Starting phenix.real_space_refine on Wed Mar 4 01:06:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f4b_28854/03_2026/8f4b_28854.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f4b_28854/03_2026/8f4b_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_28854/03_2026/8f4b_28854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f4b_28854/03_2026/8f4b_28854.map" model { file = "/net/cci-nas-00/data/ceres_data/8f4b_28854/03_2026/8f4b_28854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f4b_28854/03_2026/8f4b_28854.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.23, per 1000 atoms: 0.24 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: 0.81 Conformation dependent library (CDL) restraints added in 481.4 milliseconds 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: 0.35 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: 1.80 Time building geometry restraints manager: 1.09 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: 2.060 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG A1165 TYR 0.018 0.002 TYR A1125 PHE 0.027 0.002 PHE A 558 TRP 0.019 0.002 TRP A 553 HIS 0.007 0.002 HIS A 386 Details of bonding type rmsd covalent geometry : bond 0.01350 ( 9687) covalent geometry : angle 1.81963 (13136) hydrogen bonds : bond 0.28099 ( 559) hydrogen bonds : angle 8.47100 ( 1647) 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 : 0.330 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: 0.6577 (tppt) REVERT: A 247 GLU cc_start: 0.7550 (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: 0.7703 (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: 0.6440 (tttp) cc_final: 0.6158 (tptt) REVERT: A 1343 LYS cc_start: 0.6628 (mttm) cc_final: 0.6315 (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: 0.1216 time to fit residues: 35.5887 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 : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 432 GLN A 480 ASN A 597 ASN A 622 HIS ** A 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.160687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121259 restraints weight = 11361.728| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.99 r_work: 0.3137 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9689 Z= 0.166 Angle : 0.591 9.894 13136 Z= 0.315 Chirality : 0.041 0.168 1524 Planarity : 0.004 0.033 1640 Dihedral : 4.466 46.047 1293 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.34 % Allowed : 7.75 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.23), residues: 1188 helix: 1.04 (0.18), residues: 754 sheet: -0.24 (0.55), residues: 79 loop : -2.24 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 233 TYR 0.019 0.002 TYR A1032 PHE 0.015 0.002 PHE A 589 TRP 0.017 0.001 TRP A 520 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9687) covalent geometry : angle 0.59123 (13136) hydrogen bonds : bond 0.06456 ( 559) hydrogen bonds : angle 4.42085 ( 1647) Misc. bond : bond 0.00052 ( 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 167 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.432 Fit side-chains REVERT: A 239 THR cc_start: 0.8097 (m) cc_final: 0.7642 (p) REVERT: A 240 ASP cc_start: 0.6772 (m-30) cc_final: 0.6489 (m-30) REVERT: A 246 LYS cc_start: 0.8085 (mttt) cc_final: 0.7489 (tptt) REVERT: A 444 ILE cc_start: 0.9085 (tt) cc_final: 0.8549 (pt) REVERT: A 485 MET cc_start: 0.6497 (ttp) cc_final: 0.5987 (mmt) REVERT: A 496 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7486 (mtmt) REVERT: A 503 LYS cc_start: 0.7176 (tttm) cc_final: 0.6751 (ptmt) REVERT: A 534 GLU cc_start: 0.7887 (tt0) cc_final: 0.7505 (mt-10) REVERT: A 614 LYS cc_start: 0.7384 (tptm) cc_final: 0.7174 (tptt) REVERT: A 617 ARG cc_start: 0.7480 (ttp80) cc_final: 0.7201 (ttm110) REVERT: A 647 LYS cc_start: 0.7852 (mttt) cc_final: 0.7538 (mtmm) REVERT: A 751 GLU cc_start: 0.7478 (tp30) cc_final: 0.7257 (mt-10) REVERT: A 764 LYS