Starting phenix.real_space_refine on Tue Jun 17 18:12:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fd7_29004/06_2025/8fd7_29004.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fd7_29004/06_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_29004/06_2025/8fd7_29004.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fd7_29004/06_2025/8fd7_29004.map" model { file = "/net/cci-nas-00/data/ceres_data/8fd7_29004/06_2025/8fd7_29004.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fd7_29004/06_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-5710/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: 11.49, per 1000 atoms: 0.58 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: 5.52 Conformation dependent library (CDL) restraints added in 2.6 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: 2.36 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: 6.95 Time building geometry restraints manager: 6.43 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: 6.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.140 Set scattering table: 0.210 Process input model: 46.200 Find NCS groups from input model: 0.190 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.560 ------------------------------------------------------------------------------- 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 20145 Z= 0.263 Angle : 0.576 21.604 27327 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 2) link_NAG-ASN : angle 1.37335 ( 6) link_BETA1-4 : bond 0.00134 ( 1) link_BETA1-4 : angle 1.01962 ( 3) hydrogen bonds : bond 0.15063 ( 934) hydrogen bonds : angle 6.00684 ( 2733) SS BOND : bond 0.00180 ( 10) SS BOND : angle 0.72599 ( 20) covalent geometry : bond 0.00527 (20132) covalent geometry : angle 0.57519 (27298) *********************** 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 : 2.281 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: 0.3406 time to fit residues: 111.0693 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 : 4.182 ------------------------------------------------------------------------------- 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: 0.0980 chunk 140 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.162793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.102488 restraints weight = 37399.188| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.29 r_work: 0.3183 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20145 Z= 0.124 Angle : 0.603 23.451 27327 Z= 0.291 Chirality : 0.055 2.010 3116 Planarity : 0.004 0.048 3426 Dihedral : 10.111 178.784 3187 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.06 % Favored : 93.82 % Rotamer: Outliers : 2.38 % Allowed : 9.63 % Favored : 87.99 % 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: -0.20 (0.18), residues: 2394 helix: 1.33 (0.16), residues: 1177 sheet: -0.25 (0.34), residues: 227 loop : -1.99 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 123 HIS 0.003 0.001 HIS D1006 PHE 0.017 0.001 PHE D 29 TYR 0.021 0.001 TYR K1192 ARG 0.004 0.000 ARG D 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 2) link_NAG-ASN : angle 1.97659 ( 6) link_BETA1-4 : bond 0.00123 ( 1) link_BETA1-4 : angle 1.43509 ( 3) hydrogen bonds : bond 0.04444 ( 934) hydrogen bonds : angle 4.53119 ( 2733) SS BOND : bond 0.00218 ( 10) SS BOND : angle 0.89648 ( 20) covalent geometry : bond 0.00270 (20132) covalent geometry : angle 0.60235 (27298) *********************** 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 155 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 2.321 Fit side-chains revert: symmetry clash REVERT: D 41 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8473 (tptt) REVERT: D 272 LYS cc_start: 0.8795 (tttp) cc_final: 0.8342 (tppt) REVERT: D 726 LYS cc_start: 0.8298 (mmmt) cc_final: 0.7957 (mmtp) REVERT: D 773 ASP cc_start: 0.8465 (t0) cc_final: 0.8115 (t0) REVERT: K 570 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: K 571 MET cc_start: 0.7113 (ttt) cc_final: 0.6747 (ttp) REVERT: K 656 LEU cc_start: 0.8117 (pp) cc_final: 0.7658 (mp) REVERT: K 1098 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8100 (t80) REVERT: K 1100 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7929 (p0) REVERT: K 1278 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6984 (t80) REVERT: K 1379 MET cc_start: 0.7627 (ptp) cc_final: 0.7180 (ptm) REVERT: K 1399 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.5520 (t80) REVERT: K 1476 MET cc_start: 0.8512 (ttm) cc_final: 0.8030 (tpp) REVERT: K 1494 LEU cc_start: 0.7949 (mp) cc_final: 0.7653 (tt) REVERT: K 1586 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.6034 (mmp80) outliers start: 51 outliers final: 26 residues processed: 150 average time/residue: 0.4114 time to fit residues: 95.7953 Evaluate side-chains 127 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 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 1033 LEU 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 923 VAL Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1100 ASN 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 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: 0.9980 chunk 95 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 183 optimal weight: 30.