Starting phenix.real_space_refine on Sun Jul 27 21:48:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f4b_28854/07_2025/8f4b_28854.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f4b_28854/07_2025/8f4b_28854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f4b_28854/07_2025/8f4b_28854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f4b_28854/07_2025/8f4b_28854.map" model { file = "/net/cci-nas-00/data/ceres_data/8f4b_28854/07_2025/8f4b_28854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f4b_28854/07_2025/8f4b_28854.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6140 2.51 5 N 1585 2.21 5 O 1714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9487 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9323 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 41, 'TRANS': 1140} Chain breaks: 3 Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 161 Classifications: {'peptide': 17} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 16} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.44, per 1000 atoms: 0.68 Number of scatterers: 9487 At special positions: 0 Unit cell: (147.29, 112.27, 84.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1714 8.00 N 1585 7.00 C 6140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY B 1 " Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 5 sheets defined 68.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.603A pdb=" N ARG A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Proline residue: A 255 - end of helix removed outlier: 3.831A pdb=" N LYS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 340 removed outlier: 3.658A pdb=" N PHE A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 removed outlier: 3.686A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 410 removed outlier: 3.942A pdb=" N TYR A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.595A pdb=" N PHE A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 462 Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 466 through 511 removed outlier: 3.661A pdb=" N VAL A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.846A pdb=" N LYS A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.749A pdb=" N LEU A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 572 removed outlier: 3.665A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 548 " --> pdb=" O TYR A 544 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Proline residue: A 557 - end of helix removed outlier: 3.623A pdb=" N ALA A 561 " --> pdb=" O PRO A 557 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 621 removed outlier: 4.193A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Proline residue: A 595 - end of helix Proline residue: A 600 - end of helix Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.677A pdb=" N SER A 629 " --> pdb=" O ASP A 626 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 630 " --> pdb=" O PRO A 627 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 626 through 630' Processing helix chain 'A' and resid 683 through 692 removed outlier: 4.442A pdb=" N LEU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 744 Processing helix chain 'A' and resid 746 through 753 removed outlier: 4.020A pdb=" N ILE A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 4.217A pdb=" N GLY A 765 " --> pdb=" O GLY A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 785 removed outlier: 3.609A pdb=" N ASP A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 removed outlier: 3.504A pdb=" N GLY A 803 " --> pdb=" O ASP A 799 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS A 805 " --> pdb=" O HIS A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 860 through 867 Processing helix chain 'A' and resid 959 through 970 Processing helix chain 'A' and resid 970 through 1000 removed outlier: 4.147A pdb=" N ASP A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1057 removed outlier: 3.553A pdb=" N GLY A1022 " --> pdb=" O TYR A1018 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A1028 " --> pdb=" O SER A1024 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A1041 " --> pdb=" O SER A1037 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1056 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.968A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1084 removed outlier: 3.511A pdb=" N LEU A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A1080 " --> pdb=" O SER A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1111 removed outlier: 3.934A pdb=" N GLN A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A1091 " --> pdb=" O PRO A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 Processing helix chain 'A' and resid 1117 through 1147 removed outlier: 3.661A pdb=" N LEU A1121 " --> pdb=" O ILE A1117 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A1134 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG A1137 " --> pdb=" O VAL A1133 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1160 removed outlier: 3.903A pdb=" N TYR A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1167 Processing helix chain 'A' and resid 1169 through 1220 removed outlier: 3.522A pdb=" N LYS A1180 " --> pdb=" O GLN A1176 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A1187 " --> pdb=" O GLU A1183 " (cutoff:3.500A) Proline residue: A1190 - end of helix removed outlier: 3.726A pdb=" N ASN A1195 " --> pdb=" O SER A1191 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1237 removed outlier: 3.606A pdb=" N VAL A1229 " --> pdb=" O SER A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1257 removed outlier: 3.999A pdb=" N TYR A1242 " --> pdb=" O GLN A1238 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A1244 