Starting phenix.real_space_refine on Fri Sep 11 17:34:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7x7a_33040/09_2026/7x7a_33040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x7a_33040/09_2026/7x7a_33040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x7a_33040/09_2026/7x7a_33040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x7a_33040/09_2026/7x7a_33040.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7x7a_33040/09_2026/7x7a_33040.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7x7a_33040/09_2026/7x7a_33040.cif" model { file = "/net/cci-nas-00/data/ceres_data/7x7a_33040/09_2026/7x7a_33040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x7a_33040/09_2026/7x7a_33040.cif" } resolution = 3.2 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= 1.000 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 33 5.49 5 S 31 5.16 5 C 6436 2.51 5 N 1787 2.21 5 O 1987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10278 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1241, 9585 Classifications: {'peptide': 1241} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 59, 'TRANS': 1181} Chain breaks: 9 Unresolved non-hydrogen bonds: 447 Unresolved non-hydrogen angles: 535 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 17, 'GLN:plan1': 6, 'ASP:plan': 17, 'GLU:plan': 24, 'HIS:plan': 3, 'ARG:plan': 5, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 280 Chain: "C" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 689 Classifications: {'RNAv2': 33} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 2, 'rna3p_pyr': 11} Link IDs: {'rna2p': 19, 'rna3p': 13} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3410 SG CYS A 491 23.351 24.192 106.441 1.00 54.23 S ATOM 3478 SG CYS A 501 24.259 25.068 110.211 1.00 57.67 S ATOM 3492 SG CYS A 503 24.692 21.682 108.296 1.00 51.64 S ATOM 3514 SG CYS A 506 26.916 24.838 107.593 1.00 46.52 S ATOM 665 SG CYS A 88 31.894 31.852 138.464 1.00 76.49 S ATOM 893 SG CYS A 121 31.890 33.286 141.998 1.00 87.60 S ATOM 924 SG CYS A 127 34.614 34.130 139.355 1.00 76.29 S ATOM 948 SG CYS A 130 31.162 35.601 139.046 1.00 70.82 S ATOM 5407 SG CYS A 750 14.724 24.319 76.828 1.00 59.01 S ATOM 5420 SG CYS A 752 17.958 22.901 75.428 1.00 50.96 S ATOM 5442 SG CYS A 755 18.116 25.914 77.759 1.00 45.85 S ATOM 7328 SG CYS A1018 19.474 43.011 44.360 1.00 48.84 S ATOM 7496 SG CYS A1406 17.303 41.977 47.376 1.00 52.75 S ATOM 7547 SG CYS A1414 17.211 40.198 44.065 1.00 45.18 S ATOM 7564 SG CYS A1417 20.453 40.000 46.319 1.00 39.71 S Time building chain proxies: 2.26, per 1000 atoms: 0.22 Number of scatterers: 10278 At special positions: 0 Unit cell: (73.1499, 81.6999, 156.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 31 16.00 P 33 15.00 O 1987 8.00 N 1787 7.00 C 6436 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=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 364.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " Number of angles added : 21 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 32.2% alpha, 24.0% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 28 through 31 Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.633A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 162 through 166 removed outlier: 4.348A pdb=" N ASN A 165 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP A 166 " --> pdb=" O GLU A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 166' Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 270 through 287 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.165A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 339 through 351 Processing helix chain 'A' and resid 354 through 374 removed outlier: 3.683A pdb=" N PHE A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 4.147A pdb=" N ILE A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 509 removed outlier: 3.998A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.865A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 664 Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 723 through 740 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.630A pdb=" N GLY A 859 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 877 removed outlier: 4.380A pdb=" N PHE A 876 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 880 No H-bonds generated for 'chain 'A' and resid 878 through 880' Processing helix chain 'A' and resid 999 through 1015 removed outlier: 3.660A pdb=" N HIS A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1400 through 1404 removed outlier: 3.666A pdb=" N HIS A1404 " --> pdb=" O LYS A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1420 removed outlier: 3.665A pdb=" N LEU A1419 " --> pdb=" O PRO A1415 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A1420 " --> pdb=" O GLY