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 700 ASN D 826 ASN D 974 GLN ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1514 HIS ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1559 ASN C 301 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.159993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101013 restraints weight = 37277.684| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.93 r_work: 0.3129 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20145 Z= 0.234 Angle : 0.694 24.921 27327 Z= 0.340 Chirality : 0.056 1.807 3116 Planarity : 0.005 0.055 3426 Dihedral : 9.845 175.956 3176 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.86 % Rotamer: Outliers : 2.90 % Allowed : 10.89 % Favored : 86.21 % 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: -0.35 (0.18), residues: 2394 helix: 1.23 (0.15), residues: 1173 sheet: -0.47 (0.34), residues: 228 loop : -2.03 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 611 HIS 0.005 0.001 HIS D1006 PHE 0.021 0.002 PHE D 688 TYR 0.021 0.002 TYR D1070 ARG 0.005 0.001 ARG D 353 Details of bonding type rmsd link_NAG-ASN : bond 0.00441 ( 2) link_NAG-ASN : angle 3.10992 ( 6) link_BETA1-4 : bond 0.00731 ( 1) link_BETA1-4 : angle 1.59509 ( 3) hydrogen bonds : bond 0.05002 ( 934) hydrogen bonds : angle 4.47597 ( 2733) SS BOND : bond 0.00365 ( 10) SS BOND : angle 0.99996 ( 20) covalent geometry : bond 0.00566 (20132) covalent geometry : angle 0.69172 (27298) *********************** 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 160 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 98 time to evaluate : 2.206 Fit side-chains REVERT: D 41 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8530 (tptt) REVERT: D 272 LYS cc_start: 0.9041 (tttp) cc_final: 0.8566 (tppt) REVERT: D 370 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6550 (mtp180) REVERT: D 773 ASP cc_start: 0.8759 (t0) cc_final: 0.8373 (t0) REVERT: D 1073 CYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7733 (p) REVERT: K 570 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7082 (mm-30) REVERT: K 571 MET cc_start: 0.6955 (ttt) cc_final: 0.6624 (ptm) REVERT: K 575 MET cc_start: 0.6099 (mmm) cc_final: 0.5694 (mpp) REVERT: K 656 LEU cc_start: 0.8222 (pp) cc_final: 0.7720 (mp) REVERT: K 1098 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8133 (t80) REVERT: K 1238 MET cc_start: 0.7146 (tmm) cc_final: 0.6793 (ttt) REVERT: K 1278 TYR cc_start: 0.7127 (OUTLIER) cc_final: 0.6857 (t80) REVERT: K 1379 MET cc_start: 0.7615 (ptp) cc_final: 0.7084 (ptm) REVERT: K 1399 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5421 (t80) REVERT: K 1476 MET cc_start: 0.8623 (ttm) cc_final: 0.8161 (tpp) REVERT: K 1494 LEU cc_start: 0.8034 (mp) cc_final: 0.7754 (tt) REVERT: K 1582 ASN cc_start: 0.8645 (t0) cc_final: 0.7800 (p0) REVERT: K 1586 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.5594 (mmp80) outliers start: 62 outliers final: 39 residues processed: 156 average time/residue: 0.3106 time to fit residues: 78.3402 Evaluate side-chains 139 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 92 time to evaluate : 2.132 ------------------------------------------------------------------------------- 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 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 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 1073 CYS 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 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 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 K residue 1600 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 217 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 175 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 184 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 428 GLN ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1100 ASN ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1559 ASN C 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.159383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101331 