Starting phenix.real_space_refine on Sun Jun 22 05:07:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgh_34739/06_2025/8hgh_34739.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgh_34739/06_2025/8hgh_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/cci-nas-00/data/ceres_data/8hgh_34739/06_2025/8hgh_34739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgh_34739/06_2025/8hgh_34739.map" model { file = "/net/cci-nas-00/data/ceres_data/8hgh_34739/06_2025/8hgh_34739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgh_34739/06_2025/8hgh_34739.cif" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Time to flip 3 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.60, per 1000 atoms: 0.57 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.53 Conformation dependent library (CDL) restraints added in 3.0 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: 3.88 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: 12.71 Time building geometry restraints manager: 6.73 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: 0.00 - 1.99: 34924 1.99 - 3.97: 576 3.97 - 5.96: 53 5.96 - 7.94: 16 7.94 - 9.93: 7 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 3.040 nonbonded pdb=" O GLY B1501 " pdb=" OG1 THR B1507 " model vdw 2.301 3.040 nonbonded pdb=" OG SER A 647 " pdb=" OE1 GLU A 704 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR B 541 " pdb=" O PHE B 544 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR B1486 " pdb=" O VAL G 63 " model vdw 2.329 3.040 ... (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 Time spend for trying shortcut: 0.13 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: 1.030 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: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 65.270 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.130 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.280 ------------------------------------------------------------------------------- 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 26255 Z= 0.199 Angle : 0.619 9.926 35746 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 % Allowed : 7.96 % Favored : 86.21 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1465 HIS 0.007 0.001 HIS B 78 PHE 0.021 0.001 PHE B1315 TYR 0.012 0.001 TYR B1498 ARG 0.002 0.000 ARG C 44 Details of bonding type rmsd hydrogen bonds : bond 0.18225 ( 615) hydrogen bonds : angle 7.41850 ( 1791) metal coordination : bond 0.00139 ( 6) SS BOND : bond 0.00185 ( 85) SS BOND : angle 0.76304 ( 170) covalent geometry : bond 0.00327 (26164) covalent geometry : angle 0.61804 (35576) *********************** 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 to be fit. rotamer outliers: 167 poor density : 585 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.7924 (mm) REVERT: A 338 LYS cc_start: 0.6262 (mttt) cc_final: 0.5789 (tppp) REVERT: A 473 MET cc_start: 0.6833 (mmt) cc_final: 0.5864 (ptm) REVERT: A 508 MET cc_start: 0.7599 (ttp) cc_final: 0.6804 (ttp) REVERT: A 621 PHE cc_start: 0.8124 (m-80) cc_final: 0.7689 (m-10) REVERT: A 664 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6764 (mm-30) REVERT: A 752 ASN cc_start: 0.7596 (m110) cc_final: 0.7084 (t0) REVERT: A 785 ASP cc_start: 0.8084 (t0) cc_final: 0.7583 (t0) REVERT: A 849 THR cc_start: 0.7151 (OUTLIER) cc_final: 0.6699 (t) REVERT: A 976 ILE cc_start: 0.2985 (OUTLIER) cc_final: 0.2475 (mp) REVERT: A 1014 MET cc_start: 0.5386 (mtp) cc_final: 0.4741 (mtp) REVERT: A 1045 THR cc_start: 0.6415 (OUTLIER) cc_final: 0.6187 (t) REVERT: A 1078 HIS cc_start: 0.4643 (m-70) cc_final: 0.4152 (m170) REVERT: A 1250 MET cc_start: 0.7575 (mmm) cc_final: 0.7321 (mmm) REVERT: A 1281 ARG cc_start: 0.5797 (ptt90) cc_final: 0.4658 (tmm-80) REVERT: A 1412 CYS cc_start: -0.3279 (OUTLIER) cc_final: -0.3488 (t) REVERT: B 32 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7918 (mm) REVERT: B 78 HIS cc_start: 0.8905 (OUTLIER) cc_final: 0.8574 (p-80) REVERT: B 112 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8572 (mt) REVERT: B 239 ASP cc_start: 0.7529 (t0) cc_final: 0.7327 (p0) REVERT: B 445 LEU cc_start: 0.5656 (OUTLIER) cc_final: 0.5439 (pt) REVERT: B 465 VAL cc_start: 0.6916 (OUTLIER) cc_final: 0.6713 (m) REVERT: B 497 ILE cc_start: 0.7543 (mm) cc_final: 0.7341 (mt) REVERT: B 544 PHE cc_start: 0.6288 (OUTLIER) cc_final: 0.4590 (m-80) REVERT: B 783 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6871 (mt-10) REVERT: B 975 VAL cc_start: 0.3100 (OUTLIER) cc_final: 0.2557 (p) REVERT: B 995 PRO cc_start: 0.5490 (Cg_exo) cc_final: 0.5278 (Cg_endo) REVERT: B 1004 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5047 (m-80) REVERT: B 1056 VAL cc_start: 0.7358 (OUTLIER) cc_final: 0.5857 (p) REVERT: B 1204 ASP cc_start: 0.5927 (OUTLIER) cc_final: 0.5504 (p0) REVERT: B 1247 LEU cc_start: 0.6959 (mt) cc_final: 0.6635 (mt) REVERT: B 1257 PHE cc_start: 0.7566 (m-80) cc_final: 0.7234 (m-10) REVERT: B 1485 ASN cc_start: 0.8661 (m-40) cc_final: 0.8401 (m110) REVERT: B 1497 ASN cc_start: 0.7913 (m-40) cc_final: 0.7569 (t0) REVERT: C 73 ASN cc_start: 0.7751 (t0) cc_final: 0.7344 (p0) REVERT: C 131 MET cc_start: 0.7627 (ppp) cc_final: 0.7253 (tmm) REVERT: C 134 GLN cc_start: 0.8435 (tt0) cc_final: 0.8226 (tt0) REVERT: C 165 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8460 (pt) REVERT: C 190 THR cc_start: 0.8748 (p) cc_final: 0.8479 (p) REVERT: G 95 PHE cc_start: 0.6073 (m-80) cc_final: 0.5533 (m-10) REVERT: G 117 ARG cc_start: 0.7674 (ptp-170) cc_final: 0.7213 (ptm-80) REVERT: G 141 LEU cc_start: 0.8330 (mt) cc_final: 0.7663 (tt) REVERT: G 142 LYS cc_start: 0.7498 (ptpp) cc_final: 0.5699 (ptpt) REVERT: G 180 THR cc_start: 0.6067 (p) cc_final: 0.5793 (t) outliers start: 167 outliers final: 40 residues processed: 723 average time/residue: 0.4229 time to fit residues: 473.5180 Evaluate side-chains 298 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 2.900 ------------------------------------------------------------------------------- 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: 30.0000 chunk 247 optimal weight: 0.1980 chunk 137 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 255 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 190 optimal weight: 0.0770 chunk 296 optimal weight: 7.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 108 HIS A 198 HIS A 262 ASN A 298 GLN A 554 ASN A 620 HIS A 942 GLN ** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 ASN A1491 ASN B 198 HIS B 232 ASN B 734 ASN B1210 HIS ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.101745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.081299 restraints weight = 91133.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.080791 restraints weight = 72436.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.081658 restraints weight = 69029.504| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26255 Z= 0.122 Angle : 0.592 7.939 35746 Z= 0.306 Chirality : 0.045 0.203 3850 Planarity : 0.005 0.054 4690 Dihedral : 4.340 26.589 3492 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.31 % Allowed : 2.83 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3238 helix: -0.99 (0.23), residues: 479 sheet: -0.11 (0.22), residues: 624 loop : -0.92 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 201 HIS 0.010 0.001 HIS A1055 PHE 0.023 0.001 PHE C 162 TYR 0.019 0.001 TYR G 140 ARG 0.007 0.001 ARG A1007 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 615) hydrogen bonds : angle 5.63481 ( 1791) metal coordination : bond 0.00208 ( 6) SS BOND : bond 0.00590 ( 85) SS BOND : angle 1.61979 ( 170) covalent geometry : bond 0.00275 (26164) covalent geometry : angle 0.58323 (35576) *********************** 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 353 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 344 time to evaluate : 3.487 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: A 151 LEU cc_start: 0.8351 (mm) cc_final: 0.8018 (tp) REVERT: A 338 LYS cc_start: 0.6106 (mttt) cc_final: 0.5744 (tppp) REVERT: A 473 MET cc_start: 0.7255 (mmt) cc_final: 0.6443 (ptm) REVERT: A 508 MET cc_start: 0.7617 (ttp) cc_final: 0.7075 (ttp) REVERT: A 621 PHE cc_start: 0.8036 (m-80) cc_final: 0.7728 (m-10) REVERT: A 664 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7079 (mt-10) REVERT: A 752 ASN cc_start: 0.7473 (m110) cc_final: 0.7124 (t0) REVERT: A 1078 HIS cc_start: 0.4701 (m-70) cc_final: 0.4266 (m170) REVERT: A 1250 MET cc_start: 0.7510 (mmm) cc_final: 0.7034 (mtt) REVERT: A 1281 ARG cc_start: 0.5900 (ptt90) cc_final: 0.4507 (ttp-110) REVERT: A 1518 MET cc_start: 0.7169 (mtp) cc_final: 0.6474 (ttm) REVERT: B 668 ASP cc_start: 0.6880 (p0) cc_final: 0.6517 (t0) REVERT: B 816 MET cc_start: 0.6575 (pmm) cc_final: 0.6350 (ppp) REVERT: B 1006 LEU cc_start: 0.7871 (tt) cc_final: 0.7504 (tt) REVERT: B 1257 PHE cc_start: 0.7422 (m-80) cc_final: 0.7112 (m-10) REVERT: B 1497 ASN cc_start: 0.7739 (m-40) cc_final: 0.7458 (t0) REVERT: C 131 MET cc_start: 0.7503 (ppp) cc_final: 0.7125 (tmm) REVERT: C 160 ILE cc_start: 0.7918 (pt) cc_final: 0.7651 (pt) REVERT: G 117 ARG cc_start: 0.8290 (ptp-170) cc_final: 0.7167 (ptm-80) REVERT: G 141 LEU cc_start: 0.8239 (mt) cc_final: 0.7550 (tt) REVERT: G 180 THR cc_start: 0.6461 (p) cc_final: 0.6115 (t) outliers start: 9 outliers final: 2 residues