Starting phenix.real_space_refine on Thu Jan 23 12:10:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fd7_29004/01_2025/8fd7_29004.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fd7_29004/01_2025/8fd7_29004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fd7_29004/01_2025/8fd7_29004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fd7_29004/01_2025/8fd7_29004.map" model { file = "/net/cci-nas-00/data/ceres_data/8fd7_29004/01_2025/8fd7_29004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fd7_29004/01_2025/8fd7_29004.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 1.079 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: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 P 2 5.49 5 S 105 5.16 5 Na 1 4.78 5 C 12761 2.51 5 N 3234 2.21 5 O 3595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 19701 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 7630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 955, 7630 Classifications: {'peptide': 955} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 912} Chain breaks: 4 Chain: "K" Number of atoms: 10227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 10227 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1227} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 181} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 126 Unusual residues: {' CA': 1, ' NA': 1, 'GBN': 1, 'NAG': 8} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 172 Unusual residues: {' CA': 2, 'CLR': 3, 'WO9': 1, 'YSW': 1} Classifications: {'undetermined': 7, 'water': 3} Link IDs: {None: 9} Time building chain proxies: 11.80, per 1000 atoms: 0.60 Number of scatterers: 19701 At special positions: 0 Unit cell: (126.085, 142.785, 199.565, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 3 19.99 S 105 16.00 P 2 15.00 Na 1 11.00 O 3595 8.00 N 3234 7.00 C 12761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 305 " - pdb=" SG CYS D1046 " distance=2.03 Simple disulfide: pdb=" SG CYS D 356 " - pdb=" SG CYS D1061 " distance=2.03 Simple disulfide: pdb=" SG CYS D 406 " - pdb=" SG CYS D1073 " distance=2.03 Simple disulfide: pdb=" SG CYS D 669 " - pdb=" SG CYS D 699 " distance=2.03 Simple disulfide: pdb=" SG CYS D 906 " - pdb=" SG CYS D 976 " distance=2.03 Simple disulfide: pdb=" SG CYS D 998 " - pdb=" SG CYS D1028 " distance=2.03 Simple disulfide: pdb=" SG CYS D1001 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS K 316 " - pdb=" SG CYS K 332 " distance=2.03 Simple disulfide: pdb=" SG CYS K1058 " - pdb=" SG CYS K1069 " distance=2.03 Simple disulfide: pdb=" SG CYS K1431 " - pdb=" SG CYS K1447 " 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG D1203 " - " ASN D 94 " " NAG D1204 " - " ASN D 470 " Time building additional restraints: 4.96 Conformation dependent library (CDL) restraints added in 2.7 seconds 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4582 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 15 sheets defined 53.9% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'D' and resid 31 through 55 Processing helix chain 'D' and resid 55 through 67 removed outlier: 4.193A pdb=" N TYR D 66 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 112 removed outlier: 3.589A pdb=" N ALA D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 202 removed outlier: 4.542A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 Processing helix chain 'D' and resid 243 through 251 removed outlier: 4.148A pdb=" N GLY D 249 " --> pdb=" O TRP D 245 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 268 through 283 removed outlier: 3.547A pdb=" N LYS D 272 " --> pdb=" O GLY D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 325 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.515A pdb=" N GLY D 338 " --> pdb=" O ASP D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 379 removed outlier: 3.687A pdb=" N PHE D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 408 removed outlier: 3.674A pdb=" N ASN D 408 " --> pdb=" O MET D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 421 Processing helix chain 'D' and resid 427 through 432 removed outlier: 4.227A pdb=" N VAL D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 440 Processing helix chain 'D' and resid 441 through 444 Processing helix chain 'D' and resid 481 through 484 removed outlier: 3.858A pdb=" N GLN D 484 " --> pdb=" O LEU D 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 481 through 484' Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 562 through 567 removed outlier: 3.717A pdb=" N GLU D 567 " --> pdb=" O PHE D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 582 removed outlier: 3.690A pdb=" N ASP D 582 " --> pdb=" O ASN D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 629 Processing helix chain 'D' and resid 639 through 649 removed outlier: 3.530A pdb=" N GLN D 643 " --> pdb=" O GLU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 653 removed outlier: 5.911A pdb=" N ASP D 653 " --> pdb=" O LEU D 650 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 650 through 653' Processing helix chain 'D' and resid 654 through 659 Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 700 through 721 removed outlier: 3.906A pdb=" N ILE D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.625A