restraints weight = 36016.970| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.92 r_work: 0.3152 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20145 Z= 0.178 Angle : 0.639 24.958 27327 Z= 0.309 Chirality : 0.054 1.795 3116 Planarity : 0.004 0.057 3426 Dihedral : 9.475 176.217 3174 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.73 % Favored : 93.15 % Rotamer: Outliers : 2.76 % Allowed : 12.20 % Favored : 85.05 % 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: -0.31 (0.18), residues: 2394 helix: 1.27 (0.15), residues: 1173 sheet: -0.44 (0.34), residues: 229 loop : -2.04 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K1501 HIS 0.005 0.001 HIS D1006 PHE 0.015 0.001 PHE D 515 TYR 0.022 0.001 TYR K1223 ARG 0.003 0.000 ARG D 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 2) link_NAG-ASN : angle 2.80864 ( 6) link_BETA1-4 : bond 0.00520 ( 1) link_BETA1-4 : angle 1.70364 ( 3) hydrogen bonds : bond 0.04363 ( 934) hydrogen bonds : angle 4.29802 ( 2733) SS BOND : bond 0.00348 ( 10) SS BOND : angle 0.83436 ( 20) covalent geometry : bond 0.00427 (20132) covalent geometry : angle 0.63766 (27298) *********************** 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 154 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 95 time to evaluate : 2.178 Fit side-chains REVERT: D 41 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8532 (tptt) REVERT: D 199 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6947 (mmm-85) REVERT: D 370 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6179 (mtp85) REVERT: D 773 ASP cc_start: 0.8729 (t0) cc_final: 0.8356 (t0) REVERT: K 570 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: K 571 MET cc_start: 0.7071 (ttt) cc_final: 0.6847 (ptm) REVERT: K 656 LEU cc_start: 0.8258 (pp) cc_final: 0.7756 (mp) REVERT: K 1098 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8102 (t80) REVERT: K 1238 MET cc_start: 0.7252 (tmm) cc_final: 0.6809 (ttt) REVERT: K 1278 TYR cc_start: 0.7142 (OUTLIER) cc_final: 0.6864 (t80) REVERT: K 1379 MET cc_start: 0.7598 (ptp) cc_final: 0.7032 (ptm) REVERT: K 1399 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.5482 (t80) REVERT: K 1476 MET cc_start: 0.8517 (ttm) cc_final: 0.8152 (tpp) REVERT: K 1494 LEU cc_start: 0.8060 (mp) cc_final: 0.7766 (tt) REVERT: K 1582 ASN cc_start: 0.8613 (t0) cc_final: 0.7817 (p0) REVERT: K 1586 ARG cc_start: 0.6196 (OUTLIER) cc_final: 0.5645 (mmp80) outliers start: 59 outliers final: 40 residues processed: 148 average time/residue: 0.3079 time to fit residues: 72.4675 Evaluate side-chains 141 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 93 time to evaluate : 2.192 ------------------------------------------------------------------------------- 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 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 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 742 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 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 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 258 LEU 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 1002 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 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 1486 TRP Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 11 optimal weight: 0.9990 chunk 113 optimal weight: 30.0000 chunk 238 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 162 optimal weight: 30.0000 chunk 16 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.161139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.102326 restraints weight = 37289.324| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.63 r_work: 0.3173 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20145 Z= 0.143 Angle : 0.615 25.031 27327 Z= 0.296 Chirality : 0.053 1.801 3116 Planarity : 0.004 0.061 3426 Dihedral : 9.243 178.286 3173 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 3.22 % Allowed : 12.29 % Favored : 84.49 % 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: -0.26 (0.17), residues: 2394 helix: 1.33 (0.15), residues: 1175 sheet: -0.30 (0.34), residues: 225 loop : -2.07 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 187 HIS 0.004 0.001 HIS D1006 PHE 0.014 0.001 PHE D 515 TYR 0.020 0.001 TYR D1070 ARG 0.005 0.000 ARG D 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 2) link_NAG-ASN : angle 2.70576 ( 6) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 1.63915 ( 3) hydrogen bonds : bond 0.04014 ( 934) hydrogen bonds : angle 4.16416 ( 2733) SS BOND : bond 0.00289 ( 10) SS BOND : angle 0.75238 ( 20) covalent geometry : bond 0.00335 (20132) covalent geometry : angle 0.61392 (27298) *********************** 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 168 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 99 time to evaluate : 2.183 Fit side-chains REVERT: D 41 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8543 (tptt) REVERT: D 773 ASP cc_start: 0.8637 (t0) cc_final: 0.8311 (t0) REVERT: K 325 GLN cc_start: 0.6777 (OUTLIER) cc_final: 0.5311 (mt0) REVERT: K 570 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7121 (mm-30) REVERT: K 571 MET cc_start: 0.6981 (ttt) cc_final: 0.6639 (ptm) REVERT: K 575 MET cc_start: 0.6080 (mmm) cc_final: 0.5475 (mpp) REVERT: K 656 LEU cc_start: 0.8302 (pp) cc_final: 0.7785 (mp) REVERT: K 1098 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8137 (t80) REVERT: K 1225 MET cc_start: 0.8675 (ptp) cc_final: 0.8452 (ptp) REVERT: K 1278 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6907 (t80) REVERT: K 1379 MET cc_start: 0.7730 (ptp) cc_final: 0.7211 (ptm) REVERT: K 1399 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.5587 (t80) REVERT: K 1476 MET cc_start: 0.8544 (ttm) cc_final: 0.8207 (tpp) REVERT: K 1494 LEU cc_start: 0.8079 (mp) cc_final: 0.7792 (tt) REVERT: K 1582 ASN cc_start: 0.8616 (t0) cc_final: 0.7796 (p0) REVERT: K 1586 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5717 (mmp80) outliers start: 69 outliers final: 48 residues processed: 164 average time/residue: 0.2822 time to fit residues: 76.3002 Evaluate side-chains 148 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 93 time to evaluate : 2.166 ------------------------------------------------------------------------------- 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 72 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 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 742 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 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 1001 CYS 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 258 LEU Chi-restraints excluded: chain K residue 290 PHE Chi-restraints excluded: chain K residue 325 GLN 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 220 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 204 optimal weight: 0.4980 chunk 229 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 194 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 0.0770 chunk 180 optimal weight: 5.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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** ** K1398 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 = 0.161547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.101575 restraints weight = 37187.504| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.03 r_work: 0.3148 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20145 Z= 0.132 Angle : 0.622 25.119 27327 Z= 0.296 Chirality : 0.052 1.807 3116 Planarity : 0.004 0.055 3426 Dihedral : 9.091 179.794 3173 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.19 % Rotamer: Outliers : 3.36 % Allowed : 12.34 % Favored : 84.30 % 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: -0.21 (0.17), residues: 2394 helix: 1.38 (0.15), residues: 1176 sheet: -0.23 (0.34), residues: 225 loop : -2.08 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 187 HIS 0.004 0.001 HIS D1006 PHE 0.017 0.001 PHE K1161 TYR 0.020 0.001 TYR D1070 ARG 0.005 0.000 ARG D 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 2) link_NAG-ASN : angle 2.63432 ( 6) link_BETA1-4 : bond 0.00304 ( 1) link_BETA1-4 : angle 1.58964 ( 3) hydrogen bonds : bond 0.03838 ( 934) hydrogen bonds : angle 4.08793 ( 2733) SS BOND : bond 0.00381 ( 10) SS BOND : angle 0.91256 ( 20) covalent geometry : bond 0.00306 (20132) covalent geometry : angle 0.62020 (27298) *********************** REFINEMENT MACRO_CYCLE 6 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 169 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 97 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: D 199 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7089 (mmm-85) REVERT: D 370 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6251 (mtp85) REVERT: D 773 ASP cc_start: 0.8711 (t0) cc_final: 0.8368 (t0) REVERT: K 325 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.5220 (mt0) REVERT: K 570 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: K 656 LEU cc_start: 0.8257 (pp) cc_final: 0.7740 (mp) REVERT: K 1098 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8098 (t80) REVERT: K 1238 MET cc_start: 0.7242 (tmm) cc_final: 0.6736 (ttt) REVERT: K 1278 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6879 (t80) REVERT: K 1379 MET cc_start: 0.7578 (ptp) cc_final: 0.7009 (ptm) REVERT: K 1399 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5401 (t80) REVERT: K 1476 MET cc_start: 0.8558 (ttm) cc_final: 0.8094 (tpp) REVERT: K 1494 LEU cc_start: 0.8160 (mp) cc_final: 0.7872 (tt) REVERT: K 1582 ASN cc_start: 0.8605 (t0) cc_final: 0.7788 (p0) REVERT: K 1586 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5724 (mmp80) outliers start: 72 outliers final: 49 residues processed: 164 average time/residue: 0.3046 time to fit residues: 79.5369 Evaluate side-chains 151 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 94 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 SER 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 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 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 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 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 290 PHE Chi-restraints excluded: chain K residue 325 GLN 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 521 VAL Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 691 ASN 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 1188 GLN Chi-restraints excluded: chain K residue 1223 TYR 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 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 1589 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 130 optimal weight: 0.9990 chunk 143 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 229 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 195 optimal weight: 0.0060 chunk 148 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.162519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100474 restraints weight = 36944.063| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.86 r_work: 0.3169 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20145 Z= 0.107 Angle : 0.608 24.930 27327 Z= 0.288 Chirality : 0.052 1.820 3116 Planarity : 0.004 0.054 3426 Dihedral : 8.668 176.964 3169 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 2.85 % Allowed : 13.18 % Favored : 83.97 % 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: -0.13 (0.17), residues: 2394 helix: 1.47 (0.15), residues: 1170 sheet: -0.22 (0.34), residues: 233 loop : -2.04 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 187 HIS 0.003 0.000 HIS D1006 PHE 0.018 0.001 PHE K 748 TYR 0.020 0.001 TYR K1223 ARG 0.007 0.000 ARG D 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 2) link_NAG-ASN : angle 2.43591 ( 6) link_BETA1-4 : bond 0.00363 ( 1) link_BETA1-4 : angle 1.52048 ( 3) hydrogen bonds : bond 0.03466 ( 934) hydrogen bonds : angle 3.99911 ( 2733) SS BOND : bond 0.00213 ( 10) SS BOND : angle 0.81137 ( 20) covalent geometry : bond 0.00235 (20132) covalent geometry : angle 0.60640 (27298) *********************** REFINEMENT MACRO_CYCLE 7 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: 61 poor density : 100 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 199 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6978 (mmm-85) REVERT: D 370 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6177 (mtp85) REVERT: D 490 MET cc_start: 0.7573 (tpp) cc_final: 0.7369 (mmm) REVERT: D 773 ASP cc_start: 0.8431 (t0) cc_final: 0.8175 (t0) REVERT: K 325 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.5726 (mt0) REVERT: K 570 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: K 571 MET cc_start: 0.6631 (ptm) cc_final: 0.6161 (ptp) REVERT: K 575 MET cc_start: 0.6185 (mmm) cc_final: 0.5506 (mpp) REVERT: K 656 LEU cc_start: 0.8217 (pp) cc_final: 0.7727 (mp) REVERT: K 1098 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.7965 (t80) REVERT: K 1223 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.8018 (p90) REVERT: K 1238 MET cc_start: 0.7040 (tmm) cc_final: 0.6489 (ttt) REVERT: K 1278 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6909 (t80) REVERT: K 1379 MET cc_start: 0.7516 (ptp) cc_final: 0.6950 (ptm) REVERT: K 1399 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5351 (t80) REVERT: K 1476 MET cc_start: 0.8494 (ttm) cc_final: 0.7999 (tpp) REVERT: K 1494 LEU cc_start: 0.8101 (mp) cc_final: 0.7823 (tt) REVERT: K 1582 ASN cc_start: 0.8570 (t0) cc_final: 0.7767 (p0) REVERT: K 1586 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.5973 (mmp80) outliers start: 61 outliers final: 40 residues processed: 157 average time/residue: 0.3096 time to fit residues: 77.3664 Evaluate side-chains 146 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 97 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 72 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 