processed: 351 average time/residue: 0.4092 time to fit residues: 226.2173 Evaluate side-chains 195 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 111 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 186 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN ** A1022 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 HIS A1347 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS B 554 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 GLN B1210 HIS ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1473 HIS C 200 ASN G 98 GLN G 136 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.095298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.071569 restraints weight = 92524.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.071626 restraints weight = 63602.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071094 restraints weight = 57899.759| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 26255 Z= 0.327 Angle : 0.841 12.875 35746 Z= 0.442 Chirality : 0.052 0.273 3850 Planarity : 0.006 0.085 4690 Dihedral : 5.664 32.508 3492 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.31 % Allowed : 6.28 % Favored : 93.40 % 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: -1.43 (0.14), residues: 3238 helix: -1.02 (0.23), residues: 475 sheet: -0.52 (0.22), residues: 614 loop : -1.08 (0.13), residues: 2149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A1255 HIS 0.015 0.002 HIS B 175 PHE 0.049 0.003 PHE B 91 TYR 0.022 0.003 TYR B 275 ARG 0.008 0.001 ARG A 909 Details of bonding type rmsd hydrogen bonds : bond 0.04707 ( 615) hydrogen bonds : angle 6.02386 ( 1791) metal coordination : bond 0.00739 ( 6) SS BOND : bond 0.00740 ( 85) SS BOND : angle 2.32600 ( 170) covalent geometry : bond 0.00724 (26164) covalent geometry : angle 0.82714 (35576) *********************** 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 259 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 250 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.5747 (mttt) cc_final: 0.5210 (tptm) REVERT: A 473 MET cc_start: 0.7445 (mmt) cc_final: 0.6535 (ptp) REVERT: A 556 MET cc_start: 0.7692 (mmt) cc_final: 0.7438 (mpp) REVERT: A 575 MET cc_start: 0.7825 (mpp) cc_final: 0.7362 (mpp) REVERT: A 621 PHE cc_start: 0.8199 (m-80) cc_final: 0.7823 (m-10) REVERT: A 831 MET cc_start: 0.4606 (mmp) cc_final: 0.3833 (mtm) REVERT: A 1066 ILE cc_start: 0.8223 (mm) cc_final: 0.7957 (mm) REVERT: A 1078 HIS cc_start: 0.5773 (m-70) cc_final: 0.5535 (m170) REVERT: A 1281 ARG cc_start: 0.6299 (ptt90) cc_final: 0.4787 (ttp-110) REVERT: A 1456 ARG cc_start: 0.7339 (mpp-170) cc_final: 0.6245 (mtp85) REVERT: B 239 ASP cc_start: 0.7625 (t70) cc_final: 0.7263 (p0) REVERT: B 473 MET cc_start: 0.6973 (tmm) cc_final: 0.6751 (tmm) REVERT: B 530 LYS cc_start: 0.5972 (mmmt) cc_final: 0.5250 (mmtm) REVERT: B 668 ASP cc_start: 0.7348 (p0) cc_final: 0.6809 (p0) REVERT: B 1077 TYR cc_start: 0.8209 (p90) cc_final: 0.7793 (p90) REVERT: B 1292 PHE cc_start: 0.7670 (m-80) cc_final: 0.6273 (p90) REVERT: B 1534 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6442 (tm-30) REVERT: C 69 GLU cc_start: 0.7982 (tt0) cc_final: 0.7743 (tt0) REVERT: C 73 ASN cc_start: 0.7940 (t0) cc_final: 0.7410 (p0) REVERT: G 131 MET cc_start: 0.7704 (ppp) cc_final: 0.7378 (tpt) REVERT: G 141 LEU cc_start: 0.8274 (mt) cc_final: 0.7746 (pp) REVERT: G 198 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6713 (pp20) outliers start: 9 outliers final: 4 residues processed: 256 average time/residue: 0.6332 time to fit residues: 257.9676 Evaluate side-chains 169 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 165 time to evaluate : 5.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 250 optimal weight: 0.0770 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 315 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.0270 chunk 89 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS A 554 ASN A 584 GLN ** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1491 ASN B 136 GLN B 234 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.098347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.078491 restraints weight = 91947.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.078371 restraints weight = 82647.