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP A1245 " --> pdb=" O THR A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1263 removed outlier: 3.706A pdb=" N GLU A1261 " --> pdb=" O ILE A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1268 removed outlier: 4.524A pdb=" N GLU A1268 " --> pdb=" O GLU A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1289 removed outlier: 4.092A pdb=" N VAL A1289 " --> pdb=" O TRP A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1340 removed outlier: 3.792A pdb=" N LEU A1337 " --> pdb=" O SER A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1369 removed outlier: 3.899A pdb=" N LYS A1368 " --> pdb=" O ASP A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1388 Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1430 through 1446 removed outlier: 3.674A pdb=" N ARG A1434 " --> pdb=" O SER A1430 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A1435 " --> pdb=" O VAL A1431 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A1436 " --> pdb=" O GLY A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1475 removed outlier: 3.520A pdb=" N LEU A1466 " --> pdb=" O GLU A1462 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A1473 " --> pdb=" O SER A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1492 removed outlier: 4.065A pdb=" N ILE A1490 " --> pdb=" O ARG A1486 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A1492 " --> pdb=" O ASN A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1517 removed outlier: 3.644A pdb=" N GLN A1515 " --> pdb=" O SER A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1528 Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 664 removed outlier: 6.181A pdb=" N ALA A 649 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 644 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 661 through 664 removed outlier: 6.181A pdb=" N ALA A 649 " --> pdb=" O GLY A 663 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE A 644 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL A 704 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL A 646 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 702 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASN A 648 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY A 700 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 650 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.533A pdb=" N ALA A 709 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASP A 792 " --> pdb=" O ALA A 709 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 711 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 673 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE A 839 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 675 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N MET A 841 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL A 677 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 848 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 6.408A pdb=" N LYS A1310 " --> pdb=" O GLY A1298 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY A1298 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE A1312 " --> pdb=" O ASP A1296 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR A1297 " --> pdb=" O GLU A1347 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLU A1347 " --> pdb=" O TYR A1297 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 6.730A pdb=" N LEU A1450 " --> pdb=" O LEU A1481 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A1483 " --> pdb=" O LEU A1450 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A1452 " --> pdb=" O ILE A1483 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS A1321 " --> pdb=" O ARG A1495 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE A1497 " --> pdb=" O LYS A1321 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N GLY A1323 " --> pdb=" O ILE A1497 " (cutoff:3.500A) 562 hydrogen bonds defined for protein. 1647 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: 3.43 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1767 1.33 - 1.45: 2318 1.45 - 1.58: 5522 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9687 Sorted by residual: bond pdb=" N GLN A 234 " pdb=" CA GLN A 234 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 2.02e+01 bond pdb=" N THR A 556 " pdb=" CA THR A 556 " ideal model delta sigma weight residual 1.462 1.495 -0.033 7.70e-03 1.69e+04 1.84e+01 bond pdb=" N ILE A 829 " pdb=" CA ILE A 829 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.04e-02 9.25e+03 1.59e+01 bond pdb=" N VAL A 668 " pdb=" CA VAL A 668 " ideal model delta sigma weight residual 1.460 1.495 -0.035 9.30e-03 1.16e+04 1.42e+01 bond pdb=" N ILE A1369 " pdb=" CA ILE A1369 " ideal model delta sigma weight residual 1.457 1.499 -0.043 1.15e-02 7.56e+03 1.37e+01 ... (remaining 9682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 9895 2.15 - 4.30: 2810 4.30 - 6.45: 429 6.45 - 8.60: 1 8.60 - 10.75: 1 Bond angle restraints: 13136 Sorted by residual: angle pdb=" C MET A 476 " pdb=" N VAL A 477 " pdb=" CA VAL A 477 " ideal model delta sigma weight residual 120.33 125.50 -5.17 8.00e-01 1.56e+00 4.18e+01 angle pdb=" C ILE A1360 " pdb=" N GLY A1361 " pdb=" CA GLY A1361 " ideal model delta sigma weight residual 120.10 125.65 -5.55 9.50e-01 1.11e+00 3.41e+01 angle pdb=" C LYS A1408 " pdb=" N GLY A1409 " pdb=" CA GLY A1409 " ideal model delta sigma weight residual 120.03 125.87 -5.84 1.12e+00 7.97e-01 2.72e+01 angle pdb=" CA GLY A 700 " pdb=" C GLY A 700 " pdb=" O GLY A 700 " ideal model delta sigma weight residual 122.37 118.61 3.76 7.30e-01 1.88e+00 2.65e+01 angle pdb=" C GLN A1025 " pdb=" N GLY A1026 " pdb=" CA GLY A1026 " ideal model delta sigma weight residual 119.98 125.56 -5.58 