cc_start: 0.7400 (tptt) cc_final: 0.7093 (mtpp) REVERT: A 784 CYS cc_start: 0.8535 (t) cc_final: 0.8088 (t) REVERT: A 808 GLU cc_start: 0.8157 (tt0) cc_final: 0.7894 (tm-30) REVERT: A 1080 ASP cc_start: 0.7964 (t70) cc_final: 0.7488 (m-30) REVERT: A 1113 MET cc_start: 0.7657 (mtp) cc_final: 0.7222 (mmm) REVERT: A 1176 GLN cc_start: 0.7685 (tp40) cc_final: 0.7027 (mt0) REVERT: A 1235 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: A 1252 GLU cc_start: 0.7303 (tp30) cc_final: 0.6978 (mt-10) REVERT: A 1280 MET cc_start: 0.6331 (pmm) cc_final: 0.6131 (pmm) REVERT: A 1310 LYS cc_start: 0.6677 (tttp) cc_final: 0.6407 (tptp) REVERT: A 1368 LYS cc_start: 0.8299 (mmtp) cc_final: 0.7662 (mmmt) REVERT: A 1385 MET cc_start: 0.6342 (tmm) cc_final: 0.5408 (mmp) REVERT: B 2 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.5220 (m-80) REVERT: B 5 ASN cc_start: 0.7229 (m-40) cc_final: 0.6837 (m-40) outliers start: 14 outliers final: 7 residues processed: 165 average time/residue: 0.1141 time to fit residues: 25.5490 Evaluate side-chains 131 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 1209 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 7 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 ASN A 805 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.157933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.119260 restraints weight = 11447.569| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.99 r_work: 0.3119 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9689 Z= 0.144 Angle : 0.531 8.468 13136 Z= 0.277 Chirality : 0.040 0.155 1524 Planarity : 0.003 0.039 1640 Dihedral : 4.130 44.776 1293 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.53 % Allowed : 10.05 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1188 helix: 1.76 (0.18), residues: 762 sheet: -0.31 (0.55), residues: 75 loop : -1.98 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 633 TYR 0.013 0.001 TYR A1032 PHE 0.017 0.001 PHE A1098 TRP 0.011 0.001 TRP A 223 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9687) covalent geometry : angle 0.53071 (13136) hydrogen bonds : bond 0.05710 ( 559) hydrogen bonds : angle 3.97051 ( 1647) Misc. bond : bond 0.00024 ( 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 152 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.390 Fit side-chains REVERT: A 228 MET cc_start: 0.8726 (mmt) cc_final: 0.8463 (mmm) REVERT: A 239 THR cc_start: 0.8181 (m) cc_final: 0.7770 (p) REVERT: A 246 LYS cc_start: 0.8152 (mttt) cc_final: 0.7577 (tppt) REVERT: A 485 MET cc_start: 0.6505 (ttp) cc_final: 0.6048 (mmt) REVERT: A 503 LYS cc_start: 0.7208 (tttm) cc_final: 0.6801 (ptmt) REVERT: A 505 MET cc_start: 0.7925 (mmm) cc_final: 0.7606 (mmm) REVERT: A 534 GLU cc_start: 0.7901 (tt0) cc_final: 0.7523 (mt-10) REVERT: A 617 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7292 (ttm110) REVERT: A 647 LYS cc_start: 0.7973 (mttt) cc_final: 0.7673 (mtmm) REVERT: A 695 MET cc_start: 0.8690 (mtp) cc_final: 0.8473 (mtp) REVERT: A 725 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7307 (t0) REVERT: A 751 GLU cc_start: 0.7502 (tp30) cc_final: 0.7265 (mt-10) REVERT: A 758 ARG cc_start: 0.7541 (mtm-85) cc_final: 0.7127 (mtm-85) REVERT: A 764 LYS cc_start: 0.7481 (tptt) cc_final: 0.7163 (mtpp) REVERT: A 784 CYS cc_start: 0.8571 (t) cc_final: 0.8096 (t) REVERT: A 808 GLU cc_start: 0.8100 (tt0) cc_final: 0.7851 (tm-30) REVERT: A 819 ASN cc_start: 0.7285 (m-40) cc_final: 0.6932 (t0) REVERT: A 1080 ASP cc_start: 0.7983 (t70) cc_final: 0.7549 (m-30) REVERT: A 1113 MET cc_start: 0.7746 (mtp) cc_final: 0.7264 (mmm) REVERT: A 1176 GLN cc_start: 0.7881 (tp40) cc_final: 0.7212 (mt0) REVERT: A 1235 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: A 1252 GLU cc_start: 0.7609 (tp30) cc_final: 0.7076 (mt-10) REVERT: A 1265 GLU cc_start: 0.8396 (tp30) cc_final: 0.8194 (tp30) REVERT: A 1368 LYS cc_start: 