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.078824 restraints weight = 80403.945| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 26255 Z= 0.115 Angle : 0.596 11.048 35746 Z= 0.307 Chirality : 0.045 0.254 3850 Planarity : 0.004 0.049 4690 Dihedral : 4.688 29.524 3492 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.38 % 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: -1.08 (0.14), residues: 3238 helix: -0.74 (0.23), residues: 481 sheet: -0.18 (0.21), residues: 618 loop : -0.88 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.011 0.001 HIS A 78 PHE 0.017 0.001 PHE A 91 TYR 0.014 0.001 TYR B 776 ARG 0.005 0.000 ARG A 762 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 615) hydrogen bonds : angle 5.36169 ( 1791) metal coordination : bond 0.00074 ( 6) SS BOND : bond 0.00623 ( 85) SS BOND : angle 1.90716 ( 170) covalent geometry : bond 0.00258 (26164) covalent geometry : angle 0.58233 (35576) *********************** 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 277 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 274 time to evaluate : 6.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.5653 (mttt) cc_final: 0.5196 (tptm) REVERT: A 473 MET cc_start: 0.7469 (mmt) cc_final: 0.6645 (ptm) REVERT: A 575 MET cc_start: 0.8050 (mpp) cc_final: 0.7455 (mpp) REVERT: A 621 PHE cc_start: 0.8295 (m-80) cc_final: 0.7904 (m-80) REVERT: A 664 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7460 (mt-10) REVERT: A 670 GLU cc_start: 0.7570 (pt0) cc_final: 0.7355 (pt0) REVERT: A 711 LEU cc_start: 0.9041 (pp) cc_final: 0.8799 (pp) REVERT: A 769 GLU cc_start: 0.7361 (pt0) cc_final: 0.7100 (pt0) REVERT: A 831 MET cc_start: 0.4746 (mmp) cc_final: 0.4132 (mtm) REVERT: A 1078 HIS cc_start: 0.5705 (m-70) cc_final: 0.5268 (m170) REVERT: A 1456 ARG cc_start: 0.7159 (mpp-170) cc_final: 0.6267 (mtp180) REVERT: B 17 LEU cc_start: 0.8700 (mt) cc_final: 0.8499 (mt) REVERT: B 66 TYR cc_start: 0.7403 (m-80) cc_final: 0.7191 (m-10) REVERT: B 327 ARG cc_start: 0.7171 (ptp-170) cc_final: 0.6931 (ptp-170) REVERT: B 530 LYS cc_start: 0.5490 (mmmt) cc_final: 0.4904 (mmtm) REVERT: B 668 ASP cc_start: 0.7373 (p0) cc_final: 0.6861 (p0) REVERT: B 1077 TYR cc_start: 0.8142 (p90) cc_final: 0.7927 (p90) REVERT: B 1490 ILE cc_start: 0.8610 (tt) cc_final: 0.8209 (mm) REVERT: B 1497 ASN cc_start: 0.7950 (m-40) cc_final: 0.7726 (t0) REVERT: B 1534 GLN cc_start: 0.6941 (mm-40) cc_final: 0.6410 (tm-30) REVERT: C 69 GLU cc_start: 0.8096 (tt0) cc_final: 0.7889 (tt0) REVERT: C 73 ASN cc_start: 0.7943 (t0) cc_final: 0.7469 (p0) REVERT: C 78 ILE cc_start: 0.8081 (mm) cc_final: 0.6525 (mm) REVERT: G 117 ARG cc_start: 0.8621 (ptp-170) cc_final: 0.7220 (ptm-80) REVERT: G 141 LEU cc_start: 0.8268 (mt) cc_final: 0.7604 (tt) REVERT: G 142 LYS cc_start: 0.7664 (ptpt) cc_final: 0.7369 (ptpt) REVERT: G 199 GLN cc_start: 0.8047 (tt0) cc_final: 0.7761 (pt0) outliers start: 3 outliers final: 0 residues processed: 277 average time/residue: 0.6052 time to fit residues: 274.1203 Evaluate side-chains 177 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 9.9990 chunk 288 optimal weight: 0.0980 chunk 76 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 282 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 66 optimal weight: 0.0970 chunk 237 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1389 HIS B 301 GLN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 942 GLN ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.096170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.073938 restraints weight = 92157.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072974 restraints weight = 69738.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.072977 restraints weight = 66786.592| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26255 Z= 0.191 Angle : 0.631 11.960 35746 Z= 0.331 Chirality : 0.046 0.243 3850 Planarity : 0.004 0.052 4690 Dihedral : 4.939 29.549 3492 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3238 helix: -0.79 (0.23), residues: 492 sheet: -0.22 (0.21), residues: 631 loop : -0.91 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 658 HIS 0.007 0.001 HIS C 143 PHE 0.024 0.002 PHE A1218 TYR 0.018 0.002 TYR B 275 ARG 0.005 0.001 ARG B 69 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 615) hydrogen bonds : angle 5.39160 ( 1791) metal coordination : bond 0.00370 ( 6) SS BOND : bond 0.00421 ( 85) SS BOND : angle 1.65209 ( 170) covalent geometry : bond 0.00433 (26164) covalent geometry : angle 0.62252 (35576) *********************** 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 241 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8428 (mmtt) REVERT: A 338 LYS cc_start: 0.5857 (mttt) cc_final: 0.5335 (tppp) REVERT: A 341 ASP cc_start: 0.7011 (t0) cc_final: 0.6760 (t0) REVERT: A 347 GLU cc_start: 0.6830 (pm20) cc_final: 0.5862 (pm20) REVERT: A 473 MET cc_start: 0.7630 (mmt) cc_final: 0.6676 (ptp) REVERT: A 621 PHE cc_start: 0.8386 (m-80) cc_final: 0.7939 (m-10) REVERT: A 664 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 