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 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 290 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 544 GLU Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1188 GLN 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 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 1589 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 71 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 152 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 200 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 111 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1559 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.162394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.103549 restraints weight = 37220.252| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.32 r_work: 0.3164 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20145 Z= 0.112 Angle : 0.622 24.176 27327 Z= 0.291 Chirality : 0.052 1.846 3116 Planarity : 0.004 0.053 3426 Dihedral : 8.288 178.087 3167 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.27 % Favored : 93.61 % Rotamer: Outliers : 2.66 % Allowed : 13.36 % Favored : 83.97 % 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: -0.07 (0.17), residues: 2394 helix: 1.50 (0.15), residues: 1172 sheet: -0.16 (0.34), residues: 223 loop : -2.01 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 440 HIS 0.003 0.000 HIS D1006 PHE 0.019 0.001 PHE K1226 TYR 0.020 0.001 TYR D1070 ARG 0.007 0.000 ARG D 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 2) link_NAG-ASN : angle 2.40913 ( 6) link_BETA1-4 : bond 0.00318 ( 1) link_BETA1-4 : angle 1.42284 ( 3) hydrogen bonds : bond 0.03439 ( 934) hydrogen bonds : angle 3.95343 ( 2733) SS BOND : bond 0.00216 ( 10) SS BOND : angle 0.69293 ( 20) covalent geometry : bond 0.00253 (20132) covalent geometry : angle 0.62127 (27298) *********************** REFINEMENT MACRO_CYCLE 8 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 159 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 102 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 199 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7020 (mmm-85) REVERT: D 272 LYS cc_start: 0.8958 (tttp) cc_final: 0.8444 (tppt) REVERT: D 370 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6188 (mtp85) REVERT: D 490 MET cc_start: 0.7823 (tpp) cc_final: 0.7573 (mmm) REVERT: D 773 ASP cc_start: 0.8728 (t0) cc_final: 0.8277 (t0) REVERT: K 325 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.5145 (mt0) REVERT: K 570 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6960 (mm-30) REVERT: K 571 MET cc_start: 0.6716 (ptm) cc_final: 0.6439 (ptm) REVERT: K 656 LEU cc_start: 0.8269 (pp) cc_final: 0.7768 (mp) REVERT: K 1098 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8029 (t80) REVERT: K 1223 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.8062 (p90) REVERT: K 1238 MET cc_start: 0.7257 (tmm) cc_final: 0.6733 (ttt) REVERT: K 1278 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6903 (t80) REVERT: K 1339 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8285 (mm) REVERT: K 1379 MET cc_start: 0.7452 (ptp) cc_final: 0.6908 (ptm) REVERT: K 1399 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5215 (t80) REVERT: K 1476 MET cc_start: 0.8503 (ttm) cc_final: 0.8037 (tpp) REVERT: K 1494 LEU cc_start: 0.8115 (mp) cc_final: 0.7834 (tt) REVERT: K 1582 ASN cc_start: 0.8591 (t0) cc_final: 0.7803 (p0) REVERT: K 1586 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6243 (mmp80) outliers start: 57 outliers final: 43 residues processed: 155 average time/residue: 0.3163 time to fit residues: 78.3416 Evaluate side-chains 151 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 98 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 72 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 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 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 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 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 290 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 544 GLU Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1188 GLN Chi-restraints excluded: chain K residue 1223 TYR Chi-restraints excluded: chain K residue 1240 HIS Chi-restraints excluded: chain K residue 1278 TYR Chi-restraints excluded: chain K residue 1339 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 88 optimal weight: 3.9990 chunk 187 optimal weight: 0.9980 chunk 111 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 204 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1559 