1.11e+00 8.12e-01 2.53e+01 ... (remaining 13131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 5203 15.79 - 31.58: 456 31.58 - 47.37: 104 47.37 - 63.15: 17 63.15 - 78.94: 3 Dihedral angle restraints: 5783 sinusoidal: 2290 harmonic: 3493 Sorted by residual: dihedral pdb=" CA TYR A 318 " pdb=" C TYR A 318 " pdb=" N LYS A 319 " pdb=" CA LYS A 319 " ideal model delta harmonic sigma weight residual 180.00 154.66 25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ASN B 5 " pdb=" C ASN B 5 " pdb=" N LEU B 6 " pdb=" CA LEU B 6 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA VAL A 810 " pdb=" C VAL A 810 " pdb=" N ILE A 811 " pdb=" CA ILE A 811 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 499 0.045 - 0.089: 468 0.089 - 0.134: 390 0.134 - 0.179: 143 0.179 - 0.223: 24 Chirality restraints: 1524 Sorted by residual: chirality pdb=" CA ILE A1003 " pdb=" N ILE A1003 " pdb=" C ILE A1003 " pdb=" CB ILE A1003 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE A1316 " pdb=" N ILE A1316 " pdb=" C ILE A1316 " pdb=" CB ILE A1316 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE A 839 " pdb=" N ILE A 839 " pdb=" C ILE A 839 " pdb=" CB ILE A 839 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1521 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 558 " 0.020 2.00e-02 2.50e+03 1.34e-02 3.13e+00 pdb=" CG PHE A 558 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 558 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 558 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 558 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 558 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 558 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 553 " 0.011 2.00e-02 2.50e+03 7.16e-03 1.28e+00 pdb=" CG TRP A 553 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 553 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 553 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 553 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 553 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 553 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 553 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 553 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 553 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1125 " -0.013 2.00e-02 2.50e+03 7.94e-03 1.26e+00 pdb=" CG TYR A1125 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A1125 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A1125 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A1125 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A1125 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A1125 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A1125 " -0.003 2.00e-02 2.50e+03 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1040 2.80 - 3.33: 9850 3.33 - 3.85: 13535 3.85 - 4.38: 18251 4.38 - 4.90: 30077 Nonbonded interactions: 72753 Sorted by model distance: nonbonded pdb=" OE2 GLU A1203 " pdb=" OH TYR B 10 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR A 378 " pdb=" OE1 GLU A1203 " model vdw 2.417 3.040 nonbonded pdb=" O THR A 552 " pdb=" OG1 THR A 556 " model vdw 2.457 3.040 nonbonded pdb=" O SER B 15 " pdb=" C THR B 16 " model vdw 2.498 3.270 nonbonded pdb=" OG1 THR A1370 " pdb=" OG1 THR A1447 " model vdw 2.519 3.040 ... (remaining 72748 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: 2.690 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 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 : 0.014 0.212 9689 Z= 1.082 Angle : 1.820 10.754 13136 Z= 1.395 Chirality : 0.087 0.223 1524 Planarity : 0.003 0.015 1640 Dihedral : 12.695 78.943 3525 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.10 % Allowed : 1.82 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.20), residues: 1188 helix: -1.63 (0.15), residues: 719 sheet: -0.85 (0.57), residues: 77 loop : -2.57 (0.26), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 553 HIS 0.007 0.002 HIS A 386 PHE 0.027 0.002 PHE A 558 TYR 0.018 0.002 TYR A1125 ARG 0.005 0.001 ARG A1165 Details of bonding type rmsd hydrogen bonds : bond 0.28099 ( 559) hydrogen bonds : angle 8.47100 ( 1647) covalent geometry : bond 0.01350 ( 9687) covalent geometry : angle 1.81963 (13136) Misc. bond : bond 0.16954 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.922 Fit side-chains REVERT: A 239 THR cc_start: 0.7804 (m) cc_final: 0.7536 (p) REVERT: A 240 ASP cc_start: 0.6114 (m-30) cc_final: 0.5508 (m-30) REVERT: A 246 LYS cc_start: 0.7414 (mttt) cc_final: 0.6576 (tppt) REVERT: A 247 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7267 (pm20) REVERT: A 251 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7322 (pt0) REVERT: A 344 GLU cc_start: 0.6014 (mt-10) cc_final: 0.5615 (tt0) REVERT: A 356 LYS cc_start: 0.6995 (mttt) cc_final: 0.6527 (mmtt) REVERT: A 357 LYS cc_start: 0.7868 (mttt) cc_final: 0.7294 (mmtm) REVERT: A 444 ILE cc_start: 0.8361 (tt) cc_final: 0.7788 (pt) REVERT: A 485 MET cc_start: 0.5349 (ttp) cc_final: 0.5007 (mmt) REVERT: A 496 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6765 (mtmt) REVERT: A 503 LYS cc_start: 0.6579 (tttm) cc_final: 0.6185 (ptmt) REVERT: A 534 GLU cc_start: 0.7467 (tt0) cc_final: 0.7106 (mt-10) REVERT: A 617 ARG cc_start: 0.6637 (ttp80) cc_final: 0.6015 (ttm110) REVERT: A 652 THR cc_start: 0.7704 (p) cc_final: 0.7487 (p) REVERT: A 685 SER cc_start: 0.8391 (t) cc_final: 0.8184 (m) REVERT: A 695 MET cc_start: 0.8381 (mtp) cc_final: 0.8106 (mtm) REVERT: A 699 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6948 (pp20) REVERT: A 738 LYS cc_start: 0.7715 (tttp) cc_final: 0.7457 (mmmt) REVERT: A 751 GLU cc_start: 0.7437 (tp30) cc_final: 0.7165 (mt-10) REVERT: A 758 ARG