831 MET cc_start: 0.4665 (mmp) cc_final: 0.4053 (mtm) REVERT: A 1250 MET cc_start: 0.7879 (mtt) cc_final: 0.7659 (mtt) REVERT: A 1456 ARG cc_start: 0.7156 (mpp-170) cc_final: 0.6136 (mmm160) REVERT: B 66 TYR cc_start: 0.7650 (m-80) cc_final: 0.6993 (m-80) REVERT: B 327 ARG cc_start: 0.7396 (ptp-170) cc_final: 0.7130 (ptp-170) REVERT: B 668 ASP cc_start: 0.7783 (p0) cc_final: 0.7163 (p0) REVERT: B 1077 TYR cc_start: 0.8343 (p90) cc_final: 0.7865 (p90) REVERT: B 1497 ASN cc_start: 0.7922 (m-40) cc_final: 0.7655 (t0) REVERT: B 1534 GLN cc_start: 0.7060 (mm-40) cc_final: 0.6565 (tm-30) REVERT: C 69 GLU cc_start: 0.7994 (tt0) cc_final: 0.7732 (tt0) REVERT: C 73 ASN cc_start: 0.8108 (t0) cc_final: 0.7658 (p0) REVERT: G 117 ARG cc_start: 0.8789 (ptp-170) cc_final: 0.7219 (ptm-80) REVERT: G 141 LEU cc_start: 0.8292 (mt) cc_final: 0.7757 (pp) REVERT: G 198 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6786 (pp20) REVERT: G 199 GLN cc_start: 0.8122 (tt0) cc_final: 0.7374 (pt0) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.3680 time to fit residues: 141.8329 Evaluate side-chains 168 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 322 optimal weight: 4.9990 chunk 279 optimal weight: 0.3980 chunk 249 optimal weight: 0.9990 chunk 298 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 HIS ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 HIS B 168 ASN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1239 GLN ** B1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN G 136 GLN G 143 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.097894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.078458 restraints weight = 91522.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.077541 restraints weight = 84377.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.078253 restraints weight = 83617.276| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 26255 Z= 0.104 Angle : 0.562 11.108 35746 Z= 0.290 Chirality : 0.044 0.209 3850 Planarity : 0.004 0.048 4690 Dihedral : 4.526 27.155 3492 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.14 % Allowed : 1.50 % Favored : 98.36 % 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: -0.97 (0.15), residues: 3238 helix: -0.49 (0.24), residues: 485 sheet: -0.06 (0.22), residues: 600 loop : -0.86 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.014 0.001 HIS B 175 PHE 0.023 0.001 PHE C 162 TYR 0.014 0.001 TYR B 471 ARG 0.006 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.03058 ( 615) hydrogen bonds : angle 5.06435 ( 1791) metal coordination : bond 0.00110 ( 6) SS BOND : bond 0.00295 ( 85) SS BOND : angle 1.49094 ( 170) covalent geometry : bond 0.00239 (26164) covalent geometry : angle 0.55423 (35576) *********************** 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 263 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 259 time to evaluate : 2.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.6025 (mttt) cc_final: 0.5531 (tptm) REVERT: A 473 MET cc_start: 0.7473 (mmt) cc_final: 0.6681 (ptm) REVERT: A 621 PHE cc_start: 0.8108 (m-80) cc_final: 0.7739 (m-80) REVERT: A 664 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7080 (mt-10) REVERT: A 831 MET cc_start: 0.4459 (mmp) cc_final: 0.3875 (mtm) REVERT: A 1079 SER cc_start: 0.7576 (m) cc_final: 0.7065 (p) REVERT: B 66 TYR cc_start: 0.7371 (m-80) cc_final: 0.6844 (m-80) REVERT: B 78 HIS cc_start: 0.8840 (OUTLIER) cc_final: 0.8539 (p-80) REVERT: B 327 ARG cc_start: 0.7005 (ptp-170) cc_final: 0.6800 (ptp-170) REVERT: B 480 MET cc_start: 0.7735 (tmm) cc_final: 0.7498 (tmm) REVERT: B 499 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6528 (tm-30) REVERT: B 668 ASP cc_start: 0.7398 (p0) cc_final: 0.6894 (p0) REVERT: B 1497 ASN cc_start: 0.7706 (m-40) cc_final: 0.7500 (t0) REVERT: B 1534 GLN cc_start: 0.7038 (mm-40) cc_final: 0.6325 (tm-30) REVERT: C 73 ASN cc_start: 0.7647 (t0) cc_final: 0.7428 (p0) REVERT: C 161 HIS cc_start: 0.6599 (m-70) cc_final: 0.6293 (m-70) REVERT: G 95 PHE cc_start: 0.6551 (m-80) cc_final: 0.6307 (m-10) REVERT: G 117 ARG cc_start: 0.8480 (ptp-170) cc_final: 0.7257 (ptm-80) REVERT: G 141 LEU cc_start: 0.8326 (mt) cc_final: 0.7866 (pp) REVERT: G 154 ARG cc_start: 0.7823 (ttp80) cc_final: 0.7430 (tmm-80) REVERT: G 198 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6676 (pp20) REVERT: G 199 GLN cc_start: 0.8094 (tt0) cc_final: 0.7422 (pt0) outliers start: 4 outliers final: 0 residues processed: 263 average time/residue: 0.3595 time to fit residues: 151.2207 Evaluate side-chains 181 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 166 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 78 optimal weight: 0.0870 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 313 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 291 optimal weight: 1.9990 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN A1012 GLN B 78 HIS ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1318 GLN ** B1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.096366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.076651 restraints weight = 92233.