ASN C 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.160571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.101834 restraints weight = 37118.510| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.02 r_work: 0.3135 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20145 Z= 0.198 Angle : 0.678 25.503 27327 Z= 0.324 Chirality : 0.055 1.880 3116 Planarity : 0.004 0.053 3426 Dihedral : 8.364 161.961 3165 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.98 % Favored : 92.90 % Rotamer: Outliers : 2.90 % Allowed : 13.32 % Favored : 83.79 % 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: -0.19 (0.18), residues: 2394 helix: 1.43 (0.16), residues: 1167 sheet: -0.34 (0.34), residues: 226 loop : -2.05 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP K 440 HIS 0.006 0.001 HIS K1083 PHE 0.017 0.001 PHE K 748 TYR 0.021 0.002 TYR D1070 ARG 0.008 0.000 ARG D 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 2) link_NAG-ASN : angle 2.81419 ( 6) link_BETA1-4 : bond 0.00305 ( 1) link_BETA1-4 : angle 1.52536 ( 3) hydrogen bonds : bond 0.04199 ( 934) hydrogen bonds : angle 4.10764 ( 2733) SS BOND : bond 0.00374 ( 10) SS BOND : angle 0.89672 ( 20) covalent geometry : bond 0.00479 (20132) covalent geometry : angle 0.67671 (27298) *********************** REFINEMENT MACRO_CYCLE 9 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: 62 poor density : 96 time to evaluate : 2.123 Fit side-chains revert: symmetry clash REVERT: D 199 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.6847 (mmm-85) REVERT: D 370 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6165 (mtp85) REVERT: D 773 ASP cc_start: 0.8734 (t0) cc_final: 0.8339 (t0) REVERT: K 325 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.5122 (mt0) REVERT: K 544 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: K 570 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6950 (mm-30) REVERT: K 656 LEU cc_start: 0.8293 (pp) cc_final: 0.7769 (mp) REVERT: K 1098 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8030 (t80) REVERT: K 1223 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.8112 (p90) REVERT: K 1238 MET cc_start: 0.7218 (tmm) cc_final: 0.6695 (ttt) REVERT: K 1278 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6870 (t80) REVERT: K 1379 MET cc_start: 0.7590 (ptp) cc_final: 0.6997 (ptm) REVERT: K 1399 PHE cc_start: 0.6170 (OUTLIER) cc_final: 0.5275 (t80) REVERT: K 1476 MET cc_start: 0.8459 (ttm) cc_final: 0.8010 (tpp) REVERT: K 1494 LEU cc_start: 0.8081 (mp) cc_final: 0.7791 (tt) REVERT: K 1504 TYR cc_start: 0.4543 (OUTLIER) cc_final: 0.4192 (p90) REVERT: K 1582 ASN cc_start: 0.8610 (t0) cc_final: 0.7802 (p0) REVERT: K 1586 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.5984 (mmp80) outliers start: 62 outliers final: 44 residues processed: 154 average time/residue: 0.3024 time to fit residues: 74.0295 Evaluate side-chains 149 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 94 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 72 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 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 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 742 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 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 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1066 VAL Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 290 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 544 GLU Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 691 ASN Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1188 GLN Chi-restraints excluded: chain K residue 1223 TYR 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 1504 TYR Chi-restraints excluded: chain K residue 1586 ARG Chi-restraints excluded: chain K residue 1600 LEU Chi-restraints excluded: chain C residue 292 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 151 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 192 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 212 optimal weight: 0.0570 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.161590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100619 restraints weight = 37187.838| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.29 r_work: 0.3138 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20145 Z= 0.128 Angle : 0.624 24.701 27327 Z= 0.296 Chirality : 0.053 1.834 3116 Planarity : 0.004 0.054 3426 Dihedral : 8.223 164.672 3165 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 2.43 % Allowed : 13.74 % Favored : 83.83 % 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: -0.13 (0.18), residues: 