pdb=" N GLU D 752 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 762 Processing helix chain 'D' and resid 763 through 772 Processing helix chain 'D' and resid 819 through 829 Processing helix chain 'D' and resid 881 through 889 Processing helix chain 'D' and resid 1023 through 1026 Processing helix chain 'D' and resid 1044 through 1049 removed outlier: 3.576A pdb=" N MET D1048 " --> pdb=" O ASP D1044 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D1049 " --> pdb=" O PRO D1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1044 through 1049' Processing helix chain 'K' and resid 113 through 120 removed outlier: 3.778A pdb=" N ILE K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 144 removed outlier: 3.719A pdb=" N GLU K 127 " --> pdb=" O TRP K 123 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 182 removed outlier: 3.717A pdb=" N TYR K 164 " --> pdb=" O GLU K 160 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 211 Processing helix chain 'K' and resid 234 through 241 removed outlier: 3.754A pdb=" N ARG K 237 " --> pdb=" O LYS K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 242 through 251 removed outlier: 4.118A pdb=" N ARG K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU K 247 " --> pdb=" O ARG K 243 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL K 248 " --> pdb=" O PRO K 244 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER K 249 " --> pdb=" O LEU K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 266 Processing helix chain 'K' and resid 268 through 290 Processing helix chain 'K' and resid 349 through 361 Processing helix chain 'K' and resid 364 through 377 removed outlier: 3.584A pdb=" N VAL K 368 " --> pdb=" O GLY K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 413 removed outlier: 4.041A pdb=" N TYR K 384 " --> pdb=" O TRP K 380 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU K 413 " --> pdb=" O SER K 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 447 removed outlier: 3.650A pdb=" N LEU K 424 " --> pdb=" O ASP K 420 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU K 445 " --> pdb=" O ILE K 441 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE K 447 " --> pdb=" O GLN K 443 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 542 Processing helix chain 'K' and resid 552 through 578 removed outlier: 3.536A pdb=" N ALA K 565 " --> pdb=" O LYS K 561 " (cutoff:3.500A) Processing helix chain 'K' and resid 579 through 585 Processing helix chain 'K' and resid 589 through 606 removed outlier: 3.689A pdb=" N PHE K 594 " --> pdb=" O ARG K 590 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL K 595 " --> pdb=" O PHE K 591 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS K 597 " --> pdb=" O CYS K 593 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY K 598 " --> pdb=" O PHE K 594 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE K 604 " --> pdb=" O ILE K 600 " (cutoff:3.500A) Processing helix chain 'K' and resid 607 through 609 No H-bonds generated for 'chain 'K' and resid 607 through 609' Processing helix chain 'K' and resid 613 through 631 removed outlier: 3.877A pdb=" N LEU K 619 " --> pdb=" O GLY K 615 " (cutoff:3.500A) Processing helix chain 'K' and resid 637 through 673 removed outlier: 5.543A pdb=" N SER K 653 " --> pdb=" O ARG K 649 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU K 654 " --> pdb=" O SER K 650 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 705 Processing helix chain 'K' and resid 708 through 719 removed outlier: 3.591A pdb=" N TYR K 719 " --> pdb=" O GLY K 715 " (cutoff:3.500A) Processing helix chain 'K' and resid 723 through 728 removed outlier: 4.268A pdb=" N LEU K 728 " --> pdb=" O PHE K 724 " (cutoff:3.500A) Processing helix chain 'K' and resid 729 through 763 removed outlier: 4.082A pdb=" N PHE K 733 " --> pdb=" O VAL K 729 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY K 740 " --> pdb=" O LEU K 736 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASN K 741 " --> pdb=" O PHE K 737 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE K 751 " --> pdb=" O VAL K 747 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU K 760 " --> pdb=" O LEU K 756 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER K 761 " --> pdb=" O ALA K 757 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR K 763 " --> pdb=" O ALA K 759 " (cutoff:3.500A) Processing helix chain 'K' and resid 890 through 898 removed outlier: 3.921A pdb=" N HIS K 894 " --> pdb=" O ARG K 890 " (cutoff:3.500A) Processing helix chain 'K' and resid 900 through 919 removed outlier: 3.675A pdb=" N LEU K 917 " --> pdb=" O SER K 913 " (cutoff:3.500A) Processing helix chain 'K' and resid 928 through 951 Processing helix chain 'K' and resid 967 through 980 removed outlier: 4.084A pdb=" N ILE K 971 " --> pdb=" O ASN K 967 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP K 973 " --> pdb=" O PHE K 969 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU K 974 " --> pdb=" O ASN K 970 " (cutoff:3.500A) Processing helix chain 'K' and resid 996 through 1000 removed outlier: 3.975A pdb=" N VAL K 999 " --> pdb=" O ILE K 996 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU K1000 " --> pdb=" O LEU K 997 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 