A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 4.060A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1500 removed outlier: 3.725A pdb=" N ILE A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A1498 " --> pdb=" O GLN A1494 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A1499 " --> pdb=" O LEU A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 4.060A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1603 removed outlier: 3.558A pdb=" N LEU A1598 " --> pdb=" O GLY A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.520A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1666 removed outlier: 3.819A pdb=" N LEU A1666 " --> pdb=" O TYR A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1683 removed outlier: 3.842A pdb=" N LYS A1679 " --> pdb=" O LYS A1675 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1683 " --> pdb=" O LYS A1679 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.771A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR A 191 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 178 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG A 193 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG A 176 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TRP A 195 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N SER A 174 " --> pdb=" O TRP A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 46 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.193A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 3.522A pdb=" N PHE A 557 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY A 600 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 removed outlier: 3.522A pdb=" N PHE A 557 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.000A pdb=" N VAL A 432 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE A 460 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 539 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.799A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.799A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.111A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 805 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB6, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AB7, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB8, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.575A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A 956 " --> pdb=" O PHE A1520 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.540A pdb=" N CYS A 956 " --> pdb=" O PHE A1520 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.818A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N GLU A1510 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N TYR A 987 " --> pdb=" O GLU A1510 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A1507 " --> pdb=" O LEU A1456 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A1509 " --> pdb=" O LEU A1454 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1421 through 1422 360 hydrogen bonds defined for protein. 978 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3037 1.34 - 1.46: 1962 1.46 - 1.58: 5471 1.58 - 1.70: 65 1.70 - 1.82: 42 Bond restraints: 10577 Sorted by residual: bond pdb=" C3' U C 5 " pdb=" O3' U C 5 " ideal model delta sigma weight residual 1.415 1.445 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" CB GLU A 291 " pdb=" CG GLU A 291 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CA ASN A1544 " pdb=" CB ASN A1544 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 9.03e-01 bond pdb=" N VAL A 872 " pdb=" CA VAL A 872 " ideal model delta sigma weight residual 1.461 1.472 -0.011 1.23e-02 6.61e+03 8.19e-01 bond pdb=" CB ASN A1544 " pdb=" CG ASN A1544 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.27e-01 ... (remaining 10572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 14037 1.55 - 3.10: 325 3.10 - 4.66: 81 4.66 - 6.21: 29 6.21 - 7.76: 2 Bond angle restraints: 14474 Sorted by residual: angle pdb=" C3' U C 5 " pdb=" O3' U C 5 " pdb=" P U C 6 " ideal model delta sigma weight residual 119.70 125.77 -6.07 1.20e+00 6.94e-01 2.56e+01 angle pdb=" C ASN A 871 " pdb=" N VAL A 872 " pdb=" CA VAL A 872 " ideal model delta sigma weight residual 122.13 129.89 -7.76 1.85e+00 2.92e-01 1.76e+01 angle pdb=" N ILE A 688 " pdb=" CA ILE A 688 " pdb=" C ILE A 688 " ideal model delta sigma weight residual 112.96 109.77 3.19 1.00e+00 1.00e+00 1.02e+01 angle pdb=" C LYS A1543 " pdb=" N ASN A1544 " pdb=" CA ASN A1544 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.07e+00 angle pdb=" O3' A C -2 " pdb=" C3' A C -2 " pdb=" C2' A C -2 " ideal model delta sigma weight residual 113.80 108.69 5.11 2.00e+00 2.50e-01 6.53e+00 ... (remaining 14469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 5961 34.11 - 68.23: 219 68.23 - 102.34: 