2394 helix: 1.44 (0.15), residues: 1172 sheet: -0.21 (0.34), residues: 224 loop : -2.00 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP K 440 HIS 0.004 0.001 HIS K1083 PHE 0.024 0.001 PHE K1226 TYR 0.020 0.001 TYR D1070 ARG 0.007 0.000 ARG D 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 2) link_NAG-ASN : angle 2.56355 ( 6) link_BETA1-4 : bond 0.00334 ( 1) link_BETA1-4 : angle 1.62885 ( 3) hydrogen bonds : bond 0.03662 ( 934) hydrogen bonds : angle 3.99911 ( 2733) SS BOND : bond 0.00263 ( 10) SS BOND : angle 0.73900 ( 20) covalent geometry : bond 0.00297 (20132) covalent geometry : angle 0.62308 (27298) ********************** REFINEMENT MACRO_CYCLE 10 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 148 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 96 time to evaluate : 2.355 Fit side-chains revert: symmetry clash REVERT: D 199 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6887 (mmm-85) REVERT: D 370 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6134 (mtp85) REVERT: D 773 ASP cc_start: 0.8500 (t0) cc_final: 0.8171 (t0) REVERT: K 325 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.5152 (mt0) REVERT: K 544 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: K 570 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6930 (mm-30) REVERT: K 571 MET cc_start: 0.7097 (ptp) cc_final: 0.6879 (ptt) REVERT: K 656 LEU cc_start: 0.8228 (pp) cc_final: 0.7726 (mp) REVERT: K 1098 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.7997 (t80) REVERT: K 1238 MET cc_start: 0.7066 (tmm) cc_final: 0.6574 (ttt) REVERT: K 1278 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6944 (t80) REVERT: K 1379 MET cc_start: 0.7566 (ptp) cc_final: 0.7018 (ptm) REVERT: K 1399 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.5389 (t80) REVERT: K 1476 MET cc_start: 0.8434 (ttm) cc_final: 0.7983 (tpp) REVERT: K 1494 LEU cc_start: 0.8068 (mp) cc_final: 0.7772 (tt) REVERT: K 1582 ASN cc_start: 0.8606 (t0) cc_final: 0.7799 (p0) REVERT: K 1586 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.6112 (mmp80) outliers start: 52 outliers final: 41 residues processed: 146 average time/residue: 0.3121 time to fit residues: 72.7728 Evaluate side-chains 143 residues out of total 2141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 93 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 72 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 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 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 742 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 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 1001 CYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 175 PHE Chi-restraints excluded: chain K residue 290 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 544 GLU Chi-restraints excluded: chain K residue 570 GLU Chi-restraints excluded: chain K residue 683 GLN Chi-restraints excluded: chain K residue 1098 PHE Chi-restraints excluded: chain K residue 1125 ILE Chi-restraints excluded: chain K residue 1188 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 136 optimal weight: 0.1980 chunk 157 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 222 optimal weight: 0.1980 chunk 223 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.161898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.101832 restraints weight = 37377.985| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.43 r_work: 0.3145 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20145 Z= 0.118 Angle : 0.623 24.569 27327 Z= 0.295 Chirality : 0.053 1.851 3116 Planarity : 0.004 0.054 3426 Dihedral : 8.133 165.154 3165 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.27 % Favored : 93.61 % Rotamer: Outliers : 2.48 % Allowed : 13.74 % Favored : 83.79 % 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: -0.10 (0.18), residues: 2394 helix: 1.44 (0.15), residues: 1178 sheet: -0.08 (0.34), residues: 215 loop : -1.99 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP K 440 HIS 0.004 0.001 HIS K1083 PHE 0.018 0.001 PHE K 748 TYR 0.022 0.001 TYR K 742 ARG 0.009 0.000 ARG D 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 2) link_NAG-ASN : angle 2.51981 ( 6) link_BETA1-4 : bond 0.00332 ( 1) link_BETA1-4 : angle 1.50196 ( 3) hydrogen bonds : bond 0.03545 ( 934) hydrogen bonds : angle 3.98146 ( 2733) SS BOND : bond 0.00239 ( 10) SS BOND : angle 0.70571 ( 20) covalent geometry : bond 0.00271 (20132) covalent geometry : angle 0.62205 (27298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16026.41 seconds wall clock time: 274 minutes 40.80 seconds (16480.80 seconds total)