Starting phenix.real_space_refine on Mon Aug 25 05:29:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hgh_34739/08_2025/8hgh_34739.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hgh_34739/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hgh_34739/08_2025/8hgh_34739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hgh_34739/08_2025/8hgh_34739.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hgh_34739/08_2025/8hgh_34739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hgh_34739/08_2025/8hgh_34739.map" } resolution = 4.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.38, per 1000 atoms: 0.25 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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1601 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 486 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 482 " pdb="ZN ZN A1601 " - pdb=" NE2 HIS A 492 " pdb=" ZN B1601 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 482 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 486 " pdb="ZN ZN B1601 " - pdb=" NE2 HIS B 492 " 6476 Ramachandran restraints generated. 3238 Oldfield, 0 Emsley, 3238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6092 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 44 sheets defined 17.7% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 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: 6.82 Time building geometry restraints manager: 3.02 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: 0.05 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.140 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG C 44 TYR 0.012 0.001 TYR B1498 PHE 0.021 0.001 PHE B1315 TRP 0.010 0.001 TRP B1465 HIS 0.007 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00327 (26164) covalent geometry : angle 0.61804 (35576) SS BOND : bond 0.00185 ( 85) SS BOND : angle 0.76304 ( 170) hydrogen bonds : bond 0.18225 ( 615) hydrogen bonds : angle 7.41850 ( 1791) metal coordination : bond 0.00139 ( 6) *********************** 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 : 1.041 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: 0.7914 (mm) REVERT: A 338 LYS cc_start: 0.6262 (mttt) cc_final: 0.5790 (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: 0.6806 (ttp) REVERT: A 621 PHE cc_start: 0.8124 (m-80) cc_final: 0.7687 (m-10) REVERT: A 664 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6759 (mm-30) REVERT: A 752 ASN cc_start: 0.7596 (m110) cc_final: 0.7087 (t0) REVERT: A 785 ASP cc_start: 0.8084 (t0) cc_final: 0.7582 (t0) REVERT: A 849 THR cc_start: 0.7151 (OUTLIER) cc_final: 0.6702 (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: 0.4742 (mtp) REVERT: A 1045 THR cc_start: 0.6415 (OUTLIER) cc_final: 0.6185 (t) REVERT: A 1078 HIS cc_start: 0.4643 (m-70) cc_final: 0.4153 (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: 0.4657 (tmm-80) REVERT: A 1412 CYS cc_start: -0.3279 (OUTLIER) cc_final: -0.3499 (t) REVERT: A 1463 LEU cc_start: 0.7585 (tp) cc_final: 0.7309 (tp) 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: 0.8572 (p-80) REVERT: B 112 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8571 (mt) REVERT: B 239 ASP cc_start: 0.7529 (t0) cc_final: 0.7326 (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: 0.6712 (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: 0.4592 (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: 0.5279 (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: 0.5856 (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: 0.6589 (mt) REVERT: B 1257 PHE cc_start: 0.7566 (m-80) cc_final: 0.7236 (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: 0.7252 (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: 0.5537 (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: 0.5697 (ptpt) REVERT: G 180 THR cc_start: 0.6067 (p) cc_final: 0.5791 (t) outliers start: 167 outliers final: 40 residues processed: 723 average time/residue: 0.1919 time to fit residues: 213.9663 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 : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.4980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 198 HIS A 262 ASN A 298 GLN A 554 ASN A 942 GLN A1055 HIS 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 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 = 0.3946 r_free = 0.3946 target = 0.101706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.081182 restraints weight = 91098.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.081625 restraints weight = 76983.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.082262 restraints weight = 70112.