0.8323 (mmtp) cc_final: 0.7704 (mmmt) REVERT: A 1385 MET cc_start: 0.6465 (tmm) cc_final: 0.5535 (mmp) REVERT: A 1491 MET cc_start: 0.7266 (tpp) cc_final: 0.6975 (tpp) REVERT: A 1492 ASP cc_start: 0.7019 (t0) cc_final: 0.6691 (p0) REVERT: B 11 GLU cc_start: 0.8835 (mp0) cc_final: 0.8570 (mp0) outliers start: 16 outliers final: 10 residues processed: 151 average time/residue: 0.1043 time to fit residues: 21.6227 Evaluate side-chains 135 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 THR 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 725 ASN 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 62 optimal weight: 0.0000 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 ASN A 774 GLN A1474 GLN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.161405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124554 restraints weight = 11526.629| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.11 r_work: 0.3248 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9689 Z= 0.119 Angle : 0.506 7.056 13136 Z= 0.262 Chirality : 0.038 0.144 1524 Planarity : 0.003 0.041 1640 Dihedral : 3.952 43.539 1293 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.53 % Allowed : 11.87 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.25), residues: 1188 helix: 2.02 (0.19), residues: 761 sheet: 0.04 (0.55), residues: 80 loop : -1.88 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.013 0.001 TYR A1032 PHE 0.015 0.001 PHE A 558 TRP 0.010 0.001 TRP A1197 HIS 0.004 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9687) covalent geometry : angle 0.50573 (13136) hydrogen bonds : bond 0.05001 ( 559) hydrogen bonds : angle 3.80780 ( 1647) Misc. bond : bond 0.00025 ( 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 154 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.278 Fit side-chains REVERT: A 239 THR cc_start: 0.8279 (m) cc_final: 0.7909 (p) REVERT: A 246 LYS cc_start: 0.8233 (mttt) cc_final: 0.7799 (tppt) REVERT: A 485 MET cc_start: 0.6743 (ttp) cc_final: 0.6401 (mmt) REVERT: A 503 LYS cc_start: 0.7477 (tttm) cc_final: 0.7084 (ptmt) REVERT: A 534 GLU cc_start: 0.7960 (tt0) cc_final: 0.7662 (mt-10) REVERT: A 617 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7825 (ttm110) REVERT: A 647 LYS cc_start: 0.8205 (mttt) cc_final: 0.7985 (mtmm) REVERT: A 656 ASN cc_start: 0.7246 (t0) cc_final: 0.6812 (t0) REVERT: A 695 MET cc_start: 0.8663 (mtp) cc_final: 0.8420 (mtp) REVERT: A 725 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7612 (t0) REVERT: A 758 ARG cc_start: 0.7688 (mtm-85) cc_final: 0.7296 (mtm-85) REVERT: A 764 LYS cc_start: 0.7602 (tptt) cc_final: 0.7317 (mtpp) REVERT: A 784 CYS cc_start: 0.8599 (t) cc_final: 0.8210 (t) REVERT: A 1080 ASP cc_start: 0.8100 (t70) cc_final: 0.7684 (m-30) REVERT: A 1113 MET cc_start: 0.7880 (mtp) cc_final: 0.7497 (mmm) REVERT: A 1176 GLN cc_start: 0.8154 (tp40) cc_final: 0.7568 (mt0) REVERT: A 1235 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: A 1252 GLU cc_start: 0.7900 (tp30) cc_final: 0.7399 (mt-10) REVERT: A 1368 LYS cc_start: 0.8292 (mmtp) cc_final: 0.7657 (mmmt) REVERT: A 1385 MET cc_start: 0.6577 (tmm) cc_final: 0.5703 (mmp) REVERT: A 1491 MET cc_start: 0.7364 (tpp) cc_final: 0.7039 (tpp) REVERT: B 11 GLU cc_start: 0.8840 (mp0) cc_final: 0.8581 (mp0) outliers start: 16 outliers final: 8 residues processed: 151 average time/residue: 0.1032 time to fit residues: 21.5990 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 : 0.308 ------------------------------------------------------------------------------- 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 701 HIS Chi-restraints excluded: chain A residue 725 ASN 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 1382 SER Chi-restraints excluded: chain A residue 1474 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 107 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.158018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119600 restraints weight = 11595.820| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.00 r_work: 0.3141 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3453 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= 0.136 Angle : 0.518 8.982 13136 Z= 0.268 Chirality : 0.039 0.144 1524 Planarity : 0.003 0.043 1640 Dihedral : 3.923 43.304 1293 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.72 % Allowed : 12.