26 102.34 - 136.45: 0 136.45 - 170.57: 1 Dihedral angle restraints: 6207 sinusoidal: 2663 harmonic: 3544 Sorted by residual: dihedral pdb=" C4' A C -12 " pdb=" C3' A C -12 " pdb=" C2' A C -12 " pdb=" C1' A C -12 " ideal model delta sinusoidal sigma weight residual 36.34 -36.54 72.88 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' A C -13 " pdb=" C3' A C -13 " pdb=" C2' A C -13 " pdb=" C1' A C -13 " ideal model delta sinusoidal sigma weight residual 36.34 -35.95 72.30 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" C4' U C -3 " pdb=" C3' U C -3 " pdb=" C2' U C -3 " pdb=" C1' U C -3 " ideal model delta sinusoidal sigma weight residual 36.34 -35.91 72.25 1 3.10e+00 1.04e-01 6.94e+02 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1374 0.063 - 0.126: 156 0.126 - 0.190: 6 0.190 - 0.253: 45 0.253 - 0.316: 27 Chirality restraints: 1608 Sorted by residual: chirality pdb=" C2' U C 5 " pdb=" C3' U C 5 " pdb=" O2' U C 5 " pdb=" C1' U C 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" P U C 6 " pdb=" OP1 U C 6 " pdb=" OP2 U C 6 " pdb=" O5' U C 6 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C3' A C -2 " pdb=" C4' A C -2 " pdb=" O3' A C -2 " pdb=" C2' A C -2 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1605 not shown) Planarity restraints: 1748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 1 " 0.032 2.00e-02 2.50e+03 1.63e-02 5.96e+00 pdb=" N1 C C 1 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C C 1 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C C 1 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C C 1 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C C 1 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C C 1 " 0.012 2.00e-02 2.50e+03 pdb=" C5 C C 1 " -0.008 2.00e-02 2.50e+03 pdb=" C6 C C 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 813 " -0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 814 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 814 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 814 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C C 2 " -0.020 2.00e-02 2.50e+03 1.02e-02 2.35e+00 pdb=" N1 C C 2 " 0.021 2.00e-02 2.50e+03 pdb=" C2 C C 2 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C C 2 " 0.001 2.00e-02 2.50e+03 pdb=" N3 C C 2 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C C 2 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C C 2 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C C 2 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C C 2 " 0.002 2.00e-02 2.50e+03 ... (remaining 1745 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 234 2.69 - 3.24: 9693 3.24 - 3.79: 15748 3.79 - 4.35: 21480 4.35 - 4.90: 36560 Nonbonded interactions: 83715 Sorted by model distance: nonbonded pdb=" OG SER A 813 " pdb=" OE2 GLU A 995 " model vdw 2.134 3.040 nonbonded pdb=" O GLY A 186 " pdb=" O2' C C -1 " model vdw 2.213 3.040 nonbonded pdb=" O ILE A 531 " pdb=" O2' A C 3 " model vdw 2.229 3.040 nonbonded pdb=" NZ LYS A 804 " pdb=" OD1 ASP A 806 " model vdw 2.252 3.120 nonbonded pdb=" O SER A 494 " pdb=" N2 G C -5 " model vdw 2.264 3.120 ... (remaining 83710 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: 2.330 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.170 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.002 0.032 10593 Z= 0.112 Angle : 0.642 15.527 14495 Z= 0.298 Chirality : 0.066 0.316 1608 Planarity : 0.004 0.057 1748 Dihedral : 17.128 170.566 3935 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.24 (0.25), residues: 1221 helix: 0.83 (0.30), residues: 319 sheet: 0.31 (0.39), residues: 184 loop : -0.74 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1428 TYR 0.011 0.001 TYR A 808 PHE 0.023 0.001 PHE A 731 TRP 0.010 0.001 TRP A 113 HIS 0.009 0.001 HIS A1418 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10577) covalent geometry : angle 0.61178 / 0.30 (14474) hydrogen bonds : bond 0.22285 / 15.09 ( 325) hydrogen bonds : angle 8.13912 / 5.66 ( 978) metal coordination : bond 0.00426 / 0.27 ( 16) metal coordination : angle 5.10935 / 2.72 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.304 Fit side-chains REVERT: A 1648 LEU cc_start: 0.8316 (tt) cc_final: 0.8108 (tt) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0923 time to fit residues: 13.8499 Evaluate side-chains 71 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.0050 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN A 93 GLN A 112 GLN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115149 restraints weight = 12601.597| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.90 r_work: 0.3229 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10593 Z= 0.172 Angle : 1.011 16.556 14495 Z= 0.422 Chirality : 0.107 1.096 1608 Planarity : 0.004 0.037 1748 