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.075953 restraints weight = 87778.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076882 restraints weight = 81989.540| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26255 Z= 0.156 Angle : 0.591 10.674 35746 Z= 0.307 Chirality : 0.045 0.224 3850 Planarity : 0.004 0.047 4690 Dihedral : 4.666 27.403 3492 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3238 helix: -0.53 (0.24), residues: 483 sheet: -0.02 (0.22), residues: 609 loop : -0.89 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 658 HIS 0.005 0.001 HIS A1343 PHE 0.023 0.002 PHE G 88 TYR 0.017 0.001 TYR B 558 ARG 0.006 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.03287 ( 615) hydrogen bonds : angle 5.19261 ( 1791) metal coordination : bond 0.00308 ( 6) SS BOND : bond 0.00295 ( 85) SS BOND : angle 1.50228 ( 170) covalent geometry : bond 0.00357 (26164) covalent geometry : angle 0.58364 (35576) *********************** 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 233 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.5691 (mttt) cc_final: 0.5356 (tppp) REVERT: A 473 MET cc_start: 0.7267 (mmt) cc_final: 0.6699 (ptp) REVERT: A 621 PHE cc_start: 0.8132 (m-80) cc_final: 0.7768 (m-80) REVERT: A 664 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7126 (mt-10) REVERT: A 831 MET cc_start: 0.4483 (mmp) cc_final: 0.3912 (mtm) REVERT: A 1456 ARG cc_start: 0.7391 (mpp-170) cc_final: 0.6300 (mmm160) REVERT: B 327 ARG cc_start: 0.7043 (ptp-170) cc_final: 0.6835 (ptp-170) REVERT: B 499 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6520 (tm-30) REVERT: B 668 ASP cc_start: 0.7506 (p0) cc_final: 0.7032 (p0) REVERT: B 1077 TYR cc_start: 0.8177 (p90) cc_final: 0.7868 (p90) REVERT: B 1534 GLN cc_start: 0.7089 (mm-40) cc_final: 0.6396 (tm-30) REVERT: C 73 ASN cc_start: 0.7930 (t0) cc_final: 0.7664 (p0) REVERT: C 86 MET cc_start: 0.7504 (mmm) cc_final: 0.6861 (tpt) REVERT: C 131 MET cc_start: 0.8131 (tmm) cc_final: 0.7843 (tmm) REVERT: C 161 HIS cc_start: 0.6725 (m-70) cc_final: 0.6406 (m-70) REVERT: G 95 PHE cc_start: 0.6545 (m-80) cc_final: 0.6266 (m-10) REVERT: G 117 ARG cc_start: 0.8572 (ptp-170) cc_final: 0.7263 (ptm-80) REVERT: G 141 LEU cc_start: 0.8246 (mt) cc_final: 0.7800 (pp) REVERT: G 198 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6781 (pp20) REVERT: G 199 GLN cc_start: 0.8030 (tt0) cc_final: 0.7566 (tm-30) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.3501 time to fit residues: 132.1342 Evaluate side-chains 169 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 23 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 15 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 0.2980 chunk 115 optimal weight: 10.0000 chunk 158 optimal weight: 0.0770 chunk 268 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1078 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** ** B1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.097778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.078181 restraints weight = 92090.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.078121 restraints weight = 89131.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.078929 restraints weight = 80616.327| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 26255 Z= 0.100 Angle : 0.574 11.678 35746 Z= 0.292 Chirality : 0.044 0.232 3850 Planarity : 0.004 0.049 4690 Dihedral : 4.441 25.527 3492 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3238 helix: -0.41 (0.24), residues: 486 sheet: 0.03 (0.22), residues: 590 loop : -0.84 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.006 0.001 HIS A1343 PHE 0.016 0.001 PHE A1516 TYR 0.012 0.001 TYR B 776 ARG 0.004 0.000 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 615) hydrogen bonds : angle 5.01332 ( 1791) metal coordination : bond 0.00160 ( 6) SS BOND : bond 0.00440 ( 85) SS BOND : angle 1.74706 ( 170) covalent geometry : bond 0.00231 (26164) covalent geometry : angle 0.56213 (35576) *********************** 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 240 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 2.779 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: A 338 LYS cc_start: 