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.25), residues: 1188 helix: 2.10 (0.19), residues: 760 sheet: 0.21 (0.56), residues: 80 loop : -1.80 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 633 TYR 0.014 0.001 TYR A1032 PHE 0.015 0.001 PHE A1098 TRP 0.009 0.001 TRP A1197 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9687) covalent geometry : angle 0.51798 (13136) hydrogen bonds : bond 0.05093 ( 559) hydrogen bonds : angle 3.79635 ( 1647) Misc. bond : bond 0.00027 ( 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 149 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.443 Fit side-chains REVERT: A 239 THR cc_start: 0.8205 (m) cc_final: 0.7832 (p) REVERT: A 246 LYS cc_start: 0.8142 (mttt) cc_final: 0.7625 (tppt) REVERT: A 485 MET cc_start: 0.6482 (ttp) cc_final: 0.6085 (mmt) REVERT: A 503 LYS cc_start: 0.7140 (tttm) cc_final: 0.6760 (ptmt) REVERT: A 534 GLU cc_start: 0.7784 (tt0) cc_final: 0.7423 (mt-10) REVERT: A 617 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7518 (ttm110) REVERT: A 647 LYS cc_start: 0.8074 (mttt) cc_final: 0.7800 (mtmm) REVERT: A 656 ASN cc_start: 0.7236 (t0) cc_final: 0.6791 (t0) REVERT: A 758 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7155 (mtm-85) REVERT: A 764 LYS cc_start: 0.7634 (tptt) cc_final: 0.7301 (mtpp) REVERT: A 784 CYS cc_start: 0.8593 (t) cc_final: 0.8137 (t) REVERT: A 819 ASN cc_start: 0.7396 (m-40) cc_final: 0.7062 (t0) REVERT: A 1029 VAL cc_start: 0.7885 (t) cc_final: 0.7567 (p) REVERT: A 1080 ASP cc_start: 0.7992 (t70) cc_final: 0.7547 (m-30) REVERT: A 1113 MET cc_start: 0.7835 (mtp) cc_final: 0.7333 (mmm) REVERT: A 1176 GLN cc_start: 0.8004 (tp40) cc_final: 0.7404 (mt0) REVERT: A 1235 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7353 (m-80) REVERT: A 1368 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7469 (mmmt) REVERT: A 1385 MET cc_start: 0.6527 (tmm) cc_final: 0.5599 (mmp) REVERT: A 1446 LYS cc_start: 0.6084 (tppt) cc_final: 0.4830 (tttp) REVERT: A 1454 GLU cc_start: 0.4020 (tt0) cc_final: 0.3748 (pt0) REVERT: A 1491 MET cc_start: 0.7263 (tpp) cc_final: 0.6885 (tpp) REVERT: B 11 GLU cc_start: 0.8871 (mp0) cc_final: 0.8578 (mp0) outliers start: 18 outliers final: 12 residues processed: 143 average time/residue: 0.1043 time to fit residues: 20.7301 Evaluate side-chains 132 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 514 VAL Chi-restraints excluded: chain A residue 652 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 1377 VAL Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain B residue 5 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.157432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119156 restraints weight = 11593.824| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.99 r_work: 0.3132 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3665 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= 0.136 Angle : 0.520 8.403 13136 Z= 0.268 Chirality : 0.039 0.144 1524 Planarity : 0.003 0.043 1640 Dihedral : 3.900 42.754 1293 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.72 % Allowed : 12.73 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1188 helix: 2.19 (0.19), residues: 756 sheet: 0.34 (0.57), residues: 80 loop : -1.79 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 593 TYR 0.014 0.001 TYR A1032 PHE 0.014 0.001 PHE A1098 TRP 0.014 0.001 TRP A1507 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9687) covalent