996 through 1000' Processing helix chain 'K' and resid 1002 through 1009 removed outlier: 4.005A pdb=" N LEU K1006 " --> pdb=" O VAL K1002 " (cutoff:3.500A) Processing helix chain 'K' and resid 1017 through 1030 removed outlier: 3.627A pdb=" N ILE K1029 " --> pdb=" O ALA K1025 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY K1030 " --> pdb=" O ILE K1026 " (cutoff:3.500A) Processing helix chain 'K' and resid 1030 through 1051 Processing helix chain 'K' and resid 1104 through 1113 removed outlier: 3.768A pdb=" N LEU K1108 " --> pdb=" O ALA K1104 " (cutoff:3.500A) Processing helix chain 'K' and resid 1116 through 1126 removed outlier: 4.299A pdb=" N ASP K1126 " --> pdb=" O TYR K1122 " (cutoff:3.500A) Processing helix chain 'K' and resid 1142 through 1171 removed outlier: 4.105A pdb=" N PHE K1146 " --> pdb=" O ILE K1142 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN K1159 " --> pdb=" O PHE K1155 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N PHE K1161 " --> pdb=" O MET K1157 " (cutoff:3.500A) Processing helix chain 'K' and resid 1183 through 1193 Processing helix chain 'K' and resid 1218 through 1236 removed outlier: 4.154A pdb=" N LEU K1224 " --> pdb=" O TYR K1220 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET K1225 " --> pdb=" O PHE K1221 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU K1230 " --> pdb=" O PHE K1226 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU K1236 " --> pdb=" O ASN K1232 " (cutoff:3.500A) Processing helix chain 'K' and resid 1237 through 1240 Processing helix chain 'K' and resid 1244 through 1271 Processing helix chain 'K' and resid 1274 through 1279 removed outlier: 4.383A pdb=" N PHE K1279 " --> pdb=" O PRO K1275 " (cutoff:3.500A) Processing helix chain 'K' and resid 1281 through 1301 removed outlier: 3.551A pdb=" N THR K1285 " --> pdb=" O ASP K1281 " (cutoff:3.500A) Processing helix chain 'K' and resid 1330 through 1335 removed outlier: 3.889A pdb=" N MET K1334 " --> pdb=" O LEU K1330 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG K1335 " --> pdb=" O PHE K1331 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1330 through 1335' Processing helix chain 'K' and resid 1337 through 1343 removed outlier: 3.912A pdb=" N SER K1341 " --> pdb=" O VAL K1337 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG K1342 " --> pdb=" O LYS K1338 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY K1343 " --> pdb=" O LEU K1339 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1337 through 1343' Processing helix chain 'K' and resid 1344 through 1355 Processing helix chain 'K' and resid 1359 through 1382 removed outlier: 3.593A pdb=" N VAL K1363 " --> pdb=" O ALA K1359 " (cutoff:3.500A) Processing helix chain 'K' and resid 1401 through 1415 Processing helix chain 'K' and resid 1417 through 1425 Processing helix chain 'K' and resid 1451 through 1483 removed outlier: 3.968A pdb=" N PHE K1459 " --> pdb=" O TYR K1455 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP K1480 " --> pdb=" O MET K1476 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR K1481 " --> pdb=" O ASP K1477 " (cutoff:3.500A) Processing helix chain 'K' and resid 1485 through 1490 removed outlier: 4.440A pdb=" N LEU K1489 " --> pdb=" O ASP K1485 " (cutoff:3.500A) Processing helix chain 'K' and resid 1490 through 1504 removed outlier: 4.066A pdb=" N LEU K1494 " --> pdb=" O GLY K1490 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP K1495 " --> pdb=" O PRO K1491 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA K1502 " --> pdb=" O LYS K1498 " (cutoff:3.500A) Processing helix chain 'K' and resid 1513 through 1518 Processing helix chain 'K' and resid 1519 through 1523 removed outlier: 3.523A pdb=" N ARG K1522 " --> pdb=" O THR K1519 " (cutoff:3.500A) Processing helix chain 'K' and resid 1539 through 1543 removed outlier: 3.723A pdb=" N ARG K1542 " --> pdb=" O ALA K1539 " (cutoff:3.500A) Processing helix chain 'K' and resid 1557 through 1570 Processing helix chain 'K' and resid 1577 through 1591 removed outlier: 4.799A pdb=" N GLU K1583 " --> pdb=" O GLU K1579 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA K1587 " --> pdb=" O GLU K1583 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ILE K1588 " --> pdb=" O GLU K1584 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE K1589 " --> pdb=" O LEU K1585 " (cutoff:3.500A) Processing helix chain 'K' and resid 1600 through 1609 Proline residue: K1606 - end of helix Processing helix chain 'C' and resid 190 through 208 Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 246 through 263 removed outlier: 3.572A pdb=" N SER C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 removed outlier: 3.821A pdb=" N GLN C 279 " --> pdb=" O HIS C 276 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 281 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 removed outlier: 3.964A pdb=" N LEU C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 removed outlier: 3.879A pdb=" N THR C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 361 removed outlier: 3.535A pdb=" N TYR C 352 " --> pdb=" O HIS C 348 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 70 through 74 Processing sheet with id=AA2, first strand: chain 'D' and resid 124 through 126 Processing sheet with