cc_start: 0.7384 (ptt180) cc_final: 0.7047 (mtm-85) REVERT: A 764 LYS cc_start: 0.7570 (tptt) cc_final: 0.7247 (mtpp) REVERT: A 783 TYR cc_start: 0.7672 (t80) cc_final: 0.7385 (t80) REVERT: A 784 CYS cc_start: 0.8381 (t) cc_final: 0.8026 (m) REVERT: A 804 LYS cc_start: 0.7899 (mttt) cc_final: 0.7690 (mttm) REVERT: A 808 GLU cc_start: 0.8119 (tt0) cc_final: 0.7725 (tm-30) REVERT: A 814 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8416 (mtpp) REVERT: A 864 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7449 (mm-30) REVERT: A 971 LEU cc_start: 0.6895 (mp) cc_final: 0.6695 (mm) REVERT: A 972 PHE cc_start: 0.7227 (t80) cc_final: 0.6901 (t80) REVERT: A 1080 ASP cc_start: 0.7113 (t70) cc_final: 0.6839 (m-30) REVERT: A 1098 PHE cc_start: 0.7837 (m-80) cc_final: 0.7593 (m-80) REVERT: A 1113 MET cc_start: 0.7015 (mtp) cc_final: 0.6283 (mmm) REVERT: A 1133 VAL cc_start: 0.7723 (t) cc_final: 0.7317 (m) REVERT: A 1176 GLN cc_start: 0.6669 (tp40) cc_final: 0.5954 (mt0) REVERT: A 1252 GLU cc_start: 0.6422 (tp30) cc_final: 0.5831 (mt-10) REVERT: A 1310 LYS cc_start: 0.6439 (tttp) cc_final: 0.6158 (tptt) REVERT: A 1343 LYS cc_start: 0.6628 (mttm) cc_final: 0.6316 (mmtm) REVERT: A 1368 LYS cc_start: 0.8129 (mmtp) cc_final: 0.7453 (mmmt) REVERT: A 1377 VAL cc_start: 0.6954 (m) cc_final: 0.6691 (p) REVERT: A 1385 MET cc_start: 0.6371 (tmm) cc_final: 0.5344 (mmp) REVERT: A 1498 VAL cc_start: 0.6292 (t) cc_final: 0.5949 (p) REVERT: A 1505 GLN cc_start: 0.6907 (mm110) cc_final: 0.6698 (mp10) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.2745 time to fit residues: 79.9752 Evaluate side-chains 142 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 412 ASN A 480 ASN A 597 ASN ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.160693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121076 restraints weight = 11307.303| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.99 r_work: 0.3144 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9689 Z= 0.155 Angle : 0.578 10.002 13136 Z= 0.308 Chirality : 0.040 0.164 1524 Planarity : 0.004 0.032 1640 Dihedral : 4.427 46.113 1293 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.34 % Allowed : 7.66 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1188 helix: 1.14 (0.18), residues: 753 sheet: -0.22 (0.55), residues: 79 loop : -2.26 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 520 HIS 0.004 0.001 HIS A 985 PHE 0.014 0.002 PHE A 589 TYR 0.019 0.002 TYR A1032 ARG 0.005 0.001 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.06406 ( 559) hydrogen bonds : angle 4.41005 ( 1647) covalent geometry : bond 0.00334 ( 9687) covalent geometry : angle 0.57794 (13136) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 1.084 Fit side-chains REVERT: A 239 THR cc_start: 0.8130 (m) cc_final: 0.7689 (p) REVERT: A 246 LYS cc_start: 0.8124 (mttt) cc_final: 0.7547 (tptt) REVERT: A 444 ILE cc_start: 0.9075 (tt) cc_final: 0.8577 (pt) REVERT: A 485 MET cc_start: 0.6496 (ttp) cc_final: 0.5992 (mmt) REVERT: A 496 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7540 (mtmt) REVERT: A 503 LYS cc_start: 0.7273 (tttm) cc_final: 0.6859 (ptmt) REVERT: A 534 GLU cc_start: 0.7923 (tt0) cc_final: 0.7556 (mt-10) REVERT: A 617 ARG cc_start: 0.7515 (ttp80) cc_final: 0.7264 (ttm110) REVERT: A 647 LYS cc_start: 0.7882 (mttt) cc_final: 0.7539 (mtmm) REVERT: A 764 LYS cc_start: 0.7418 (tptt) cc_final: 0.7128 (mtpp) REVERT: A 784 CYS cc_start: 0.8551 (t) cc_final: 0.8114 (t) REVERT: A 808 GLU cc_start: 0.8180 (tt0) cc_final: 0.7931 (tm-30) REVERT: A 1080 ASP cc_start: 0.7986 (t70) cc_final: 0.7506 (m-30) REVERT: A 1113 MET cc_start: 0.7696 (mtp) cc_final: 0.7276 (mmm) REVERT: A 1176 GLN cc_start: 0.7777 (tp40) cc_final: 0.7121 (mt0) REVERT: A 1235 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7492 (m-80) REVERT: A 1252 GLU cc_start: 0.7396 (tp30) cc_final: 0.7045 (mt-10) REVERT: A 1310 LYS cc_start: 0.6668 (tttp) cc_final: 0.6436 (tptp) REVERT: A 1368 LYS cc_start: 0.8407 (mmtp) cc_final: 0.7773 (mmmt) REVERT: A 1385 MET cc_start: 0.6390 (tmm) cc_final: 0.5464 (mmp) REVERT: B 2 PHE cc_start: 0.5929 (OUTLIER) cc_final: 0.5258 (m-80) REVERT: B 5 ASN cc_start: 0.7242 (m-40) cc_final: 0.6864 (m-40) outliers start: 14 outliers final: 6 residues processed: 167 average time/residue: 0.2423 time to fit residues: 54.8766 Evaluate side-chains 131 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain B residue 2 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 622 HIS ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.162036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124680 restraints weight = 11443.091| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.06 r_work: 0.3147 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9689 Z= 0.131 Angle : 0.518 8.229 13136 Z= 0.270 Chirality : 0.039 0.159 1524 Planarity : 0.003 0.038 1640 Dihedral : 4.083 44.724 1293 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.15 % Allowed : 10.05 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1188 helix: 1.89 (0.18), residues: 755 sheet: -0.30 (0.56), residues: 74 loop : -1.97 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 223 HIS 0.004 0.001 HIS A 382 PHE 0.016 0.001 PHE A 558 TYR 0.013 0.001 TYR A1032 ARG 0.005 0.000 ARG A 617 Details of bonding type rmsd hydrogen bonds : bond 0.05513 ( 559) hydrogen bonds : angle 3.96041 ( 1647) covalent geometry : bond 0.00277 ( 9687) covalent geometry : angle 0.51787 (13136) Misc. bond : bond 0.00022 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.996 Fit side-chains REVERT: A 228 MET cc_start: 0.8774 (mmt) cc_final: 0.8542 (mmm) REVERT: A 239 THR cc_start: 0.8120 (m) cc_final: 0.7734 (p) REVERT: A 246 