0.6020 (mttt) cc_final: 0.5367 (tttt) REVERT: A 473 MET cc_start: 0.7381 (mmt) cc_final: 0.6776 (ptp) REVERT: A 621 PHE cc_start: 0.8401 (m-80) cc_final: 0.7972 (m-80) REVERT: A 664 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7298 (mt-10) REVERT: A 752 ASN cc_start: 0.7786 (m110) cc_final: 0.7055 (t0) REVERT: A 831 MET cc_start: 0.4567 (mmp) cc_final: 0.3862 (mtm) REVERT: A 1456 ARG cc_start: 0.7424 (mpp-170) cc_final: 0.6366 (mmm160) REVERT: A 1518 MET cc_start: 0.6763 (mmp) cc_final: 0.5904 (mtt) REVERT: B 327 ARG cc_start: 0.7082 (ptp-170) cc_final: 0.6864 (ptp-170) REVERT: B 668 ASP cc_start: 0.7616 (p0) cc_final: 0.7084 (p0) REVERT: B 1077 TYR cc_start: 0.8242 (p90) cc_final: 0.7806 (p90) REVERT: B 1534 GLN cc_start: 0.7129 (mm-40) cc_final: 0.6404 (tm-30) REVERT: C 73 ASN cc_start: 0.8006 (t0) cc_final: 0.7606 (p0) REVERT: C 131 MET cc_start: 0.8237 (tmm) cc_final: 0.7941 (tmm) REVERT: C 144 ASP cc_start: 0.6928 (t0) cc_final: 0.6523 (t70) REVERT: C 161 HIS cc_start: 0.6913 (m-70) cc_final: 0.6571 (m-70) REVERT: G 57 LEU cc_start: 0.8478 (tt) cc_final: 0.7877 (mt) REVERT: G 95 PHE cc_start: 0.6807 (m-80) cc_final: 0.6549 (m-10) REVERT: G 117 ARG cc_start: 0.8702 (ptp-170) cc_final: 0.7308 (ptm-80) REVERT: G 141 LEU cc_start: 0.8307 (mt) cc_final: 0.7804 (pp) REVERT: G 198 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6757 (pp20) REVERT: G 199 GLN cc_start: 0.7852 (tt0) cc_final: 0.7512 (tm-30) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.3633 time to fit residues: 141.0226 Evaluate side-chains 171 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 307 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 297 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN ** A1078 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1473 HIS A1485 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 873 GLN ** B1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1491 ASN C 48 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.095605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.071921 restraints weight = 93540.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.072422 restraints weight = 66001.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.072325 restraints weight = 52336.425| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26255 Z= 0.184 Angle : 0.632 11.984 35746 Z= 0.328 Chirality : 0.046 0.194 3850 Planarity : 0.004 0.048 4690 Dihedral : 4.833 27.398 3492 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.07 % Allowed : 0.56 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 3238 helix: -0.46 (0.24), residues: 480 sheet: -0.13 (0.22), residues: 599 loop : -0.85 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 658 HIS 0.006 0.001 HIS A1343 PHE 0.023 0.002 PHE A 91 TYR 0.014 0.001 TYR A 642 ARG 0.006 0.001 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 615) hydrogen bonds : angle 5.23018 ( 1791) metal coordination : bond 0.00399 ( 6) SS BOND : bond 0.00351 ( 85) SS BOND : angle 1.58152 ( 170) covalent geometry : bond 0.00417 (26164) covalent geometry : angle 0.62420 (35576) *********************** 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 225 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 2.915 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: A 338 LYS cc_start: 0.5589 (mttt) cc_final: 0.4946 (tttt) REVERT: A 473 MET cc_start: 0.7392 (mmt) cc_final: 0.6745 (ptp) REVERT: A 621 PHE cc_start: 0.8482 (m-80) cc_final: 0.8050 (m-80) REVERT: A 664 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7214 (mt-10) REVERT: A 752 ASN cc_start: 0.7919 (m110) cc_final: 0.7145 (t0) REVERT: A 831 MET cc_start: 0.4700 (mmp) cc_final: 0.3929 (mtm) REVERT: A 1014 MET cc_start: 0.6695 (mmm) cc_final: 0.6398 (mpp) REVERT: A 1438 MET cc_start: -0.2733 (tmm) cc_final: -0.3158 (tmm) REVERT: A 1485 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8289 (t0) REVERT: A 1518 MET cc_start: 0.6862 (mmp) cc_final: 0.6077 (mtt) REVERT: B 327 ARG cc_start: 0.7394 (ptp-170) cc_final: 0.7136 (ptp-170) REVERT: B 668 ASP cc_start: 0.7659 (p0) cc_final: 0.6963 (p0) REVERT: B 1534 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6435 (tm-30) REVERT: C 159 MET cc_start: 0.7707 (tpp) cc_final: 0.7442 (mmt) REVERT: G 117 ARG cc_start: 0.8707 (ptp-170) cc_final: 0.7293 (ptm-80) REVERT: G 141 LEU cc_start: 0.8281 (mt) cc_final: 0.7743 (pp) REVERT: G 198 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6759 (pp20) REVERT: G 199 GLN cc_start: 0.7997 (tt0) cc_final: 0.7388 (tm-30) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.5129 time to fit residues: 185.4710 Evaluate side-chains 160 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 200 optimal weight: 6.9990 chunk 307 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 299 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 288 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 281 optimal weight: 30.0000 chunk 280 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 423 ASN B 476 HIS B 529 HIS B 554 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.093979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.069864 restraints weight = 93494.