geometry : angle 0.51983 (13136) hydrogen bonds : bond 0.05050 ( 559) hydrogen bonds : angle 3.77905 ( 1647) Misc. bond : bond 0.00017 ( 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: 18 poor density : 129 time to evaluate : 0.367 Fit side-chains REVERT: A 239 THR cc_start: 0.8208 (m) cc_final: 0.7845 (p) REVERT: A 246 LYS cc_start: 0.8152 (mttt) cc_final: 0.7565 (tppt) REVERT: A 485 MET cc_start: 0.6449 (ttp) cc_final: 0.6019 (mmt) REVERT: A 503 LYS cc_start: 0.7166 (tttm) cc_final: 0.6831 (ptmt) REVERT: A 534 GLU cc_start: 0.7651 (tt0) cc_final: 0.7295 (mt-10) REVERT: A 617 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7506 (ttm110) REVERT: A 647 LYS cc_start: 0.8153 (mttt) cc_final: 0.7882 (mtmm) REVERT: A 656 ASN cc_start: 0.7257 (t0) cc_final: 0.6810 (t0) REVERT: A 758 ARG cc_start: 0.7565 (mtm-85) cc_final: 0.7246 (mtm-85) REVERT: A 764 LYS cc_start: 0.7747 (tptt) cc_final: 0.7431 (mtpp) REVERT: A 819 ASN cc_start: 0.7409 (m-40) cc_final: 0.7104 (t0) REVERT: A 1080 ASP cc_start: 0.8004 (t70) cc_final: 0.7555 (m-30) REVERT: A 1113 MET cc_start: 0.7810 (mtp) cc_final: 0.7311 (mmm) REVERT: A 1176 GLN cc_start: 0.8069 (tp40) cc_final: 0.7330 (mt0) REVERT: A 1235 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: A 1368 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7399 (mmmt) REVERT: A 1385 MET cc_start: 0.6602 (tmm) cc_final: 0.5628 (mmp) REVERT: A 1446 LYS cc_start: 0.6091 (tppt) cc_final: 0.5269 (tttp) REVERT: A 1454 GLU cc_start: 0.3759 (tt0) cc_final: 0.3487 (pt0) REVERT: A 1491 MET cc_start: 0.7355 (tpp) cc_final: 0.6920 (tpp) REVERT: B 11 GLU cc_start: 0.8868 (mp0) cc_final: 0.8581 (mp0) outliers start: 18 outliers final: 14 residues processed: 140 average time/residue: 0.1076 time to fit residues: 20.7213 Evaluate side-chains 138 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 514 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS 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 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 51 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.122093 restraints weight = 11589.923| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.00 r_work: 0.3151 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9689 Z= 0.125 Angle : 0.509 8.262 13136 Z= 0.263 Chirality : 0.039 0.143 1524 Planarity : 0.003 0.043 1640 Dihedral : 3.823 42.234 1293 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.01 % Allowed : 13.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.25), residues: 1188 helix: 2.26 (0.19), residues: 756 sheet: 0.43 (0.57), residues: 80 loop : -1.78 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.014 0.001 TYR A1032 PHE 0.014 0.001 PHE A1098 TRP 0.014 0.001 TRP A1507 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9687) covalent geometry : angle 0.50853 (13136) hydrogen bonds : bond 0.04845 ( 559) hydrogen bonds : angle 3.72868 ( 1647) Misc. bond : bond 0.00018 ( 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 148 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.354 Fit side-chains REVERT: A 239 THR cc_start: 0.8172 (m) cc_final: 0.7788 (p) REVERT: A 246 LYS cc_start: 0.8100 (mttt) cc_final: 0.7468 (tppt) REVERT: A 485 MET cc_start: 0.6350 (ttp) cc_final: 0.5940 (mmt) REVERT: A 503 LYS cc_start: 0.7097 (tttm) cc_final: 0.6749 (ptmt) REVERT: A 534 GLU cc_start: 0.7503 (tt0) cc_final: 0.7201 (mt-10) REVERT: A 617 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7354 (ttm110) REVERT: A 647 LYS cc_start: 0.8107 (mttt) cc_final: 0.7831 (mtmm) REVERT: A 656 ASN cc_start: 0.7230 (t0) cc_final: 0.6843 (t0) REVERT: A 731 GLN cc_start: 0.7874 (pm20) cc_final: 0.7502 (pm20) REVERT: A 758 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7268 (mtm-85) REVERT: A 764 LYS cc_start: 0.7706 (tptt) cc_final: 0.7354 (mtpp) REVERT: A 784 CYS cc_start: 0.8599 (t) cc_final: 0.8176 (t) REVERT: A 819 ASN cc_start: 0.7423 (m-40) cc_final: 0.7046 (t0) REVERT: A 1080 ASP cc_start: 0.7973 (t70) cc_final: 0.7512 (m-30) REVERT: A 1113 MET cc_start: 0.7766 (mtp) cc_final: 0.7212 (mmm) REVERT: A 1176 GLN cc_start: 0.7957 (tp40) cc_final: 0.7270 (mt0) REVERT: A 1235 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: A 1368 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7340 (mmmt) REVERT: A 1385 MET cc_start: 0.6595 (tmm) cc_final: 0.5612 (mmp) REVERT: A 1446 LYS cc_start: 0.6102 (tppt) cc_final: 0.5392 (tttp) REVERT: A 1454 GLU cc_start: 0.3777 (tt0) cc_final: 0.3574 (pt0) REVERT: A 1474 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6420 (mm110) REVERT: A 1491 MET cc_start: 0.7341 (tpp) cc_final: 0.6917 (tpp) REVERT: B 11 GLU cc_start: 0.8854 (mp0) cc_final: 0.8557 (mp0) outliers start: 21 outliers final: 13 residues processed: 139 average time/residue: 0.0990 time to fit residues: 19.1287 Evaluate side-chains 138 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 514 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS 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 Chi-restraints excluded: chain A residue 1474 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 10 optimal weight: 0.0970 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 GLN A1474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.158676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120809 restraints weight = 11557.945| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.00 r_work: 0.3156 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9689 Z= 0.116 Angle : 0.500 8.144 13136 Z= 0.257 Chirality : 0.038 0.143 1524 Planarity : 0.003 0.042 1640 Dihedral : 3.753 41.749 1293 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.72 % Allowed : 13.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.25), residues: 1188 helix: 2.35 (0.19), residues: 756 sheet: 0.50 (0.58), residues: 80 loop : -1.74 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 233 TYR 0.013 0.001 TYR A1032 PHE 0.013 0.001 PHE A 558 TRP 0.015 0.001 TRP A1507 HIS 0.003 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9687) covalent geometry : angle 0.50010 (13136) hydrogen bonds : bond 0.04654 ( 559) hydrogen bonds : angle 3.66007 ( 1647) Misc. bond : bond 0.00014 ( 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 145 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 239 THR cc_start: 0.8264 (m) cc_final: 0.7883 (p) REVERT: A 485 MET cc_start: 0.6466 (ttp) cc_final: 0.6071 (mmt) REVERT: A 503 LYS cc_start: 0.7208 (tttm) cc_final: 0.6874 (ptmt) REVERT: A 534 GLU cc_start: 0.7534 (tt0) cc_final: 0.7253 (mt-10) REVERT: A 617 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7483 (ttm110) REVERT: A 647 LYS cc_start: 0.8138 (mttt) cc_final: 0.7881 (mtmm) REVERT: A 656 ASN cc_start: 0.7221 (t0) cc_final: 0.6827 (t0) REVERT: A 731 GLN cc_start: 0.7909 (pm20) cc_final: 0.7521 (pm20) REVERT: A 758 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7356 (mtm-85) REVERT: A 764 LYS cc_start: 0.7655 (tptt) cc_final: 0.7370 (mtpp) REVERT: A 784 CYS cc_start: 0.8668 (t) cc_final: 0.8330 (t) REVERT: A 819 ASN cc_start: 0.7372 (m-40) cc_final: 0.7031 (t0) REVERT: A 1080 ASP cc_start: 0.8031 (t70) cc_final: 0.7574 (m-30) REVERT: A 1113 MET cc_start: 0.7801 (mtp) cc_final: 0.7283 (mmm) REVERT: A 1176 GLN cc_start: 0.8066 (tp40) cc_final: 0.7393 (mt0) REVERT: A 1235 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: A 1368 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7395 (mmmt) REVERT: A 1385 MET cc_start: 0.6684 (tmm) cc_final: 0.5724 (mmp) REVERT: A 1446 LYS cc_start: 0.5981 (tppt) cc_final: 0.5413 (tttp) REVERT: A 1491 MET cc_start: 0.7262 (tpp) cc_final: 0.6844 (tpp) REVERT: B 11 GLU cc_start: 0.8862 (mp0) cc_final: 0.8586 (mp0) outliers start: 18 outliers final: 15 residues processed: 139 average time/residue: 0.1038 