id=AA3, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AA4, first strand: chain 'D' and resid 167 through 169 removed outlier: 3.903A pdb=" N GLY D 488 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 492 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 167 through 169 removed outlier: 3.903A pdb=" N GLY D 488 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 492 " --> pdb=" O GLY D 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 300 through 302 removed outlier: 6.471A pdb=" N ILE D 258 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N PHE D 296 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL D 260 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYR D 413 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR D 388 " --> pdb=" O TYR D 413 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE D 415 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER D 390 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 523 through 525 removed outlier: 6.227A pdb=" N ALA D 516 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 515 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 610 " --> pdb=" O LEU D 623 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 743 through 745 removed outlier: 6.603A pdb=" N LYS D 817 " --> pdb=" O LYS D 732 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG D 734 " --> pdb=" O GLY D 815 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLY D 815 " --> pdb=" O ARG D 734 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL D 736 " --> pdb=" O VAL D 813 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL D 813 " --> pdb=" O VAL D 736 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N THR D 738 " --> pdb=" O PRO D 811 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS D 810 " --> pdb=" O ILE D 802 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE D 802 " --> pdb=" O LYS D 810 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA D 812 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET D 795 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 861 through 863 removed outlier: 6.777A pdb=" N LEU D 861 " --> pdb=" O ASP D 856 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP D 856 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET D 863 " --> pdb=" O ILE D 854 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 895 through 906 removed outlier: 4.613A pdb=" N GLN D 903 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N CYS D 976 " --> pdb=" O GLN D 903 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL D 905 " --> pdb=" O GLN D 974 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN D 974 " --> pdb=" O VAL D 905 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE D 977 " --> pdb=" O SER D1040 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 994 through 996 removed outlier: 3.647A pdb=" N GLY D 994 " --> pdb=" O PHE D1005 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE D1005 " --> pdb=" O GLY D 994 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1056 through 1058 Processing sheet with id=AB4, first strand: chain 'K' and resid 1072 through 1075 Processing sheet with id=AB5, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.519A pdb=" N VAL C 290 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 292 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE C 289 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU C 337 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE C 291 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 213 through 216 removed outlier: 7.019A pdb=" N SER C 213 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ASP C 270 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR C 215 " --> pdb=" O ASP C 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 952 hydrogen bonds defined for protein. 2733 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: 7.90 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3174 1.30 - 1.43: 5184 1.43 - 1.56: 11546 1.56 - 1.69: 66 1.69 - 1.82: 162 Bond restraints: 20132 Sorted by residual: bond pdb=" C18 WO9 K1701 " pdb=" O20 WO9 K1701 " ideal model delta sigma weight residual 1.331 1.470 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C33 WO9 K1701 " pdb=" O32 WO9 K1701 " ideal model delta sigma weight residual 1.334 1.467 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" C10 YSW K1702 " pdb=" C11 YSW K1702 " ideal model delta sigma weight residual 1.544 1.437 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C17 WO9 K1701 " pdb=" C18 WO9 K1701 " ideal model delta sigma weight residual 1.504 1.603 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C33 WO9 K1701 " pdb=" C35 WO9 K1701 " ideal model delta sigma weight residual 1.505 1.603 -0.098 2.00e-02 2.50e+03 2.42e+01 ... (remaining 20127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 27242 4.32 - 8.64: 52 8.64 - 12.96: 3 12.96 - 17.28: 0 17.28 - 21.60: 1 Bond angle restraints: 27298 Sorted by residual: angle pdb=" O26 WO9 K1701 " pdb=" P25 WO9 K1701 " pdb=" O27 WO9 K1701 " ideal model delta sigma weight residual 122.85 101.25 21.60 3.00e+00 1.11e-01 5.19e+01 angle pdb=" O18 YSW K1702 " pdb=" P19 YSW K1702 " pdb=" O22 YSW K1702 " ideal model delta sigma weight residual 96.75 107.23 -10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C17 WO9 K1701 " pdb=" C18 WO9 K1701 " pdb=" O20 WO9 K1701 " ideal model delta sigma weight residual 110.76 120.05 -9.29 3.00e+00 1.11e-01 9.58e+00 angle pdb=" C01 YSW K1702 " pdb=" C02 YSW K1702 " pdb=" C03 YSW K1702 " ideal model delta sigma weight residual 112.88 103.76 9.12 3.00e+00 1.11e-01 9.24e+00 angle pdb=" O18 YSW K1702 " pdb=" P19 YSW K1702 " pdb=" O20 YSW K1702 " ideal model delta sigma weight residual 111.48 102.85 8.63 3.00e+00 1.11e-01 8.27e+00 ... (remaining 27293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.76: 11979 26.76 - 53.51: 342 53.51 - 80.27: 35 80.27 - 107.03: 5 107.03 - 133.78: 4 Dihedral angle restraints: 12365 sinusoidal: 5283 harmonic: 7082 Sorted by residual: dihedral pdb=" C2 GBN D1202 " pdb=" C1R GBN D1202 " pdb=" C6R GBN D1202 " pdb=" C5R GBN D1202 " ideal model delta sinusoidal sigma weight residual -66.69 67.09 -133.78 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" C2 GBN D1202 " pdb=" C1R GBN D1202 " pdb=" C2R GBN D1202 " pdb=" C3R GBN D1202 " ideal model delta sinusoidal sigma weight residual 69.31 -61.61 130.92 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C1R GBN D1202 " pdb=" C2R GBN D1202 " pdb=" C3R GBN D1202 " pdb=" C4R GBN D1202 " ideal model delta sinusoidal sigma weight residual 53.40 -60.21 113.61 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 12362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.106: 3115 1.106 - 2.212: 0 2.212 - 3.318: 0 3.318 - 4.424: 0 4.424 - 5.531: 1 Chirality restraints: 3116 Sorted by residual: chirality pdb=" C1R GBN D1202 " pdb=" C2R GBN D1202 " pdb=" C3 GBN D1202 " pdb=" C6R GBN D1202 " both_signs ideal model delta sigma weight residual False -2.69 2.84 -5.53 2.00e-01 2.50e+01 7.65e+02 chirality pdb=" C22 WO9 K1701 " pdb=" C21 WO9 K1701 " pdb=" C23 WO9 K1701 " pdb=" O32 WO9 K1701 " both_signs ideal model delta sigma weight residual False 2.61 2.90 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.42e+00 ... (remaining 3113 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K1526 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO K1527 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO K1527 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO K1527 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K1606 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO K1607 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO K1607 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO K1607 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 693 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO D 694 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 694 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 694 " 0.024 5.00e-02 4.00e+02 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3035 2.76 - 3.29: 19985 3.29 - 3.83: 31794 3.83 - 4.36: 37204 4.36 - 4.90: 62896 Nonbonded interactions: 154914 Sorted by model distance: nonbonded pdb=" OD1 ASP D 598 " pdb=" OG SER D 764 " model vdw 2.223 3.040 nonbonded pdb=" O LEU C 303 " pdb=" OG SER C 306 " model vdw 2.268 3.040 nonbonded pdb=" OG SER C 186 " pdb=" OE1 GLN C 318 " model vdw 2.269 3.040 nonbonded pdb=" NH2 ARG D 768 " pdb=" OD2 ASP D 857 " model vdw 2.276 3.120 nonbonded pdb=" O LEU K1230 " pdb=" OG1 THR K1233 " model vdw 2.280 3.040 ... (remaining 154909 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.500 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: 0.030 Extract box with map and model: 0.820 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 45.030 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 20132 Z= 0.345 Angle : 0.575 21.604 27298 Z= 0.268 Chirality : 0.108 5.531 3116 Planarity : 0.004 0.045 3426 Dihedral : 12.341 133.783 7753 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 2.76 % Allowed : 7.24 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2394 helix: 1.07 (0.16), residues: 1178 sheet: -0.18 (0.35), residues: 221 loop : -1.99 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 123 HIS 0.004 0.000 HIS K1240 PHE 0.012 0.001 PHE D 515 TYR 0.014 0.001 TYR D1070 ARG 0.002 0.000 ARG K1511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7234 (ttpt) REVERT: D 272 LYS cc_start: 0.8463 (tttp) cc_final: 0.8129 (tppt) REVERT: D 726 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7757 (mmtp) REVERT: D 773 ASP cc_start: 0.8169 (t0) cc_final: 0.7848 (t0) REVERT: D 996 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8262 (tp) REVERT: K 570 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: K 571 MET cc_start: 0.7063 (ttt) cc_final: 0.5891 (tmm) REVERT: K 656 LEU cc_start: 0.7838 (pp) cc_final: 0.7467 (mp) REVERT: K 1098 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8573 (t80) REVERT: K 1223 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8466 (t80) REVERT: K 1226 PHE cc_start: 0.7633 (m-80) cc_final: 0.7407 (m-80) REVERT: K 1278 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.7004 (t80) REVERT: K 1379 MET cc_start: 0.7905 (ptp) cc_final: 0.7618 (ptm) REVERT: K 1399 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5846 (t80) REVERT: K 1494 LEU cc_start: 0.8019 (mp) cc_final: 0.7714 (tt) REVERT: K 1586 ARG cc_start: 0.6191 (OUTLIER) cc_final: 0.5371 (mmp80) REVERT: C 312 MET cc_start: 0.4571 (mtt) cc_final: 0.3880 (ttm) outliers start: 59 outliers final: 24 residues processed: 213 average time/residue: 0.3509 time to fit residues: 114.2377 Evaluate side-chains 133 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 671 ASP Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 748 PHE Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1100 ASN Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1586 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 123 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 145 GLN D 165 HIS D 186 ASN D 528 ASN D 696 ASN D 700 ASN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 ASN K 892 GLN K 898 ASN ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1083 HIS K1087 GLN K1358 GLN ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1580 GLN C 251 GLN C 276 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.160981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102192 restraints weight = 37395.021| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 3.13 r_work: 0.3147 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20132 Z= 0.263 Angle : 0.642 24.450 27298 Z= 0.313 Chirality : 0.056 1.978 3116 Planarity : 0.004 0.051 3426 Dihedral : 10.232 175.201 3187 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.64 % Favored : 93.23 % Rotamer: Outliers : 2.62 % Allowed : 9.77 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2394 helix: 1.25 (0.16), residues: 1179 sheet: -0.25 (0.35), residues: 217 loop : -2.05 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 123 HIS 0.003 0.001 HIS D1006 PHE 0.017 0.001 PHE D 515 TYR 0.022 0.001 TYR K1192 ARG 0.004 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 101 time to evaluate : 2.250 Fit side-chains revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8509 (tptt) REVERT: D 272 LYS cc_start: 0.8996 (tttp) cc_final: 0.8501 (tppt) REVERT: D 688 PHE cc_start: 0.7446 (t80) cc_final: 0.7224 (t80) REVERT: D 773 ASP cc_start: 0.8724 (t0) cc_final: 0.8280 (t0) REVERT: D 996 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8092 (tp) REVERT: K 570 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: K 571 MET cc_start: 0.7125 (ttt) cc_final: 0.6736 (ttp) REVERT: K 656 LEU cc_start: 0.8181 (pp) cc_final: 0.7708 (mp) REVERT: K 1098 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8082 (t80) REVERT: K 1100 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7991 (p0) REVERT: K 1223 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8348 (p90) REVERT: K 1238 MET cc_start: 0.6555 (mmm) cc_final: 0.6318 (tmm) REVERT: K 1278 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.6908 (t80) REVERT: K 1379 MET cc_start: 0.7631 (ptp) cc_final: 0.7150 (ptm) REVERT: K 1399 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.5391 (t80) REVERT: K 1476 MET cc_start: 0.8595 (ttm) cc_final: 0.8113 (tpp) REVERT: K 1494 LEU cc_start: 0.8038 (mp) cc_final: 0.7724 (tt) REVERT: K 1586 ARG cc_start: 0.6424 (OUTLIER) cc_final: 0.5742 (mmp80) outliers start: 56 outliers final: 34 residues processed: 150 average time/residue: 0.3277 time to fit residues: 77.0386 Evaluate side-chains 136 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 93 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 987 ASN Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1066 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 258 LEU Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 748 PHE Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1100 ASN Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1233 THR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1422 MET Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 15 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 239 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 223 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 183 optimal weight: 30.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 974 GLN ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1559 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.161543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103104 restraints weight = 37287.800| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.45 r_work: 0.3224 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20132 Z= 0.190 Angle : 0.599 24.938 27298 Z= 0.288 Chirality : 0.052 1.812 3116 Planarity : 0.004 0.052 3426 Dihedral : 9.598 175.863 3183 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.57 % Rotamer: Outliers : 2.76 % Allowed : 10.89 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2394 helix: 1.38 (0.15), residues: 1173 sheet: -0.24 (0.34), residues: 222 loop : -1.97 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 187 HIS 0.004 0.001 HIS D1006 PHE 0.014 0.001 PHE D 515 TYR 0.018 0.001 TYR D1070 ARG 0.005 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 99 time to evaluate : 2.175 Fit side-chains REVERT: D 41 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8507 (tptt) REVERT: D 272 LYS cc_start: 0.8898 (tttp) cc_final: 0.8420 (tppt) REVERT: D 370 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6180 (mtp85) REVERT: D 773 ASP cc_start: 0.8635 (t0) cc_final: 0.8241 (t0) REVERT: K 570 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: K 571 MET cc_start: 0.6990 (ttt) cc_final: 0.6606 (ttp) REVERT: K 656 LEU cc_start: 0.8186 (pp) cc_final: 0.7709 (mp) REVERT: K 1098 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8165 (t80) REVERT: K 1278 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6839 (t80) REVERT: K 1379 MET cc_start: 0.7607 (ptp) cc_final: 0.7114 (ptm) REVERT: K 1399 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5461 (t80) REVERT: K 1476 MET cc_start: 0.8551 (ttm) cc_final: 0.8133 (tpp) REVERT: K 1494 LEU cc_start: 0.8013 (mp) cc_final: 0.7685 (tt) REVERT: K 1582 ASN cc_start: 0.8606 (t0) cc_final: 0.7798 (p0) REVERT: K 1586 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.5815 (mmp80) outliers start: 59 outliers final: 35 residues processed: 153 average time/residue: 0.3157 time to fit residues: 77.6203 Evaluate side-chains 138 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 726 LYS Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 987 ASN Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1066 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1227 VAL Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1394 ASN Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 343 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 217 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 228 optimal weight: 30.0000 chunk 5 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 184 optimal weight: 20.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 428 GLN ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1100 ASN ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1514 HIS ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.160349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100344 restraints weight = 37413.878| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.71 r_work: 0.3170 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20132 Z= 0.261 Angle : 0.627 25.102 27298 Z= 0.304 Chirality : 0.053 1.802 3116 Planarity : 0.004 0.062 3426 Dihedral : 9.357 177.373 3175 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.11 % Rotamer: Outliers : 3.08 % Allowed : 11.40 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.17), residues: 2394 helix: 1.34 (0.15), residues: 1174 sheet: -0.32 (0.35), residues: 218 loop : -2.02 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 187 HIS 0.004 0.001 HIS D1006 PHE 0.023 0.001 PHE D 688 TYR 0.021 0.001 TYR D1070 ARG 0.004 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 98 time to evaluate : 2.391 Fit side-chains revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8518 (tptt) REVERT: D 272 LYS cc_start: 0.8983 (tttp) cc_final: 0.8510 (tppt) REVERT: D 370 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6595 (mtp180) REVERT: D 773 ASP cc_start: 0.8715 (t0) cc_final: 0.8397 (t0) REVERT: D 997 ASP cc_start: 0.8053 (m-30) cc_final: 0.7604 (m-30) REVERT: K 570 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: K 575 MET cc_start: 0.6035 (mmm) cc_final: 0.5244 (mtt) REVERT: K 656 LEU cc_start: 0.8207 (pp) cc_final: 0.7699 (mp) REVERT: K 1098 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8191 (t80) REVERT: K 1223 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.8004 (p90) REVERT: K 1278 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6835 (t80) REVERT: K 1379 MET cc_start: 0.7549 (ptp) cc_final: 0.7019 (ptm) REVERT: K 1399 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.5496 (t80) REVERT: K 1476 MET cc_start: 0.8537 (ttm) cc_final: 0.7998 (tpp) REVERT: K 1494 LEU cc_start: 0.8076 (mp) cc_final: 0.7766 (tt) REVERT: K 1582 ASN cc_start: 0.8635 (t0) cc_final: 0.7860 (p0) REVERT: K 1586 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5781 (mmp80) outliers start: 66 outliers final: 42 residues processed: 155 average time/residue: 0.3203 time to fit residues: 79.7829 Evaluate side-chains 145 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 95 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 726 LYS Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 987 ASN Chi-restraints excluded: chain D residue 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1066 VAL Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 396 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1394 ASN Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 343 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 11 optimal weight: 0.8980 chunk 113 optimal weight: 30.0000 chunk 238 optimal weight: 0.9980 chunk 94 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 230 optimal weight: 10.0000 chunk 220 optimal weight: 30.0000 chunk 162 optimal weight: 20.0000 chunk 16 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 428 GLN ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1559 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.161269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103804 restraints weight = 35896.381| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.94 r_work: 0.3203 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20132 Z= 0.158 Angle : 0.592 24.935 27298 Z= 0.281 Chirality : 0.052 1.813 3116 Planarity : 0.004 0.060 3426 Dihedral : 9.009 179.461 3174 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.68 % Favored : 94.19 % Rotamer: Outliers : 2.80 % Allowed : 12.06 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.17), residues: 2394 helix: 1.42 (0.15), residues: 1174 sheet: -0.21 (0.34), residues: 223 loop : -2.00 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 187 HIS 0.003 0.000 HIS D1006 PHE 0.021 0.001 PHE K1226 TYR 0.019 0.001 TYR D1070 ARG 0.005 0.000 ARG D 501 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4788 Ramachandran restraints generated. 