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.070391 restraints weight = 64020.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.070423 restraints weight = 53860.716| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 26255 Z= 0.258 Angle : 0.723 12.608 35746 Z= 0.379 Chirality : 0.049 0.205 3850 Planarity : 0.005 0.051 4690 Dihedral : 5.501 29.216 3492 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.07 % Allowed : 0.56 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3238 helix: -0.66 (0.24), residues: 482 sheet: -0.44 (0.22), residues: 581 loop : -1.06 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1325 HIS 0.008 0.001 HIS A 951 PHE 0.033 0.002 PHE G 88 TYR 0.019 0.002 TYR A 642 ARG 0.006 0.001 ARG A 292 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 615) hydrogen bonds : angle 5.62347 ( 1791) metal coordination : bond 0.00538 ( 6) SS BOND : bond 0.00407 ( 85) SS BOND : angle 1.80899 ( 170) covalent geometry : bond 0.00584 (26164) covalent geometry : angle 0.71347 (35576) ********************** 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 222 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 3.465 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: A 338 LYS cc_start: 0.5288 (mttt) cc_final: 0.4910 (tppp) REVERT: A 341 ASP cc_start: 0.7177 (t0) cc_final: 0.6963 (t0) REVERT: A 473 MET cc_start: 0.7476 (mmt) cc_final: 0.6858 (ptp) REVERT: A 556 MET cc_start: 0.7494 (mmt) cc_final: 0.7052 (mmm) REVERT: A 621 PHE cc_start: 0.8369 (m-80) cc_final: 0.7969 (m-80) REVERT: A 664 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7293 (mt-10) REVERT: A 752 ASN cc_start: 0.8009 (m110) cc_final: 0.7247 (t0) REVERT: A 831 MET cc_start: 0.4661 (mmp) cc_final: 0.3875 (mtm) REVERT: A 1411 GLN cc_start: 0.6019 (mp10) cc_final: 0.5807 (pm20) REVERT: A 1518 MET cc_start: 0.6795 (mmp) cc_final: 0.6488 (mtt) REVERT: B 220 MET cc_start: 0.7204 (mmt) cc_final: 0.6931 (mmt) REVERT: B 327 ARG cc_start: 0.7412 (ptp-170) cc_final: 0.7163 (ptp-170) REVERT: B 668 ASP cc_start: 0.7614 (p0) cc_final: 0.7090 (p0) REVERT: B 1534 GLN cc_start: 0.6953 (mm-40) cc_final: 0.6548 (tm-30) REVERT: G 117 ARG cc_start: 0.8745 (ptp-170) cc_final: 0.7224 (ptm-80) REVERT: G 141 LEU cc_start: 0.8066 (mt) cc_final: 0.7685 (pp) REVERT: G 199 GLN cc_start: 0.8058 (tt0) cc_final: 0.7519 (tm-30) outliers start: 2 outliers final: 1 residues processed: 222 average time/residue: 0.4425 time to fit residues: 159.7112 Evaluate side-chains 160 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 185 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 319 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN ** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 GLN A1468 HIS B 476 HIS B 571 GLN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1180 GLN G 98 GLN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.094600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070845 restraints weight = 93194.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.071149 restraints weight = 62331.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071257 restraints weight = 48633.956| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26255 Z= 0.189 Angle : 0.649 10.456 35746 Z= 0.338 Chirality : 0.047 0.202 3850 Planarity : 0.005 0.118 4690 Dihedral : 5.272 28.553 3492 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.03 % Allowed : 0.45 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 3238 helix: -0.62 (0.24), residues: 488 sheet: -0.47 (0.22), residues: 593 loop : -1.05 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1325 HIS 0.015 0.001 HIS A1055 PHE 0.020 0.002 PHE A 91 TYR 0.017 0.002 TYR G 140 ARG 0.014 0.001 ARG A 413 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 615) hydrogen bonds : angle 5.46871 ( 1791) metal coordination : bond 0.00332 ( 6) SS BOND : bond 0.00334 ( 85) SS BOND : angle 1.61251 ( 170) covalent geometry : bond 0.00431 (26164) covalent geometry : angle 0.64053 (35576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8761.90 seconds wall clock time: 160 minutes 14.16 seconds (9614.16 seconds total)