LYS cc_start: 0.8124 (mttt) cc_final: 0.7563 (tppt) REVERT: A 485 MET cc_start: 0.6449 (ttp) cc_final: 0.6023 (mmt) REVERT: A 503 LYS cc_start: 0.7186 (tttm) cc_final: 0.6783 (ptmt) REVERT: A 505 MET cc_start: 0.7871 (mmm) cc_final: 0.7582 (mmm) REVERT: A 534 GLU cc_start: 0.7876 (tt0) cc_final: 0.7499 (mt-10) REVERT: A 617 ARG cc_start: 0.7850 (ttp80) cc_final: 0.7372 (ttm110) REVERT: A 647 LYS cc_start: 0.7946 (mttt) cc_final: 0.7649 (mtmm) REVERT: A 656 ASN cc_start: 0.7139 (t0) cc_final: 0.6761 (t0) REVERT: A 751 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6944 (mm-30) REVERT: A 758 ARG cc_start: 0.7531 (mtm-85) cc_final: 0.7141 (mtm-85) REVERT: A 764 LYS cc_start: 0.7481 (tptt) cc_final: 0.7145 (mtpp) REVERT: A 784 CYS cc_start: 0.8489 (t) cc_final: 0.8021 (t) REVERT: A 808 GLU cc_start: 0.8087 (tt0) cc_final: 0.7832 (tm-30) REVERT: A 1080 ASP cc_start: 0.7962 (t70) cc_final: 0.7535 (m-30) REVERT: A 1113 MET cc_start: 0.7741 (mtp) cc_final: 0.7273 (mmm) REVERT: A 1176 GLN cc_start: 0.7827 (tp40) cc_final: 0.7182 (mt0) REVERT: A 1235 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: A 1252 GLU cc_start: 0.7501 (tp30) cc_final: 0.7056 (mt-10) REVERT: A 1265 GLU cc_start: 0.8405 (tp30) cc_final: 0.8197 (tp30) REVERT: A 1310 LYS cc_start: 0.6753 (tttp) cc_final: 0.6402 (tmtt) REVERT: A 1368 LYS cc_start: 0.8266 (mmtp) cc_final: 0.7673 (mmmt) REVERT: A 1385 MET cc_start: 0.6423 (tmm) cc_final: 0.5487 (mmp) REVERT: A 1491 MET cc_start: 0.7191 (tpp) cc_final: 0.6871 (tpp) REVERT: A 1492 ASP cc_start: 0.7082 (t0) cc_final: 0.6740 (p0) outliers start: 12 outliers final: 7 residues processed: 147 average time/residue: 0.2588 time to fit residues: 51.6275 Evaluate side-chains 131 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1209 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 106 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 805 HIS A1474 GLN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.161948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123247 restraints weight = 11354.252| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.00 r_work: 0.3170 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9689 Z= 0.125 Angle : 0.506 7.163 13136 Z= 0.262 Chirality : 0.039 0.144 1524 Planarity : 0.003 0.041 1640 Dihedral : 3.925 43.693 1293 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.44 % Allowed : 11.58 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1188 helix: 2.08 (0.19), residues: 761 sheet: -0.01 (0.56), residues: 79 loop : -1.89 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1197 HIS 0.004 0.001 HIS A 382 PHE 0.014 0.001 PHE A 558 TYR 0.014 0.001 TYR A1032 ARG 0.003 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 559) hydrogen bonds : angle 3.79156 ( 1647) covalent geometry : bond 0.00269 ( 9687) covalent geometry : angle 0.50632 (13136) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.982 Fit side-chains REVERT: A 228 MET cc_start: 0.8694 (mmt) cc_final: 0.8478 (mmm) REVERT: A 239 THR cc_start: 0.8072 (m) cc_final: 0.7702 (p) REVERT: A 246 LYS cc_start: 0.8128 (mttt) cc_final: 0.7588 (tppt) REVERT: A 485 MET cc_start: 0.6386 (ttp) cc_final: 0.6033 (mmt) REVERT: A 503 LYS cc_start: 0.7100 (tttm) cc_final: 0.6714 (ptmt) REVERT: A 534 GLU cc_start: 0.7751 (tt0) cc_final: 0.7391 (mt-10) REVERT: A 617 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7220 (ttm110) REVERT: A 647 LYS cc_start: 0.7983 (mttt) cc_final: 0.7701 (mtmm) REVERT: A 656 ASN cc_start: 0.7189 (t0) cc_final: 0.6815 (t0) REVERT: A 751 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6961 (mm-30) REVERT: A 758 ARG cc_start: 0.7540 (mtm-85) cc_final: 0.7134 (mtm-85) REVERT: A 764 LYS cc_start: 0.7527 (tptt) cc_final: 0.7139 (mtpp) REVERT: A 784 CYS cc_start: 0.8513 (t) cc_final: 0.8055 (t) REVERT: A 808 GLU cc_start: 0.8057 (tt0) cc_final: 0.7814 (tm-30) REVERT: A 1080 ASP cc_start: 0.7995 (t70) cc_final: 0.7547 (m-30) REVERT: A 1113 MET cc_start: 0.7744 (mtp) cc_final: 0.7250 (mmm) REVERT: A 1176 GLN cc_start: 0.7819 (tp40) cc_final: 0.7221 (mt0) REVERT: A 1235 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: A 1252 GLU cc_start: 0.7590 (tp30) cc_final: 0.7055 (mt-10) REVERT: A 1265 GLU cc_start: 0.8420 (tp30) cc_final: 0.8215 (tp30) REVERT: A 1368 LYS cc_start: 0.8095 (mmtp) cc_final: 0.7455 (mmmt) REVERT: A 1385 MET cc_start: 0.6427 (tmm) cc_final: 0.5473 (mmp) REVERT: A 1446 LYS cc_start: 0.6162 (tppt) cc_final: 0.4839 (tttp) REVERT: A 1491 MET cc_start: 0.7125 (tpp) cc_final: 0.6847 (tpp) outliers start: 15 outliers final: 9 residues processed: 144 average time/residue: 0.2394 time to fit residues: 47.3925 Evaluate side-chains 133 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 39 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116952 restraints weight = 11577.113| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.96 r_work: 0.3101 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9689 Z= 0.195 Angle : 0.568 6.730 13136 Z= 0.295 Chirality : 0.042 0.166 1524 Planarity : 0.004 0.045 1640 Dihedral : 4.124 44.476 1293 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.39 % Allowed : 11.58 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1188 helix: 1.81 (0.18), residues: 762 sheet: 0.06 (0.58), residues: 75 loop : -1.92 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1197 HIS 0.007 0.001 HIS A 382 PHE 0.015 0.002 PHE A 558 TYR 0.018 0.002 TYR A1032 ARG 0.003 0.001 ARG A1165 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 559) hydrogen bonds : angle 3.95182 ( 1647) covalent geometry : bond 0.00467 ( 9687) covalent geometry : angle 0.56844 (13136) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.088 Fit