihedral : 4.487 31.510 3492 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3238 helix: -0.54 (0.24), residues: 472 sheet: -0.13 (0.21), residues: 640 loop : -0.85 (0.13), residues: 2126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 286 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 293 average time/residue: 0.3839 time to fit residues: 177.8774 Evaluate side-chains 176 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 2.844 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2187 time to fit residues: 4.7675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 0.0870 chunk 222 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 32 optimal weight: 0.0000 chunk 141 optimal weight: 20.0000 chunk 199 optimal weight: 20.0000 chunk 297 optimal weight: 7.9990 chunk 315 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 282 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.7766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 HIS ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN A1078 HIS A1347 GLN ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1491 ASN B 136 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B1210 HIS ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 26164 Z= 0.199 Angle : 0.555 11.124 35576 Z= 0.286 Chirality : 0.044 0.236 3850 Planarity : 0.004 0.042 4690 Dihedral : 4.404 30.419 3492 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.87 (0.15), residues: 3238 helix: -0.45 (0.25), residues: 470 sheet: -0.03 (0.21), residues: 624 loop : -0.77 (0.13), residues: 2144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 266 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 269 average time/residue: 0.3590 time to fit residues: 158.0211 Evaluate side-chains 169 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 168 time to evaluate : 2.922 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2242 time to fit residues: 4.5576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 262 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 268 optimal weight: 0.0070 chunk 217 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 79 optimal weight: 0.4980 overall best weight: 1.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 HIS A1078 HIS ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1210 HIS ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN G 143 HIS ** G 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 26164 Z= 0.202 Angle : 0.552 10.028 35576 Z= 0.284 Chirality : 0.044 0.280 3850 Planarity : 0.004 0.043 4690 Dihedral : 4.442 28.909 3492 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.03 % 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: -0.81 (0.15), residues: 3238 helix: -0.34 (0.25), residues: 468 sheet: 0.02 (0.22), residues: 626 loop : -0.75 (0.13), residues: 2144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.3742 time to fit residues: 150.1435 Evaluate side-chains 160 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.938 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 8.9990 chunk 283 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 185 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 301 GLN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 GLN B1210 HIS ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 26164 Z= 0.210 Angle : 0.553 9.557 35576 Z= 0.285 Chirality : 0.044 0.247 3850 Planarity : 0.004 0.042 4690 Dihedral : 4.433 27.752 3492 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3238 helix: -0.35 (0.25), residues: 468 sheet: 0.02 (0.21), residues: 631 loop : -0.76 (0.13), residues: 2139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.3770 time to fit residues: 144.5079 Evaluate side-chains 153 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.875 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 179 optimal weight: 0.5980 chunk 230 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 265 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 942 GLN ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 HIS A1078 HIS A1389 HIS ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1473 HIS B1491 ASN C 91 ASN G 143 HIS ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 26164 Z= 0.270 Angle : 0.599 11.056 35576 Z= 0.312 Chirality : 0.045 0.225 3850 Planarity : 0.004 0.045 4690 Dihedral : 4.716 27.835 3492 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 0.03 % 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: -0.88 (0.15), residues: 3238 helix: -0.37 (0.25), residues: 467 sheet: 0.05 (0.22), residues: 618 loop : -0.83 (0.13), residues: 2153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 3.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.3710 time to fit residues: 144.3167 Evaluate side-chains 155 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 2.878 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 187 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 199 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN B 301 GLN B 423 ASN ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 942 GLN ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 26164 Z= 0.178 Angle : 0.561 11.656 35576 Z= 0.288 Chirality : 0.044 0.210 3850 Planarity : 0.004 0.043 4690 Dihedral : 4.477 26.400 3492 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.03 % 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: -0.80 (0.15), residues: 3238 helix: -0.33 (0.25), residues: 473 sheet: 0.11 (0.22), residues: 611 loop : -0.77 (0.13), residues: 2154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 223 average time/residue: 0.3510 time to fit residues: 131.7240 Evaluate side-chains 154 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 2.926 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2264 time to fit residues: 4.3937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 9.9990 chunk 301 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 chunk 292 optimal weight: 9.9990 chunk 300 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 264 optimal weight: 4.9990 chunk 276 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS ** A1405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 26164 Z= 0.192 Angle : 0.556 10.083 35576 Z= 0.287 Chirality : 0.044 0.196 3850 Planarity : 0.004 0.042 4690 Dihedral : 4.475 27.697 3492 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.81 (0.15), residues: 3238 helix: -0.30 (0.25), residues: 473 sheet: 0.10 (0.22), residues: 611 loop : -0.79 (0.13), residues: 2154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.3528 time to fit residues: 124.0550 Evaluate side-chains 146 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 3.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 324 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 258 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 199 optimal weight: 0.0470 overall best weight: 2.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN A1078 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1318 GLN C 91 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 26164 Z= 0.225 Angle : 0.582 13.250 35576 Z= 0.300 Chirality : 0.045 0.194 3850 Planarity : 0.004 0.077 4690 Dihedral : 4.593 26.259 3492 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.83 (0.15), residues: 3238 helix: -0.22 (0.25), residues: 467 sheet: 0.04 (0.21), residues: 619 loop : -0.82 (0.13), residues: 2152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.3544 time to fit residues: 127.5725 Evaluate side-chains 146 residues out of total 2864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 3.072 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 158 optimal weight: 2.9990 chunk 205 optimal weight: 0.3980 chunk 275 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 259 optimal weight: 0.0870 chunk 108 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** 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 = 0.3858 r_free = 0.3858 target = 0.097321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.077917 restraints weight = 92903.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.077353 restraints weight = 86883.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.078015 restraints weight = 84287.007| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 26164 Z= 0.159 Angle : 0.552 9.586 35576 Z= 0.281 Chirality : 0.044 0.188 3850 Planarity : 0.004 0.043 4690 Dihedral : 4.436 30.272 3492 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3238 helix: -0.18 (0.25), residues: 474 sheet: 0.06 (0.21), residues: 618 loop : -0.78 (0.13), residues: 2146 =============================================================================== Job complete usr+sys time: 4357.52 seconds wall clock time: 80 minutes 50.50 seconds (4850.50 seconds total)