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082823 restraints weight = 46880.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.083363 restraints weight = 42053.010| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 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 0.053 26255 Z= 0.121 Angle : 0.591 8.263 35746 Z= 0.305 Chirality : 0.045 0.194 3850 Planarity : 0.005 0.054 4690 Dihedral : 4.339 26.667 3492 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.35 % Allowed : 2.83 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.14), residues: 3238 helix: -1.04 (0.23), residues: 485 sheet: -0.12 (0.22), residues: 624 loop : -0.91 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1007 TYR 0.020 0.001 TYR G 140 PHE 0.028 0.001 PHE C 162 TRP 0.029 0.001 TRP C 201 HIS 0.010 0.001 HIS A1055 Details of bonding type rmsd covalent geometry : bond 0.00277 (26164) covalent geometry : angle 0.57970 (35576) SS BOND : bond 0.00419 ( 85) SS BOND : angle 1.73935 ( 170) hydrogen bonds : bond 0.03888 ( 615) hydrogen bonds : angle 5.64111 ( 1791) metal coordination : bond 0.00265 ( 6) *********************** 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 352 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 342 time to evaluate : 0.922 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: 0.8424 (mm) cc_final: 0.8076 (tp) REVERT: A 159 MET cc_start: 0.6978 (mtp) cc_final: 0.6641 (mmt) REVERT: A 338 LYS cc_start: 0.6072 (mttt) cc_final: 0.5791 (tptm) REVERT: A 473 MET cc_start: 0.7330 (mmt) cc_final: 0.6466 (ptm) REVERT: A 508 MET cc_start: 0.7662 (ttp) cc_final: 0.7115 (ttp) REVERT: A 621 PHE cc_start: 0.8254 (m-80) cc_final: 0.7949 (m-10) REVERT: A 664 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 752 ASN cc_start: 0.7516 (m110) cc_final: 0.7015 (t0) REVERT: A 776 TYR cc_start: 0.7988 (m-80) cc_final: 0.7696 (m-10) REVERT: A 1078 HIS cc_start: 0.5032 (m-70) cc_final: 0.4604 (m170) REVERT: A 1250 MET cc_start: 0.7589 (mmm) cc_final: 0.7154 (mtt) REVERT: A 1281 ARG cc_start: 0.6005 (ptt90) cc_final: 0.4552 (ttp-110) REVERT: A 1518 MET cc_start: 0.7254 (mtp) cc_final: 0.6635 (ttm) REVERT: B 480 MET cc_start: 0.7700 (tmm) cc_final: 0.7468 (tmm) REVERT: B 668 ASP cc_start: 0.7139 (p0) cc_final: 0.6595 (t0) REVERT: B 816 MET cc_start: 0.6742 (pmm) cc_final: 0.6459 (ppp) REVERT: B 831 MET cc_start: 0.7598 (mtt) cc_final: 0.7373 (pmm) REVERT: B 1006 LEU cc_start: 0.8039 (tt) cc_final: 0.7692 (tt) REVERT: B 1257 PHE cc_start: 0.7391 (m-80) cc_final: 0.6979 (m-10) REVERT: B 1497 ASN cc_start: 0.7696 (m-40) cc_final: 0.7397 (t0) REVERT: C 131 MET cc_start: 0.7738 (ppp) cc_final: 0.7373 (tmm) REVERT: C 160 ILE cc_start: 0.7870 (pt) cc_final: 0.7600 (pt) REVERT: G 117 ARG cc_start: 0.8447 (ptp-170) cc_final: 0.7214 (ptm-80) REVERT: G 141 LEU cc_start: 0.8261 (mt) cc_final: 0.7577 (tt) REVERT: G 142 LYS cc_start: 0.7526 (ptpp) cc_final: 0.6694 (ptpt) REVERT: G 180 THR cc_start: 0.6539 (p) cc_final: 0.6260 (t) outliers start: 10 outliers final: 2 residues processed: 349 average time/residue: 0.1824 time to fit residues: 98.7795 Evaluate side-chains 194 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 269 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 313 optimal weight: 0.0270 chunk 30 optimal weight: 9.9990 chunk 273 optimal weight: 8.9990 chunk 314 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 275 optimal weight: 30.0000 overall best weight: 3.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 234 HIS A 355 HIS A 942 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 734 ASN B1210 HIS ** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS G 98 GLN G 143 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.098600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074090 restraints weight = 92540.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.074143 restraints weight = 59852.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074379 restraints weight = 50721.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.074673 restraints weight = 51900.