side-chains REVERT: A 239 THR cc_start: 0.8201 (m) cc_final: 0.7829 (p) REVERT: A 246 LYS cc_start: 0.8162 (mttt) cc_final: 0.7584 (tppt) REVERT: A 485 MET cc_start: 0.6655 (ttp) cc_final: 0.6091 (mmt) REVERT: A 503 LYS cc_start: 0.7182 (tttm) cc_final: 0.6805 (ptmt) REVERT: A 505 MET cc_start: 0.8069 (mmm) cc_final: 0.7767 (mmm) REVERT: A 534 GLU cc_start: 0.7830 (tt0) cc_final: 0.7456 (mt-10) REVERT: A 617 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7548 (ttm110) REVERT: A 647 LYS cc_start: 0.8195 (mttt) cc_final: 0.7923 (mtmm) REVERT: A 656 ASN cc_start: 0.7395 (t0) cc_final: 0.7000 (t0) REVERT: A 751 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6960 (mm-30) REVERT: A 758 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7266 (mtm-85) REVERT: A 764 LYS cc_start: 0.7686 (tptt) cc_final: 0.7303 (mtpp) REVERT: A 808 GLU cc_start: 0.8129 (tt0) cc_final: 0.7894 (tm-30) REVERT: A 819 ASN cc_start: 0.7527 (m-40) cc_final: 0.7297 (t0) REVERT: A 1029 VAL cc_start: 0.7921 (t) cc_final: 0.7595 (p) REVERT: A 1080 ASP cc_start: 0.8008 (t70) cc_final: 0.7571 (m-30) REVERT: A 1113 MET cc_start: 0.7797 (mtp) cc_final: 0.7347 (mmm) REVERT: A 1176 GLN cc_start: 0.8093 (tp40) cc_final: 0.7386 (mt0) REVERT: A 1235 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: A 1265 GLU cc_start: 0.8439 (tp30) cc_final: 0.8194 (tp30) REVERT: A 1368 LYS cc_start: 0.8142 (mmtp) cc_final: 0.7487 (mmmt) REVERT: A 1385 MET cc_start: 0.6581 (tmm) cc_final: 0.5687 (mmp) REVERT: A 1446 LYS cc_start: 0.6145 (tppt) cc_final: 0.5131 (tttp) REVERT: A 1491 MET cc_start: 0.7581 (tpp) cc_final: 0.7188 (tpp) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 0.2404 time to fit residues: 50.5397 Evaluate side-chains 140 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1505 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1474 GLN A1505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.123257 restraints weight = 11506.572| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.95 r_work: 0.3146 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9689 Z= 0.117 Angle : 0.498 9.198 13136 Z= 0.257 Chirality : 0.038 0.141 1524 Planarity : 0.003 0.042 1640 Dihedral : 3.881 42.852 1293 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.82 % Allowed : 12.44 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1188 helix: 2.17 (0.19), residues: 756 sheet: 0.38 (0.58), residues: 80 loop : -1.81 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1507 HIS 0.004 0.001 HIS A 827 PHE 0.013 0.001 PHE A 558 TYR 0.013 0.001 TYR A1032 ARG 0.003 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 559) hydrogen bonds : angle 3.71991 ( 1647) covalent geometry : bond 0.00245 ( 9687) covalent geometry : angle 0.49793 (13136) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.839 Fit side-chains REVERT: A 239 THR cc_start: 0.8187 (m) cc_final: 0.7816 (p) REVERT: A 246 LYS cc_start: 0.8076 (mttt) cc_final: 0.7489 (tppt) REVERT: A 485 MET cc_start: 0.6320 (ttp) cc_final: 0.5889 (mmt) REVERT: A 503 LYS cc_start: 0.7047 (tttm) cc_final: 0.6719 (ptmt) REVERT: A 534 GLU cc_start: 0.7525 (tt0) cc_final: 0.7210 (mt-10) REVERT: A 617 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7291 (ttm110) REVERT: A 647 LYS cc_start: 0.8106 (mttt) cc_final: 0.7824 (mtmm) REVERT: A 656 ASN cc_start: 0.7242 (t0) cc_final: 0.6816 (t0) REVERT: A 758 ARG cc_start: 0.7571 (mtm-85) cc_final: 0.7232 (mtm-85) REVERT: A 764 LYS cc_start: 0.7704 (tptt) cc_final: 0.7374 (mtpp) REVERT: A 784 CYS cc_start: 0.8597 (t) cc_final: 0.8172 (t) REVERT: A 808 GLU cc_start: 0.8110 (tt0) cc_final: 0.7828 (tm-30) REVERT: A 819 ASN cc_start: 0.7407 (m-40) cc_final: 0.7026 (t0) REVERT: A 1080 ASP cc_start: 0.7943 (t70) cc_final: 0.7483 (m-30) REVERT: A 1113 MET cc_start: 0.7745 (mtp) cc_final: 0.7199 (mmm) REVERT: A 1176 GLN cc_start: 0.7941 (tp40) cc_final: 0.7201 (mt0) REVERT: A 1235 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: A 1252 GLU cc_start: 0.7556 (tp30) cc_final: 0.6933 (mt-10) REVERT: A 1265 GLU cc_start: 0.8368 (tp30) cc_final: 0.8122 (tp30) REVERT: A 1368 LYS cc_start: 0.8036 (mmtp) cc_final: 0.7379 (mmmt) REVERT: A 1385 MET cc_start: 0.6533 (tmm) cc_final: 0.5600 (mmp) REVERT: A 1446 LYS cc_start: 0.6021 (tppt) cc_final: 0.5241 (tttp) REVERT: A 1491 MET cc_start: 0.7499 (tpp) cc_final: 0.7100 (tpp) outliers start: 19 outliers final: 12 residues processed: 141 average time/residue: 0.2723 time to fit residues: 52.4130 Evaluate side-chains 135 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1474 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 93 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.0070 chunk 99 optimal weight: 0.0020 chunk 108 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 0.0170 chunk 111 optimal weight: 0.0070 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 overall best weight: 0.