2394 Oldfield, 0 Emsley, 2394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 101 time to evaluate : 2.026 Fit side-chains REVERT: D 41 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8554 (tptt) REVERT: D 199 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7138 (mmm-85) REVERT: D 272 LYS cc_start: 0.8948 (tttp) cc_final: 0.8474 (tppt) REVERT: D 370 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6226 (mtp85) REVERT: D 773 ASP cc_start: 0.8681 (t0) cc_final: 0.8297 (t0) REVERT: D 997 ASP cc_start: 0.8024 (m-30) cc_final: 0.7548 (m-30) REVERT: K 325 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.5945 (mt0) REVERT: K 570 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7011 (mm-30) REVERT: K 571 MET cc_start: 0.6732 (ptm) cc_final: 0.6353 (ptm) REVERT: K 656 LEU cc_start: 0.8201 (pp) cc_final: 0.7707 (mp) REVERT: K 1098 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8107 (t80) REVERT: K 1223 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.8075 (p90) REVERT: K 1225 MET cc_start: 0.8615 (ptp) cc_final: 0.8335 (ptp) REVERT: K 1226 PHE cc_start: 0.8351 (t80) cc_final: 0.8131 (t80) REVERT: K 1278 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6891 (t80) REVERT: K 1379 MET cc_start: 0.7591 (ptp) cc_final: 0.7037 (ptm) REVERT: K 1399 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.5371 (t80) REVERT: K 1476 MET cc_start: 0.8479 (ttm) cc_final: 0.7971 (tpp) REVERT: K 1494 LEU cc_start: 0.8045 (mp) cc_final: 0.7760 (tt) REVERT: K 1582 ASN cc_start: 0.8549 (t0) cc_final: 0.7732 (p0) REVERT: K 1586 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5850 (mmp80) REVERT: C 177 MET cc_start: -0.4454 (tpp) cc_final: -0.4706 (mmm) outliers start: 60 outliers final: 38 residues processed: 158 average time/residue: 0.3283 time to fit residues: 81.6822 Evaluate side-chains 144 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 96 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 538 ILE Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 726 LYS Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 870 THR Chi-restraints excluded: chain D residue 873 ILE Chi-restraints excluded: chain D residue 880 ILE Chi-restraints excluded: chain D residue 889 VAL Chi-restraints excluded: chain D residue 987 ASN Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 325 GLN Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 399 LEU Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 917 LEU Chi-restraints excluded: chain K residue 923 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1236 LEU Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1395 ARG Chi-restraints excluded: chain K residue 1399 PHE Chi-restraints excluded: chain K residue 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 343 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.0217 > 50: distance: 44 - 45: 5.156 distance: 45 - 46: 16.954 distance: 45 - 48: 8.510 distance: 46 - 47: 13.188 distance: 46 - 55: 23.780 distance: 47 - 72: 24.676 distance: 48 - 49: 8.951 distance: 49 - 50: 9.778 distance: 50 - 51: 10.188 distance: 51 - 52: 9.699 distance: 52 - 53: 11.666 distance: 52 - 54: 11.392 distance: 55 - 56: 17.714 distance: 56 - 57: 8.807 distance: 56 - 59: 25.773 distance: 57 - 58: 21.257 distance: 57 - 61: 9.795 distance: 58 - 83: 26.010 distance: 59 - 60: 3.841 distance: 61 - 62: 9.335 distance: 62 - 63: 13.961 distance: 62 - 65: 11.402 distance: 63 - 64: 17.300 distance: 63 - 67: 13.850 distance: 65 - 66: 11.619 distance: 67 - 68: 9.556 distance: 68 - 69: 19.734 distance: 68 - 71: 8.627 distance: 69 - 70: 39.883 distance: 69 - 72: 17.226 distance: 72 - 73: 17.351 distance: 73 - 74: 5.106 distance: 73 - 76: 9.525 distance: 74 - 75: 15.678 distance: 76 - 77: 8.422 distance: 77 - 78: 8.618 distance: 78 - 79: 6.970 distance: 79 - 80: 6.827 distance: 83 - 84: 14.059 distance: 84 - 85: 5.354 distance: 84 - 87: 13.290 distance: 85 - 86: 19.218 distance: 85 - 89: 11.088 distance: 87 - 88: 23.519 distance: 89 - 90: 14.433 distance: 90 - 91: 13.064 distance: 90 - 93: 22.166 distance: 91 - 92: 6.988 distance: 91 - 95: 18.529 distance: 92 - 117: 22.359 distance: 93 - 94: 16.938 distance: 95 - 96: 15.860 distance: 96 - 97: 7.044 distance: 96 - 99: 24.351 distance: 97 - 98: 7.904 distance: 97 - 103: 13.275 distance: 98 - 124: 8.221 distance: 99 - 101: 14.428 distance: 100 - 102: 19.575 distance: 103 - 104: 18.107 distance: 104 - 105: 12.247 distance: 104 - 107: 7.720 distance: 105 - 106: 9.799 distance: 105 - 108: 9.757 distance: 106 - 132: 27.257 distance: 108 - 109: 14.799 distance: 109 - 110: 11.437 distance: 109 - 112: 17.678 distance: 110 - 111: 8.096 distance: 110 - 117: 3.105 distance: 111 - 138: 4.293 distance: 112 - 113: 13.185 distance: 113 - 114: 18.849 distance: 114 - 115: 17.497 distance: 114 - 116: 12.357