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.074747 restraints weight = 43541.762| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 26255 Z= 0.184 Angle : 0.629 10.339 35746 Z= 0.327 Chirality : 0.046 0.284 3850 Planarity : 0.005 0.051 4690 Dihedral : 4.594 29.794 3492 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.14 % Allowed : 4.50 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 3238 helix: -0.60 (0.24), residues: 474 sheet: -0.18 (0.21), residues: 637 loop : -0.82 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 123 TYR 0.015 0.002 TYR B 18 PHE 0.024 0.002 PHE A 544 TRP 0.011 0.002 TRP B 210 HIS 0.010 0.001 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00415 (26164) covalent geometry : angle 0.61804 (35576) SS BOND : bond 0.00417 ( 85) SS BOND : angle 1.76857 ( 170) hydrogen bonds : bond 0.03692 ( 615) hydrogen bonds : angle 5.43093 ( 1791) metal coordination : bond 0.00311 ( 6) *********************** 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 287 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 283 time to evaluate : 0.980 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: A 292 ARG cc_start: 0.7442 (tmt-80) cc_final: 0.6683 (tpt90) REVERT: A 296 ASP cc_start: 0.7323 (t0) cc_final: 0.7091 (p0) REVERT: A 338 LYS cc_start: 0.5799 (mttt) cc_final: 0.5423 (tptm) REVERT: A 341 ASP cc_start: 0.6599 (t0) cc_final: 0.6362 (t0) REVERT: A 347 GLU cc_start: 0.6890 (pm20) cc_final: 0.6634 (pm20) REVERT: A 473 MET cc_start: 0.7453 (mmt) cc_final: 0.6552 (ptm) REVERT: A 575 MET cc_start: 0.7991 (mpp) cc_final: 0.7422 (mpp) REVERT: A 621 PHE cc_start: 0.8429 (m-80) cc_final: 0.8001 (m-10) REVERT: A 664 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7338 (mt-10) REVERT: A 752 ASN cc_start: 0.7824 (m110) cc_final: 0.7245 (t0) REVERT: A 769 GLU cc_start: 0.7189 (pt0) cc_final: 0.6877 (pt0) REVERT: A 1078 HIS cc_start: 0.5811 (m-70) cc_final: 0.5428 (m-70) REVERT: A 1281 ARG cc_start: 0.6131 (ptt90) cc_final: 0.4641 (ttp-110) REVERT: B 530 LYS cc_start: 0.6184 (mmmt) cc_final: 0.5219 (mmtm) REVERT: B 668 ASP cc_start: 0.7325 (p0) cc_final: 0.6652 (p0) REVERT: B 816 MET cc_start: 0.6914 (pmm) cc_final: 0.6639 (ppp) REVERT: B 831 MET cc_start: 0.7737 (mtt) cc_final: 0.7373 (pmm) REVERT: B 1077 TYR cc_start: 0.8199 (p90) cc_final: 0.7981 (p90) REVERT: B 1257 PHE cc_start: 0.7650 (m-80) cc_final: 0.7020 (m-10) REVERT: B 1534 GLN cc_start: 0.6939 (mm-40) cc_final: 0.6109 (tm-30) REVERT: C 73 ASN cc_start: 0.7961 (t0) cc_final: 0.7335 (p0) REVERT: C 78 ILE cc_start: 0.8143 (mm) cc_final: 0.7250 (mm) REVERT: C 159 MET cc_start: 0.6765 (ttm) cc_final: 0.6018 (mtt) REVERT: C 160 ILE cc_start: 0.7942 (pt) cc_final: 0.7682 (pt) REVERT: G 117 ARG cc_start: 0.8863 (ptp-170) cc_final: 0.7249 (ptm-80) REVERT: G 141 LEU cc_start: 0.8255 (mt) cc_final: 0.7619 (pp) REVERT: G 154 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7926 (tmm160) outliers start: 4 outliers final: 1 residues processed: 286 average time/residue: 0.1856 time to fit residues: 83.2237 Evaluate side-chains 182 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 241 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 201 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 300 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 160 optimal weight: 8.9990 chunk 286 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 460 HIS ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1491 ASN B 136 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 GLN B1210 HIS B1239 GLN ** C 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.098951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.079117 restraints weight = 90795.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.078669 restraints weight = 81483.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.079573 restraints weight = 74694.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.079856 restraints weight = 51885.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.081217 restraints weight = 46556.476| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26255 Z= 0.130 Angle : 0.574 9.678 35746 Z= 0.295 Chirality : 0.044 0.251 3850 Planarity : 0.004 0.046 4690 Dihedral : 4.458 29.149 3492 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.15), residues: 3238 helix: -0.52 (0.24), residues: 482 sheet: -0.14 (0.21), residues: 630 loop : -0.75 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 44 TYR 0.023 0.001 TYR G 140 PHE 0.024 0.001 PHE A1218 TRP 0.014 0.001 TRP A 658 HIS 0.015 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00306 (26164) covalent geometry : angle 0.56303 (35576) SS BOND : bond 0.00324 ( 85) SS BOND : angle 1.74762 ( 170) hydrogen bonds : bond 0.03272 ( 615) hydrogen bonds : angle 5.24477 ( 1791) metal coordination : bond 0.00188 ( 6) *********************** 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 278 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 275 time to evaluate : 1.082 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: A 292 ARG cc_start: 0.7426 (tmt-80) cc_final: 0.6881 (tpt90) REVERT: A 338 LYS cc_start: 0.5968 (mttt) cc_final: 