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 GLN A1474 GLN A1505 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127249 restraints weight = 11513.388| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.01 r_work: 0.3205 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9689 Z= 0.107 Angle : 0.482 8.628 13136 Z= 0.249 Chirality : 0.037 0.141 1524 Planarity : 0.003 0.042 1640 Dihedral : 3.672 41.653 1293 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.44 % Allowed : 12.92 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.25), residues: 1188 helix: 2.43 (0.19), residues: 762 sheet: 0.46 (0.58), residues: 80 loop : -1.77 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1507 HIS 0.004 0.001 HIS A 827 PHE 0.013 0.001 PHE A 558 TYR 0.011 0.001 TYR A1032 ARG 0.002 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 559) hydrogen bonds : angle 3.55842 ( 1647) covalent geometry : bond 0.00207 ( 9687) covalent geometry : angle 0.48226 (13136) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 239 THR cc_start: 0.8069 (m) cc_final: 0.7836 (p) REVERT: A 240 ASP cc_start: 0.6975 (m-30) cc_final: 0.6654 (t70) REVERT: A 485 MET cc_start: 0.6260 (ttp) cc_final: 0.5900 (mmt) REVERT: A 503 LYS cc_start: 0.7047 (tttm) cc_final: 0.6717 (ptmt) REVERT: A 534 GLU cc_start: 0.7453 (tt0) cc_final: 0.7162 (mt-10) REVERT: A 617 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7325 (ttm110) REVERT: A 647 LYS cc_start: 0.7990 (mttt) cc_final: 0.7720 (mtmm) REVERT: A 656 ASN cc_start: 0.7111 (t0) cc_final: 0.6731 (t0) REVERT: A 758 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7243 (mtm-85) REVERT: A 764 LYS cc_start: 0.7641 (tptt) cc_final: 0.7341 (mtpp) REVERT: A 784 CYS cc_start: 0.8550 (t) cc_final: 0.8195 (t) REVERT: A 804 LYS cc_start: 0.7698 (mmtp) cc_final: 0.7380 (mmtp) REVERT: A 808 GLU cc_start: 0.8054 (tt0) cc_final: 0.7767 (tm-30) REVERT: A 819 ASN cc_start: 0.7268 (m-40) cc_final: 0.6952 (t0) REVERT: A 1080 ASP cc_start: 0.7991 (t70) cc_final: 0.7527 (m-30) REVERT: A 1113 MET cc_start: 0.7738 (mtp) cc_final: 0.7201 (mmm) REVERT: A 1176 GLN cc_start: 0.7878 (tp40) cc_final: 0.7241 (mt0) REVERT: A 1235 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7280 (m-80) REVERT: A 1252 GLU cc_start: 0.7469 (tp30) cc_final: 0.6837 (mt-10) REVERT: A 1265 GLU cc_start: 0.8326 (tp30) cc_final: 0.8075 (tp30) REVERT: A 1368 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7349 (mmmt) REVERT: A 1385 MET cc_start: 0.6534 (tmm) cc_final: 0.5599 (mmp) REVERT: A 1474 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6413 (mm110) outliers start: 15 outliers final: 7 residues processed: 145 average time/residue: 0.2544 time to fit residues: 51.4544 Evaluate side-chains 135 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1474 GLN Chi-restraints excluded: chain A residue 1505 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 26 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 0.0270 chunk 95 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 HIS A1474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124545 restraints weight = 11701.406| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.99 r_work: 0.3183 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9689 Z= 0.120 Angle : 0.495 8.465 13136 Z= 0.253 Chirality : 0.038 0.144 1524 Planarity : 0.003 0.043 1640 Dihedral : 3.664 41.617 1293 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.44 % Allowed : 13.40 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1188 helix: 2.40 (0.19), residues: 762 sheet: 0.53 (0.58), residues: 80 loop : -1.74 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1507 HIS 0.008 0.001 HIS A 827 PHE 0.013 0.001 PHE A 558 TYR 0.013 0.001 TYR A1032 ARG 0.004 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04463 ( 559) hydrogen bonds : angle 3.60340 ( 1647) covalent geometry : bond 0.00268 ( 9687) covalent geometry : angle 0.49526 (13136) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 239 THR cc_start: 0.8067 (m) cc_final: 0.7839 (p) REVERT: A 485 MET cc_start: 0.6249 (ttp) cc_final: 0.5870 (mmt) REVERT: A 503 LYS cc_start: 0.7005 (tttm) cc_final: 0.6673 (ptmt) REVERT: A 534 GLU cc_start: 0.7419 (tt0) cc_final: 0.7126 (mt-10) REVERT: A 617 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7317 (ttm110) REVERT: A 647 LYS cc_start: 0.7986 (mttt) cc_final: 0.7702 (mtmm) REVERT: A 656 ASN cc_start: 0.7163 (t0) cc_final: 0.6794 (t0) REVERT: A 758 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7249 (mtm-85) REVERT: A 764 LYS cc_start: 0.7664 (tptt) cc_final: 0.7412 (mtpp) REVERT: A 784 CYS cc_start: 0.8508 (t) cc_final: 0.8107 (t) REVERT: A 808 GLU cc_start: 0.8061 (tt0) cc_final: 0.7791 (tm-30) REVERT: A 819 ASN cc_start: 0.7414 (m-40) cc_final: 0.7048 (t0) REVERT: A 1080 ASP cc_start: 0.8032 (t70) cc_final: 0.7551 (m-30) REVERT: A 1113 MET cc_start: 0.7756 (mtp) cc_final: 0.7190 (mmm) REVERT: A 1133 VAL cc_start: 0.8689 (t) cc_final: 0.8281 (m) REVERT: A 1176 GLN cc_start: 0.7834 (tp40) cc_final: 0.7178 (mt0) REVERT: A 1235 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: A 1252 GLU cc_start: 0.7459 (tp30) cc_final: 0.6805 (mt-10) REVERT: A 1265 GLU cc_start: 0.8339 (tp30) cc_final: 0.8097 (tp30) REVERT: A 1368 LYS cc_start: 0.7993 (mmtp) cc_final: 0.7309 (mmmt) REVERT: A 1385 MET cc_start: 0.6520 (tmm) cc_final: 0.5577 (mmp) REVERT: A 1446 LYS cc_start: 0.7090 (tptt) cc_final: 0.6025 (tttp) outliers start: 15 outliers final: 11 residues processed: 138 average time/residue: 0.2411 time to fit residues: 46.1787 Evaluate side-chains 140 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1403 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 27 optimal weight: 0.0050 chunk 113 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1505 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.121520 restraints weight = 11541.324| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.02 r_work: 0.3283 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9689 Z= 0.131 Angle : 0.516 10.938 13136 Z= 0.262 Chirality : 0.039 0.145 1524 Planarity : 0.003 0.043 1640 Dihedral : 3.735 41.508 1293 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.63 % Allowed : 13.40 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.25), residues: 1188 helix: 2.35 (0.19), residues: 758 sheet: 0.57 (0.58), residues: 80 loop : -1.68 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1507 HIS 0.005 0.001 HIS A 382 PHE 0.013 0.001 PHE A 583 TYR 0.014 0.001 TYR A1032 ARG 0.004 