time to fit residues: 20.0846 Evaluate side-chains 139 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 514 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 1032 TYR 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 Chi-restraints excluded: chain A residue 1305 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123564 restraints weight = 11605.722| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.99 r_work: 0.3136 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3914 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 : 0.520 9.659 13136 Z= 0.268 Chirality : 0.039 0.160 1524 Planarity : 0.003 0.043 1640 Dihedral : 3.748 41.591 1293 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.91 % Allowed : 13.68 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.25), residues: 1188 helix: 2.33 (0.19), residues: 756 sheet: 0.50 (0.58), residues: 80 loop : -1.73 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.014 0.001 TYR A1032 PHE 0.013 0.001 PHE A 558 TRP 0.016 0.001 TRP A1507 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9687) covalent geometry : angle 0.51965 (13136) hydrogen bonds : bond 0.04824 ( 559) hydrogen bonds : angle 3.68150 ( 1647) 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 146 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.340 Fit side-chains REVERT: A 239 THR cc_start: 0.8242 (m) cc_final: 0.7981 (p) REVERT: A 246 LYS cc_start: 0.8086 (mttt) cc_final: 0.7493 (tppt) REVERT: A 485 MET cc_start: 0.6388 (ttp) cc_final: 0.5998 (mmt) REVERT: A 503 LYS cc_start: 0.7118 (tttm) cc_final: 0.6783 (ptmt) REVERT: A 534 GLU cc_start: 0.7468 (tt0) cc_final: 0.7186 (mt-10) REVERT: A 617 ARG cc_start: 0.8003 (ttp80) cc_final: 0.7392 (ttm110) REVERT: A 647 LYS cc_start: 0.8115 (mttt) cc_final: 0.7802 (mtmm) REVERT: A 656 ASN cc_start: 0.7221 (t0) cc_final: 0.6827 (t0) REVERT: A 731 GLN cc_start: 0.7891 (pm20) cc_final: 0.7470 (pm20) REVERT: A 758 ARG cc_start: 0.7630 (mtm-85) cc_final: 0.7290 (mtm-85) REVERT: A 764 LYS cc_start: 0.7623 (tptt) cc_final: 0.7372 (mtpp) REVERT: A 784 CYS cc_start: 0.8520 (t) cc_final: 0.8126 (t) REVERT: A 819 ASN cc_start: 0.7478 (m-40) cc_final: 0.7201 (t0) REVERT: A 1080 ASP cc_start: 0.7987 (t70) cc_final: 0.7528 (m-30) REVERT: A 1113 MET cc_start: 0.7785 (mtp) cc_final: 0.7236 (mmm) REVERT: A 1176 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7348 (mt0) REVERT: A 1235 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: A 1368 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7321 (mmmt) REVERT: A 1385 MET cc_start: 0.6655 (tmm) cc_final: 0.5684 (mmp) REVERT: A 1446 LYS cc_start: 0.5982 (tppt) cc_final: 0.5505 (tttp) REVERT: A 1491 MET cc_start: 0.7250 (tpp) cc_final: 0.6826 (tpp) REVERT: B 11 GLU cc_start: 0.8847 (mp0) cc_final: 0.8556 (mp0) outliers start: 20 outliers final: 15 residues processed: 139 average time/residue: 0.0993 time to fit residues: 19.2927 Evaluate side-chains 140 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 514 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS 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 1209 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 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 63 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.0010 chunk 74 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 0.0570 chunk 4 optimal weight: 0.6980 overall best weight: 0.