0.5601 (tppp) REVERT: A 473 MET cc_start: 0.7267 (mmt) cc_final: 0.6520 (ptm) REVERT: A 575 MET cc_start: 0.7791 (mpp) cc_final: 0.7330 (mpp) REVERT: A 621 PHE cc_start: 0.8123 (m-80) cc_final: 0.7716 (m-10) REVERT: A 664 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7299 (mt-10) REVERT: A 711 LEU cc_start: 0.8949 (pp) cc_final: 0.8681 (pp) REVERT: A 752 ASN cc_start: 0.7782 (m110) cc_final: 0.7088 (t0) REVERT: A 831 MET cc_start: 0.4376 (mmp) cc_final: 0.3846 (mtm) REVERT: A 1014 MET cc_start: 0.6219 (mtp) cc_final: 0.5968 (mmm) REVERT: A 1078 HIS cc_start: 0.5144 (m-70) cc_final: 0.4745 (m170) REVERT: A 1281 ARG cc_start: 0.6042 (ptt90) cc_final: 0.4632 (ttp-110) REVERT: B 668 ASP cc_start: 0.7179 (p0) cc_final: 0.6633 (p0) REVERT: B 816 MET cc_start: 0.6514 (pmm) cc_final: 0.6307 (ppp) REVERT: B 1239 GLN cc_start: 0.5797 (OUTLIER) cc_final: 0.4586 (mp10) REVERT: C 73 ASN cc_start: 0.7780 (t0) cc_final: 0.7438 (p0) REVERT: C 160 ILE cc_start: 0.8202 (pt) cc_final: 0.7969 (pt) REVERT: G 117 ARG cc_start: 0.8541 (ptp-170) cc_final: 0.7198 (ptm-80) REVERT: G 141 LEU cc_start: 0.8194 (mt) cc_final: 0.7683 (pp) REVERT: G 142 LYS cc_start: 0.7634 (ptpt) cc_final: 0.6743 (ptpt) outliers start: 3 outliers final: 0 residues processed: 278 average time/residue: 0.1865 time to fit residues: 81.8422 Evaluate side-chains 187 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 219 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 256 optimal weight: 20.0000 chunk 284 optimal weight: 0.0470 chunk 323 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 112 optimal weight: 0.0570 chunk 315 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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 584 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN C 143 HIS G 143 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.099421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.079751 restraints weight = 90972.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.078983 restraints weight = 83012.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.079871 restraints weight = 80315.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.080338 restraints weight = 53611.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.081048 restraints weight = 48068.512| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 26255 Z= 0.102 Angle : 0.550 10.074 35746 Z= 0.282 Chirality : 0.044 0.250 3850 Planarity : 0.004 0.051 4690 Dihedral : 4.268 27.545 3492 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.03 % Allowed : 2.48 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.15), residues: 3238 helix: -0.42 (0.24), residues: 479 sheet: -0.03 (0.21), residues: 621 loop : -0.70 (0.13), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 44 TYR 0.022 0.001 TYR G 140 PHE 0.019 0.001 PHE A1218 TRP 0.010 0.001 TRP A 943 HIS 0.007 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00239 (26164) covalent geometry : angle 0.53983 (35576) SS BOND : bond 0.00375 ( 85) SS BOND : angle 1.64221 ( 170) hydrogen bonds : bond 0.03061 ( 615) hydrogen bonds : angle 5.06222 ( 1791) metal coordination : bond 0.00098 ( 6) *********************** 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 272 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 1.020 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 292 ARG cc_start: 0.7178 (tmt-80) cc_final: 0.6918 (tpt90) REVERT: A 338 LYS cc_start: 0.5918 (mttt) cc_final: 0.5489 (tptm) REVERT: A 347 GLU cc_start: 0.6344 (pm20) cc_final: 0.5651 (pm20) REVERT: A 473 MET cc_start: 0.7408 (mmt) cc_final: 0.6586 (ptm) REVERT: A 621 PHE cc_start: 0.8296 (m-80) cc_final: 0.7851 (m-10) REVERT: A 664 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7281 (mt-10) REVERT: A 752 ASN cc_start: 0.7771 (m110) cc_final: 0.7119 (t0) REVERT: A 1014 MET cc_start: 0.6335 (mtp) cc_final: 0.6126 (mmm) REVERT: A 1078 HIS cc_start: 0.5295 (m-70) cc_final: 0.5006 (m170) REVERT: A 1281 ARG cc_start: 0.6102 (ptt90) cc_final: 0.4712 (ttp-110) REVERT: B 327 ARG cc_start: 0.7113 (ptp-170) cc_final: 0.6827 (ptp-170) REVERT: B 668 ASP cc_start: 0.7200 (p0) cc_final: 0.6559 (p0) REVERT: B 816 MET cc_start: 0.6693 (pmm) cc_final: 0.6463 (ppp) REVERT: B 1257 PHE cc_start: 0.7493 (m-80) cc_final: 0.6972 (m-10) REVERT: C 73 ASN cc_start: 0.7927 (t0) cc_final: 0.7256 (p0) REVERT: G 57 LEU cc_start: 0.8481 (tt) cc_final: 0.7905 (mt) REVERT: G 117 ARG cc_start: 0.8653 (ptp-170) cc_final: 0.7207 (ptm-80) REVERT: G 142 LYS cc_start: 0.7481 (ptpt) cc_final: 0.7159 (ptpt) outliers start: 1 outliers final: 0 residues processed: 272 average time/residue: 0.1744 time to fit residues: 75.6988 Evaluate side-chains 180 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 201 optimal weight: 0.4980 chunk 306 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 304 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 403 GLN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1347 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 942 GLN ** 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 = 0.3869 r_free = 0.3869 target = 0.097825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.078109 restraints weight = 91655.