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 559) hydrogen bonds : angle 3.63369 ( 1647) covalent geometry : bond 0.00298 ( 9687) covalent geometry : angle 0.51552 (13136) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.129 Fit side-chains REVERT: A 485 MET cc_start: 0.6814 (ttp) cc_final: 0.6461 (mmt) REVERT: A 503 LYS cc_start: 0.7465 (tttm) cc_final: 0.7138 (ptmt) REVERT: A 617 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7826 (ttm110) REVERT: A 647 LYS cc_start: 0.8307 (mttt) cc_final: 0.8061 (mtmm) REVERT: A 656 ASN cc_start: 0.7235 (t0) cc_final: 0.6858 (t0) REVERT: A 758 ARG cc_start: 0.7804 (mtm-85) cc_final: 0.7507 (mtm-85) REVERT: A 764 LYS cc_start: 0.7776 (tptt) cc_final: 0.7568 (mtpp) REVERT: A 784 CYS cc_start: 0.8637 (t) cc_final: 0.8310 (t) REVERT: A 819 ASN cc_start: 0.7399 (m-40) cc_final: 0.7172 (t0) REVERT: A 1066 THR cc_start: 0.7523 (m) cc_final: 0.6989 (p) REVERT: A 1080 ASP cc_start: 0.8198 (t70) cc_final: 0.7756 (m-30) REVERT: A 1113 MET cc_start: 0.7955 (mtp) cc_final: 0.7517 (mmm) REVERT: A 1133 VAL cc_start: 0.8912 (t) cc_final: 0.8532 (m) REVERT: A 1176 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7546 (mt0) REVERT: A 1235 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: A 1265 GLU cc_start: 0.8400 (tp30) cc_final: 0.8180 (tp30) REVERT: A 1368 LYS cc_start: 0.8250 (mmtp) cc_final: 0.7612 (mmmt) REVERT: A 1385 MET cc_start: 0.6702 (tmm) cc_final: 0.5837 (mmp) REVERT: A 1446 LYS cc_start: 0.7151 (tptt) cc_final: 0.6023 (tttp) outliers start: 17 outliers final: 12 residues processed: 141 average time/residue: 0.2383 time to fit residues: 46.6127 Evaluate side-chains 137 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 0.0020 chunk 66 optimal weight: 0.0770 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.4546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.161480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123531 restraints weight = 11689.037| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.04 r_work: 0.3210 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9689 Z= 0.113 Angle : 0.513 12.124 13136 Z= 0.262 Chirality : 0.038 0.196 1524 Planarity : 0.003 0.042 1640 Dihedral : 3.668 40.616 1293 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.44 % Allowed : 13.78 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.25), residues: 1188 helix: 2.46 (0.19), residues: 758 sheet: 0.58 (0.58), residues: 80 loop : -1.68 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1507 HIS 0.008 0.001 HIS A 827 PHE 0.013 0.001 PHE A 558 TYR 0.012 0.001 TYR A1032 ARG 0.006 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 559) hydrogen bonds : angle 3.56323 ( 1647) covalent geometry : bond 0.00239 ( 9687) covalent geometry : angle 0.51342 (13136) Misc. bond : bond 0.00014 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.056 Fit side-chains REVERT: A 485 MET cc_start: 0.6785 (ttp) cc_final: 0.6415 (mmt) REVERT: A 503 LYS cc_start: 0.7443 (tttm) cc_final: 0.7122 (ptmt) REVERT: A 617 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7826 (ttm110) REVERT: A 647 LYS cc_start: 0.8305 (mttt) cc_final: 0.8063 (mtmm) REVERT: A 656 ASN cc_start: 0.7208 (t0) cc_final: 0.6885 (t0) REVERT: A 758 ARG cc_start: 0.7812 (mtm-85) cc_final: 0.7513 (mtm-85) REVERT: A 764 LYS cc_start: 0.7751 (tptt) cc_final: 0.7527 (mtpp) REVERT: A 784 CYS cc_start: 0.8590 (t) cc_final: 0.8260 (t) REVERT: A 819 ASN cc_start: 0.7351 (m-40) cc_final: 0.7024 (t0) REVERT: A 1080 ASP cc_start: 0.8189 (t70) cc_final: 0.7748 (m-30) REVERT: A 1113 MET cc_start: 0.7909 (mtp) cc_final: 0.7457 (mmm) REVERT: A 1133 VAL cc_start: 0.8916 (t) cc_final: 0.8545 (m) REVERT: A 1176 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: A 1235 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: A 1265 GLU cc_start: 0.8365 (tp30) cc_final: 0.8148 (tp30) REVERT: A 1368 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7541 (mmmt) REVERT: A 1385 MET cc_start: 0.6724 (tmm) cc_final: 0.5831 (mmp) REVERT: A 1446 LYS cc_start: 0.7162 (tptt) cc_final: 0.6128 (tttp) outliers start: 15 outliers final: 12 residues processed: 134 average time/residue: 0.2306 time to fit residues: 43.0428 Evaluate side-chains 138 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 847 SER Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1176 GLN Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 99 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 0.0060 chunk 58 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 0.0270 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 827 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.161366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123809 restraints weight = 11573.563| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.01 r_work: 0.3282 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9689 Z= 0.111 Angle : 0.507 11.835 13136 Z= 0.258 Chirality : 0.038 0.144 1524 Planarity : 0.003 0.042 1640 Dihedral : 3.577 39.528 1293 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.63 % Allowed : 13.78 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.25), residues: 1188 helix: 2.53 (0.19), residues: 758 sheet: 0.65 (0.57), residues: 80 loop : -1.61 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1507 HIS 0.008 0.001 HIS A 827 PHE 0.012 0.001 PHE A 558 TYR 0.012 0.001 TYR A1032 ARG 0.005 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 559) hydrogen bonds : angle 3.51056 ( 1647) covalent geometry : bond 0.00236 ( 9687) covalent geometry : angle 0.50710 (13136) Misc. bond : bond 0.00012 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6028.81 seconds wall clock time: 105 minutes 11.05 seconds (6311.05 seconds total)