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 725 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122933 restraints weight = 11521.298| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.01 r_work: 0.3157 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9689 Z= 0.115 Angle : 0.509 10.161 13136 Z= 0.263 Chirality : 0.039 0.287 1524 Planarity : 0.003 0.042 1640 Dihedral : 3.664 40.823 1293 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.82 % Allowed : 13.68 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.25), residues: 1188 helix: 2.44 (0.19), residues: 757 sheet: 0.50 (0.57), residues: 80 loop : -1.67 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 233 TYR 0.012 0.001 TYR A1032 PHE 0.013 0.001 PHE A 558 TRP 0.018 0.001 TRP A1507 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9687) covalent geometry : angle 0.50914 (13136) hydrogen bonds : bond 0.04537 ( 559) hydrogen bonds : angle 3.67368 ( 1647) Misc. bond : bond 0.00013 ( 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 152 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.289 Fit side-chains REVERT: A 240 ASP cc_start: 0.7707 (t70) cc_final: 0.7504 (t70) REVERT: A 485 MET cc_start: 0.6459 (ttp) cc_final: 0.6061 (mmt) REVERT: A 503 LYS cc_start: 0.7157 (tttm) cc_final: 0.6790 (ptmt) REVERT: A 534 GLU cc_start: 0.7547 (tt0) cc_final: 0.7272 (mt-10) REVERT: A 617 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7433 (ttm110) REVERT: A 647 LYS cc_start: 0.8124 (mttt) cc_final: 0.7805 (mtmm) REVERT: A 656 ASN cc_start: 0.7067 (t0) cc_final: 0.6748 (t0) REVERT: A 725 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7257 (t0) REVERT: A 731 GLN cc_start: 0.7911 (pm20) cc_final: 0.7517 (pm20) REVERT: A 758 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7320 (mtm-85) REVERT: A 764 LYS cc_start: 0.7710 (tptt) cc_final: 0.7401 (mtpp) REVERT: A 784 CYS cc_start: 0.8532 (t) cc_final: 0.8187 (t) REVERT: A 819 ASN cc_start: 0.7386 (m-40) cc_final: 0.7029 (t0) REVERT: A 1080 ASP cc_start: 0.8019 (t70) cc_final: 0.7565 (m-30) REVERT: A 1113 MET cc_start: 0.7789 (mtp) cc_final: 0.7231 (mmm) REVERT: A 1176 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7345 (mt0) REVERT: A 1235 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: A 1252 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6827 (mt-10) REVERT: A 1368 LYS cc_start: 0.8043 (mmtp) cc_final: 0.7340 (mmmt) REVERT: A 1385 MET cc_start: 0.6687 (tmm) cc_final: 0.5730 (mmp) REVERT: A 1474 GLN cc_start: 0.6500 (mp10) cc_final: 0.6161 (pm20) REVERT: A 1491 MET cc_start: 0.7201 (tpp) cc_final: 0.6790 (tpp) REVERT: B 11 GLU cc_start: 0.8833 (mp0) cc_final: 0.8558 (mp0) outliers start: 19 outliers final: 15 residues processed: 146 average time/residue: 0.0929 time to fit residues: 19.2233 Evaluate side-chains 141 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 652 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 725 ASN 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 1209 ILE Chi-restraints excluded: chain A residue 1235 TYR Chi-restraints excluded: chain A residue 1249 MET 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 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 9 optimal weight: 0.0270 chunk 118 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.161259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123543 restraints weight = 11494.868| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.01 r_work: 0.3160 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 9689 Z= 0.164 Angle : 0.844 59.199 13136 Z= 0.488 Chirality : 0.039 0.266 1524 Planarity : 0.003 0.042 1640 Dihedral : 3.690 40.822 1293 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.53 % Allowed : 14.16 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.25), residues: 1188 helix: 2.41 (0.19), residues: 757 sheet: 0.50 (0.57), residues: 80 loop : -1.67 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.013 0.001 TYR A1032 PHE 0.021 0.001 PHE A 651 TRP 0.016 0.001 TRP A1507 HIS 0.007 0.001 HIS A 827 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9687) covalent geometry : angle 0.84354 (13136) hydrogen bonds : bond 0.04612 ( 559) hydrogen bonds : angle 3.71060 ( 1647) Misc. bond : bond 0.00018 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.99 seconds wall clock time: 44 minutes 57.59 seconds (2697.59 seconds total)