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.077611 restraints weight = 81438.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.078085 restraints weight = 81189.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.078564 restraints weight = 55658.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.079919 restraints weight = 48431.730| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26255 Z= 0.152 Angle : 0.586 11.510 35746 Z= 0.303 Chirality : 0.045 0.249 3850 Planarity : 0.004 0.048 4690 Dihedral : 4.483 27.217 3492 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.15), residues: 3238 helix: -0.26 (0.24), residues: 465 sheet: 0.01 (0.21), residues: 623 loop : -0.70 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 154 TYR 0.018 0.001 TYR B1486 PHE 0.018 0.002 PHE A1218 TRP 0.012 0.001 TRP C 201 HIS 0.008 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00351 (26164) covalent geometry : angle 0.57603 (35576) SS BOND : bond 0.00398 ( 85) SS BOND : angle 1.66439 ( 170) hydrogen bonds : bond 0.03343 ( 615) hydrogen bonds : angle 5.09727 ( 1791) metal coordination : bond 0.00298 ( 6) *********************** 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 257 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.020 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: A 292 ARG cc_start: 0.7167 (tmt-80) cc_final: 0.6883 (tpt90) REVERT: A 338 LYS cc_start: 0.5913 (mttt) cc_final: 0.5518 (tptm) REVERT: A 341 ASP cc_start: 0.6645 (t0) cc_final: 0.6435 (t0) REVERT: A 473 MET cc_start: 0.7464 (mmt) cc_final: 0.6587 (ptp) REVERT: A 621 PHE cc_start: 0.8316 (m-80) cc_final: 0.7900 (m-10) REVERT: A 664 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7382 (mt-10) REVERT: A 1014 MET cc_start: 0.6554 (mtp) cc_final: 0.6348 (mmm) REVERT: A 1078 HIS cc_start: 0.5521 (m-70) cc_final: 0.5234 (m-70) REVERT: A 1250 MET cc_start: 0.7463 (mtt) cc_final: 0.7139 (mtt) REVERT: A 1281 ARG cc_start: 0.6130 (ptt90) cc_final: 0.4729 (ttp-110) REVERT: B 668 ASP cc_start: 0.7316 (p0) cc_final: 0.6704 (p0) REVERT: B 1490 ILE cc_start: 0.8584 (tt) cc_final: 0.8241 (mm) REVERT: B 1497 ASN cc_start: 0.7919 (m-40) cc_final: 0.7608 (t0) REVERT: B 1534 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6358 (tm-30) REVERT: C 73 ASN cc_start: 0.7870 (t0) cc_final: 0.7493 (p0) REVERT: G 117 ARG cc_start: 0.8640 (ptp-170) cc_final: 0.7171 (ptm-80) REVERT: G 141 LEU cc_start: 0.8151 (mt) cc_final: 0.7601 (pp) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1816 time to fit residues: 73.9493 Evaluate side-chains 179 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 210 optimal weight: 0.0070 chunk 284 optimal weight: 0.3980 chunk 133 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 285 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 316 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- 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 168 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN ** B1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN G 143 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.098796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.079134 restraints weight = 91649.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.078346 restraints weight = 83793.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.079079 restraints weight = 84192.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.079496 restraints weight = 56339.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.080383 restraints weight = 50240.337| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 26255 Z= 0.101 Angle : 0.555 12.480 35746 Z= 0.283 Chirality : 0.044 0.215 3850 Planarity : 0.004 0.049 4690 Dihedral : 4.301 25.464 3492 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.03 % Allowed : 1.15 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.15), residues: 3238 helix: -0.03 (0.25), residues: 457 sheet: 0.07 (0.22), residues: 613 loop : -0.65 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 154 TYR 0.015 0.001 TYR G 140 PHE 0.015 0.001 PHE A1516 TRP 0.032 0.001 TRP C 201 HIS 0.006 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00237 (26164) covalent geometry : angle 0.54418 (35576) SS BOND : bond 0.00292 ( 85) SS BOND : angle 1.65993 ( 170) hydrogen bonds : bond 0.03041 ( 615) hydrogen bonds : angle 4.91889 ( 1791) metal coordination : bond 0.00079 ( 6) *********************** 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 251 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 1.054 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: 0.5986 (mttt) cc_final: 0.5469 (tptm) REVERT: A 347 GLU cc_start: 0.6535 (pm20) cc_final: 0.5626 (pm20) REVERT: A 473 MET cc_start: 0.7335 (mmt) cc_final: 0.6565 (ptm) REVERT: A 621 PHE cc_start: 0.8082 (m-80) cc_final: 0.7706 (m-10) REVERT: A 664 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7243 (mt-10) REVERT: A 752 ASN cc_start: 0.7721 (m110) cc_final: 0.7096 (t0) REVERT: A 1066 ILE cc_start: 0.7557 (mm) cc_final: 0.7315 (mm) REVERT: A 1250 MET cc_start: 0.7517 (mtt) cc_final: 0.7230 (mtt) REVERT: A 1281 ARG cc_start: 0.6117 (ptt90) cc_final: 0.4725 (ttp-110) REVERT: A 1456 ARG cc_start: 0.7123 (mpp-170) cc_final: 0.6175 (mtp85) REVERT: B 327 ARG cc_start: 0.7066 (ptp-170) cc_final: 0.6811 (ptp-170) REVERT: B 668 ASP cc_start: 0.7147 (p0) cc_final: 0.6572 (p0) REVERT: B 1497 ASN cc_start: 0.7894 (m-40) cc_final: 0.7648 (t0) REVERT: B 1534 GLN cc_start: 0.6954 (mm-40) cc_final: 0.6435 (tm-30) REVERT: C 73 ASN cc_start: 0.7748 (t0) cc_final: 0.7297 (p0) REVERT: C 86 MET cc_start: 0.7685 (mmm) cc_final: 0.7076 (tpt) REVERT: G 57 LEU cc_start: 0.8438 (tt) cc_final: 0.7820 (mt) REVERT: G 117 ARG cc_start: 0.8494 (ptp-170) cc_final: 0.7143 (ptm-80) REVERT: G 154 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7324 (tmm-80) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.1733 time to fit residues: 70.3366 Evaluate side-chains 176 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 266 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 269 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN A 476 HIS ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 GLN A 942 GLN ** A 964 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 GLN A1473 HIS A1485 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS B 476 HIS ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 873 GLN B1491 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.094568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.070942 restraints weight = 93462.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.071125 restraints weight = 63142.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070677 restraints weight = 57146.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.070943 restraints weight = 59814.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.070987 restraints weight = 55458.290| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 26255 Z= 0.294 Angle : 0.774 11.853 35746 Z= 0.407 Chirality : 0.050 0.219 3850 Planarity : 0.006 0.053 4690 Dihedral : 5.477 30.659 3492 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.03 % Allowed : 1.61 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.15), residues: 3238 helix: -0.67 (0.24), residues: 474 sheet: -0.24 (0.22), residues: 617 loop : -0.96 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 89 TYR 0.024 0.002 TYR A1166 PHE 0.041 0.003 PHE A 91 TRP 0.023 0.002 TRP A 658 HIS 0.009 0.002 HIS A 951 Details of bonding type rmsd covalent geometry : bond 0.00653 (26164) covalent geometry : angle 0.76428 (35576) SS BOND : bond 0.00447 ( 85) SS BOND : angle 1.96345 ( 170) hydrogen bonds : bond 0.04179 ( 615) hydrogen bonds : angle 5.65948 ( 1791) metal coordination : bond 0.00642 ( 6) *********************** 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 225 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.030 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: 0.5375 (mttt) cc_final: 0.4940 (tptm) REVERT: A 473 MET cc_start: 0.7400 (mmt) cc_final: 0.6764 (ptm) REVERT: A 621 PHE cc_start: 0.8446 (m-80) cc_final: 0.8029 (m-80) REVERT: A 664 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7561 (mt-10) REVERT: A 752 ASN cc_start: 0.8077 (m110) cc_final: 0.7363 (t0) REVERT: A 1079 SER cc_start: 0.8144 (m) cc_final: 0.7415 (p) REVERT: A 1281 ARG cc_start: 0.6261 (ptt90) cc_final: 0.4802 (ttp-110) REVERT: A 1485 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8250 (t0) REVERT: B 159 MET cc_start: 0.8222 (mmm) cc_final: 0.8017 (tpp) REVERT: B 239 ASP cc_start: 0.7714 (t70) cc_final: 0.7215 (p0) REVERT: B 668 ASP cc_start: 0.7455 (p0) cc_final: 0.6789 (p0) REVERT: B 1153 TYR cc_start: 0.3836 (p90) cc_final: 0.3581 (p90) REVERT: B 1277 LEU cc_start: 0.4777 (mp) cc_final: 0.4461 (mp) REVERT: B 1497 ASN cc_start: 0.7936 (m-40) cc_final: 0.7698 (t0) REVERT: B 1534 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6546 (tm-30) REVERT: C 73 ASN cc_start: 0.8135 (t0) cc_final: 0.7847 (p0) REVERT: C 131 MET cc_start: 0.8227 (tmm) cc_final: 0.7951 (tmm) REVERT: G 131 MET cc_start: 0.7782 (ppp) cc_final: 0.7372 (tpp) REVERT: G 141 LEU cc_start: 0.8193 (mt) cc_final: 0.7680 (pp) REVERT: G 198 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6820 (pp20) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1794 time to fit residues: 64.5657 Evaluate side-chains 164 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 316 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 262 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 273 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 318 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN A 942 GLN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN B 301 GLN B 476 HIS B 554 ASN ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.095825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072281 restraints weight = 92505.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072017 restraints weight = 69917.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072416 restraints weight = 58917.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.072551 restraints weight = 55142.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072646 restraints weight = 50242.281| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26255 Z= 0.164 Angle : 0.630 12.330 35746 Z= 0.328 Chirality : 0.046 0.205 3850 Planarity : 0.004 0.052 4690 Dihedral : 5.086 29.487 3492 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.03 % Allowed : 0.70 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.15), residues: 3238 helix: -0.53 (0.24), residues: 472 sheet: -0.21 (0.22), residues: 604 loop : -0.90 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1283 TYR 0.018 0.001 TYR B1029 PHE 0.018 0.002 PHE C 162 TRP 0.013 0.001 TRP A 943 HIS 0.005 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00376 (26164) covalent geometry : angle 0.62042 (35576) SS BOND : bond 0.00429 ( 85) SS BOND : angle 1.67186 ( 170) hydrogen bonds : bond 0.03474 ( 615) hydrogen bonds : angle 5.29862 ( 1791) metal coordination : bond 0.00296 ( 6) *********************** 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 226 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 1.015 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: 0.5493 (mttt) cc_final: 0.4972 (tptm) REVERT: A 347 GLU cc_start: 0.7024 (pm20) cc_final: 0.5976 (pm20) REVERT: A 473 MET cc_start: 0.7204 (mmt) cc_final: 0.6778 (ptm) REVERT: A 621 PHE cc_start: 0.8148 (m-80) cc_final: 0.7685 (m-80) REVERT: A 664 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 752 ASN cc_start: 0.7950 (m110) cc_final: 0.7294 (t0) REVERT: A 1066 ILE cc_start: 0.7791 (mm) cc_final: 0.7397 (mm) REVERT: A 1079 SER cc_start: 0.7885 (m) cc_final: 0.7231 (p) REVERT: A 1281 ARG cc_start: 0.6039 (ptt90) cc_final: 0.4708 (ttp-110) REVERT: A 1438 MET cc_start: -0.2632 (tmm) cc_final: -0.3035 (tmm) REVERT: B 327 ARG cc_start: 0.7281 (ptp-170) cc_final: 0.7016 (ptp-170) REVERT: B 499 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6485 (tm-30) REVERT: B 668 ASP cc_start: 0.7148 (p0) cc_final: 0.6641 (p0) REVERT: B 1277 LEU cc_start: 0.4995 (mp) cc_final: 0.4327 (tp) REVERT: B 1534 GLN cc_start: 0.7085 (mm-40) cc_final: 0.6588 (tm-30) REVERT: C 73 ASN cc_start: 0.7924 (t0) cc_final: 0.7710 (p0) REVERT: C 131 MET cc_start: 0.7992 (tmm) cc_final: 0.7742 (tmm) REVERT: G 117 ARG cc_start: 0.8604 (ptp-170) cc_final: 0.7230 (ptm-80) REVERT: G 198 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6847 (pp20) REVERT: G 199 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7427 (tm-30) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.1767 time to fit residues: 64.6482 Evaluate side-chains 174 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 29 optimal weight: 0.0170 chunk 131 optimal weight: 20.0000 chunk 296 optimal weight: 2.9990 chunk 225 optimal weight: 0.3980 chunk 226 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 overall best weight: 0.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS B 571 GLN ** B1169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** 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 = 0.3857 r_free = 0.3857 target = 0.097230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077976 restraints weight = 92416.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.077597 restraints weight = 84021.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.078052 restraints weight = 81812.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.078492 restraints weight = 56274.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.079863 restraints weight = 49133.138| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 26255 Z= 0.107 Angle : 0.594 12.017 35746 Z= 0.304 Chirality : 0.045 0.186 3850 Planarity : 0.004 0.051 4690 Dihedral : 4.675 27.237 3492 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.15), residues: 3238 helix: -0.34 (0.24), residues: 474 sheet: -0.06 (0.22), residues: 581 loop : -0.80 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1283 TYR 0.015 0.001 TYR B 471 PHE 0.012 0.001 PHE B1516 TRP 0.017 0.001 TRP B1194 HIS 0.006 0.001 HIS A1343 Details of bonding type rmsd covalent geometry : bond 0.00248 (26164) covalent geometry : angle 0.58461 (35576) SS BOND : bond 0.00292 ( 85) SS BOND : angle 1.62443 ( 170) hydrogen bonds : bond 0.03198 ( 615) hydrogen bonds : angle 5.05316 ( 1791) metal coordination : bond 0.00220 ( 6) ********************** 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 224 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.090 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: A 338 LYS cc_start: 0.5592 (mttt) cc_final: 0.5070 (tptm) REVERT: A 347 GLU cc_start: 0.6941 (pm20) cc_final: 0.5960 (pm20) REVERT: A 473 MET cc_start: 0.7087 (mmt) cc_final: 0.6596 (ptm) REVERT: A 621 PHE cc_start: 0.8130 (m-80) cc_final: 0.7719 (m-80) REVERT: A 664 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 752 ASN cc_start: 0.7767 (m110) cc_final: 0.7060 (t0) REVERT: A 1066 ILE cc_start: 0.7685 (mm) cc_final: 0.7331 (mm) REVERT: A 1079 SER cc_start: 0.7854 (m) cc_final: 0.7113 (t) REVERT: A 1438 MET cc_start: -0.3142 (tmm) cc_final: -0.3513 (tmm) REVERT: B 115 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7642 (mp10) REVERT: B 668 ASP cc_start: 0.7445 (p0) cc_final: 0.6873 (p0) REVERT: B 1277 LEU cc_start: 0.4711 (mp) cc_final: 0.4330 (mp) REVERT: B 1534 GLN cc_start: 0.7005 (mm-40) cc_final: 0.6470 (tm-30) REVERT: C 73 ASN cc_start: 0.7885 (t0) cc_final: 0.7627 (p0) REVERT: C 131 MET cc_start: 0.7773 (tmm) cc_final: 0.7549 (tmm) REVERT: G 117 ARG cc_start: 0.8437 (ptp-170) cc_final: 0.7282 (ptm-80) REVERT: G 198 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6817 (pp20) REVERT: G 199 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7458 (tm-30) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1740 time to fit residues: 63.3996 Evaluate side-chains 170 residues out of total 2864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 69 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 257 optimal weight: 20.0000 chunk 137 optimal weight: 0.0980 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN A1078 HIS A1468 HIS ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN B 476 HIS ** B1169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.096628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077019 restraints weight = 92215.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.076571 restraints weight = 80890.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.077089 restraints weight = 81563.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.077642 restraints weight = 53991.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.078797 restraints weight = 47402.788| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26255 Z= 0.127 Angle : 0.592 11.715 35746 Z= 0.304 Chirality : 0.045 0.183 3850 Planarity : 0.004 0.050 4690 Dihedral : 4.642 27.056 3492 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.03 % Allowed : 0.38 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.15), residues: 3238 helix: -0.25 (0.24), residues: 474 sheet: -0.07 (0.22), residues: 594 loop : -0.82 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 413 TYR 0.012 0.001 TYR B 776 PHE 0.013 0.001 PHE B 91 TRP 0.018 0.001 TRP B1194 HIS 0.007 0.001 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00296 (26164) covalent geometry : angle 0.58332 (35576) SS BOND : bond 0.00288 ( 85) SS BOND : angle 1.56651 ( 170) hydrogen bonds : bond 0.03190 ( 615) hydrogen bonds : angle 5.01483 ( 1791) metal coordination : bond 0.00200 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4085.22 seconds wall clock time: 71 minutes 47.62 seconds (4307.62 seconds total)