Dihedral : 12.979 171.597 1731 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 0.83 % Allowed : 8.27 % Favored : 90.90 % 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: -0.13 (0.25), residues: 1221 helix: 1.16 (0.30), residues: 328 sheet: 0.26 (0.40), residues: 172 loop : -0.77 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1528 TYR 0.013 0.001 TYR A1436 PHE 0.019 0.001 PHE A 731 TRP 0.010 0.001 TRP A 113 HIS 0.004 0.001 HIS A 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (10577) covalent geometry : angle 0.99761 / 0.42 (14474) hydrogen bonds : bond 0.04472 / 2.90 ( 325) hydrogen bonds : angle 5.52504 / 3.82 ( 978) metal coordination : bond 0.00495 / 0.32 ( 16) metal coordination : angle 4.37205 / 2.30 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 622 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8243 (mp) outliers start: 8 outliers final: 4 residues processed: 86 average time/residue: 0.0635 time to fit residues: 8.8080 Evaluate side-chains 76 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 946 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111819 restraints weight = 12594.657| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.85 r_work: 0.3193 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10593 Z= 0.203 Angle : 0.843 12.800 14495 Z= 0.369 Chirality : 0.078 0.730 1608 Planarity : 0.004 0.037 1748 Dihedral : 13.223 179.811 1731 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.02 % Rotamer: Outliers : 1.34 % Allowed : 11.79 % Favored : 86.87 % 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: -0.24 (0.24), residues: 1221 helix: 1.28 (0.29), residues: 320 sheet: -0.04 (0.40), residues: 175 loop : -0.87 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1528 TYR 0.015 0.001 TYR A1436 PHE 0.027 0.002 PHE A 731 TRP 0.013 0.001 TRP A 113 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (10577) covalent geometry : angle 0.82361 / 0.37 (14474) hydrogen bonds : bond 0.04094 / 2.68 ( 325) hydrogen bonds : angle 5.02264 / 3.47 ( 978) metal coordination : bond 0.00733 / 0.47 ( 16) metal coordination : angle 4.78390 / 2.44 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 374 THR cc_start: 0.7262 (OUTLIER) cc_final: 0.6972 (p) REVERT: A 622 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8438 (mp) REVERT: A 1006 MET cc_start: 0.8853 (tmm) cc_final: 0.8621 (ttp) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.0816 time to fit residues: 11.0233 Evaluate side-chains 87 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1507 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 52 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113249 restraints weight = 12613.714| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.90 r_work: 0.3205 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10593 Z= 0.157 Angle : 0.765 11.309 14495 Z= 0.338 Chirality : 0.070 0.658 1608 Planarity : 0.004 0.036 1748 Dihedral : 13.008 164.269 1731 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 2.07 % Allowed : 12.51 % Favored : 85.42 % 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: -0.19 (0.24), residues: 1221 helix: 1.31 (0.29), residues: 327 sheet: -0.12 (0.40), residues: 177 loop : -0.82 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 106 TYR 0.014 0.001 TYR A1436 PHE 0.014 0.001 PHE A1520 TRP 0.021 0.001 TRP A 113 HIS 0.003 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (10577) covalent geometry : angle 0.74984 / 0.34 (14474) hydrogen bonds : bond 0.03535 / 2.32 ( 325) hydrogen bonds : angle 4.80739 / 3.32 ( 978) metal coordination : bond 0.00578 / 0.32 ( 16) metal coordination : angle 4.08250 / 2.15 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 622 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 688 ILE cc_start: 0.8651 (pt) cc_final: 0.8442 (mm) REVERT: A 846 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7850 (ttm-80) REVERT: A 939 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.7791 (pt) REVERT: A 1006 MET cc_start: 0.8852 (tmm) cc_final: 0.8610 (ttp) outliers start: 20 outliers final: 9 residues processed: 89 average time/residue: 0.0904 time to fit residues: 12.4380 Evaluate side-chains 84 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 846 ARG Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1419 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 335 GLN A 993 ASN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108787 restraints weight = 12690.215| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.87 r_work: 0.3141 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10593 Z= 0.258 Angle : 0.828 12.903 14495 Z= 0.371 Chirality : 0.074 0.742 1608 Planarity : 0.004 0.038 1748 Dihedral : 13.174 145.198 1731 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.72 % Favored : 93.12 % Rotamer: Outliers : 2.79 % Allowed : 13.24 % Favored : 83.97 % 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: -0.43 (0.24), residues: 1221 helix: 1.20 (0.29), residues: 320 sheet: -0.32 (0.40), residues: 177 loop : -0.97 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 476 TYR 0.018 0.002 TYR A 860 PHE 0.018 0.002 PHE A 731 TRP 0.034 0.001 TRP A 113 HIS 0.005 0.001 HIS A 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.26 (10577) covalent geometry : angle 0.80552 / 0.37 (14474) hydrogen bonds : bond 0.04027 / 2.63 ( 325) hydrogen bonds : angle 4.92822 / 3.40 ( 978) metal coordination : bond 0.00957 / 0.61 ( 16) metal coordination : angle 5.10654 / 2.67 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 374 THR cc_start: 0.7365 (OUTLIER) cc_final: 0.7037 (p) REVERT: A 622 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8477 (mp) REVERT: A 939 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.7822 (pt) REVERT: A 1002 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8635 (tp30) REVERT: A 1463 ARG cc_start: 0.8385 (mtt-85) cc_final: 0.8176 (mtt-85) outliers start: 27 outliers final: 17 residues processed: 98 average time/residue: 0.0992 time to fit residues: 14.4340 Evaluate side-chains 96 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 756 ILE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1507 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 61 optimal weight: 0.0060 chunk 79 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 335 GLN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1544 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114766 restraints weight = 12633.266| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.90 r_work: 0.3229 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10593 Z= 0.123 Angle : 0.702 10.964 14495 Z= 0.313 Chirality : 0.063 0.519 1608 Planarity : 0.004 0.041 1748 Dihedral : 12.923 150.937 1731 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.49 % Favored : 94.35 % Rotamer: Outliers : 1.96 % Allowed : 14.48 % Favored : 83.56 % 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: -0.16 (0.24), residues: 1221 helix: 1.51 (0.29), residues: 320 sheet: -0.19 (0.40), residues: 177 loop : -0.85 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.014 0.001 TYR A1436 PHE 0.013 0.001 PHE A1520 TRP 0.025 0.001 TRP A 113 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10577) covalent geometry : angle 0.68735 / 0.31 (14474) hydrogen bonds : bond 0.03199 / 2.10 ( 325) hydrogen bonds : angle 4.58587 / 3.16 ( 978) metal coordination : bond 0.00463 / 0.30 ( 16) metal coordination : angle 3.84637 / 2.13 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8812 (tpp) cc_final: 0.8468 (tpp) REVERT: A 374 THR cc_start: 0.7233 (OUTLIER) cc_final: 0.6993 (p) REVERT: A 390 TYR cc_start: 0.8115 (m-80) cc_final: 0.7902 (m-80) REVERT: A 622 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8479 (mp) REVERT: A 637 MET cc_start: 0.7359 (ppp) cc_final: 0.6334 (ppp) REVERT: A 788 ASP cc_start: 0.8365 (p0) cc_final: 0.8154 (p0) REVERT: A 939 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.7756 (pt) outliers start: 19 outliers final: 9 residues processed: 92 average time/residue: 0.0851 time to fit residues: 12.0315 Evaluate side-chains 85 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1544 ASN Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 138 ASN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1544 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112288 restraints weight = 12603.701| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.87 r_work: 0.3195 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10593 Z= 0.184 Angle : 0.730 11.270 14495 Z= 0.326 Chirality : 0.065 0.571 1608 Planarity : 0.004 0.042 1748 Dihedral : 12.914 148.830 1731 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.31 % Favored : 93.53 % Rotamer: Outliers : 2.69 % Allowed : 14.48 % Favored : 82.83 % 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: -0.21 (0.24), residues: 1221 helix: 1.58 (0.30), residues: 314 sheet: -0.16 (0.39), residues: 177 loop : -0.93 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 106 TYR 0.015 0.001 TYR A1436 PHE 0.014 0.001 PHE A1520 TRP 0.024 0.001 TRP A 113 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (10577) covalent geometry : angle 0.71336 / 0.33 (14474) hydrogen bonds : bond 0.03469 / 2.29 ( 325) hydrogen bonds : angle 4.61402 / 3.19 ( 978) metal coordination : bond 0.00620 / 0.36 ( 16) metal coordination : angle 4.15547 / 2.22 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.348 Fit side-chains REVERT: A 36 MET cc_start: 0.8849 (tpp) cc_final: 0.8428 (tpp) REVERT: A 138 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7803 (t0) REVERT: A 374 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.7033 (p) REVERT: A 475 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8390 (tp) REVERT: A 622 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8528 (mp) REVERT: A 637 MET cc_start: 0.7421 (ppp) cc_final: 0.6376 (ppp) REVERT: A 788 ASP cc_start: 0.8366 (p0) cc_final: 0.8146 (p0) REVERT: A 939 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.7763 (pt) outliers start: 26 outliers final: 16 residues processed: 93 average time/residue: 0.0796 time to fit residues: 11.1844 Evaluate side-chains 91 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1525 GLU Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 40 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 138 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114578 restraints weight = 12529.156| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.88 r_work: 0.3225 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10593 Z= 0.126 Angle : 0.692 10.642 14495 Z= 0.310 Chirality : 0.062 0.519 1608 Planarity : 0.003 0.042 1748 Dihedral : 12.831 150.251 1731 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.73 % Favored : 94.10 % Rotamer: Outliers : 2.48 % Allowed : 14.68 % Favored : 82.83 % 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: -0.08 (0.24), residues: 1221 helix: 1.69 (0.30), residues: 314 sheet: -0.08 (0.40), residues: 177 loop : -0.85 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 106 TYR 0.016 0.001 TYR A1436 PHE 0.013 0.001 PHE A1520 TRP 0.024 0.001 TRP A 113 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10577) covalent geometry : angle 0.67762 / 0.31 (14474) hydrogen bonds : bond 0.03236 / 2.14 ( 325) hydrogen bonds : angle 4.50702 / 3.12 ( 978) metal coordination : bond 0.00408 / 0.23 ( 16) metal coordination : angle 3.72423 / 2.08 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8778 (tpp) cc_final: 0.8382 (tpp) REVERT: A 286 GLN cc_start: 0.8766 (tp40) cc_final: 0.8437 (tm-30) REVERT: A 374 THR cc_start: 0.7288 (OUTLIER) cc_final: 0.7064 (p) REVERT: A 390 TYR cc_start: 0.8098 (m-80) cc_final: 0.7887 (m-80) REVERT: A 622 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8535 (mp) REVERT: A 637 MET cc_start: 0.7403 (ppp) cc_final: 0.6399 (ppp) REVERT: A 788 ASP cc_start: 0.8338 (p0) cc_final: 0.8130 (p0) REVERT: A 939 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.7744 (pt) outliers start: 24 outliers final: 14 residues processed: 90 average time/residue: 0.0828 time to fit residues: 11.4132 Evaluate side-chains 87 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 105 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.136475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113724 restraints weight = 12577.177| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.93 r_work: 0.3219 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10593 Z= 0.151 Angle : 0.702 10.913 14495 Z= 0.315 Chirality : 0.063 0.538 1608 Planarity : 0.004 0.042 1748 Dihedral : 12.838 149.438 1731 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.22 % Favored : 93.61 % Rotamer: Outliers : 2.38 % Allowed : 14.68 % Favored : 82.94 % 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: -0.10 (0.24), residues: 1221 helix: 1.62 (0.30), residues: 316 sheet: -0.10 (0.39), residues: 177 loop : -0.84 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 476 TYR 0.017 0.001 TYR A1436 PHE 0.013 0.001 PHE A1570 TRP 0.024 0.001 TRP A 113 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10577) covalent geometry : angle 0.68623 / 0.31 (14474) hydrogen bonds : bond 0.03310 / 2.18 ( 325) hydrogen bonds : angle 4.51693 / 3.12 ( 978) metal coordination : bond 0.00508 / 0.29 ( 16) metal coordination : angle 3.91511 / 2.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.8838 (tpp) cc_final: 0.8434 (tpp) REVERT: A 374 THR cc_start: 0.7251 (OUTLIER) cc_final: 0.6989 (p) REVERT: A 622 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 637 MET cc_start: 0.7331 (ppp) cc_final: 0.6290 (ppp) REVERT: A 788 ASP cc_start: 0.8334 (p0) cc_final: 0.8108 (p0) REVERT: A 939 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.7720 (pt) REVERT: A 1002 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8002 (tp30) outliers start: 23 outliers final: 16 residues processed: 87 average time/residue: 0.0845 time to fit residues: 11.3985 Evaluate side-chains 90 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 83 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111076 restraints weight = 12584.241| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.90 r_work: 0.3175 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10593 Z= 0.204 Angle : 0.750 11.730 14495 Z= 0.337 Chirality : 0.066 0.602 1608 Planarity : 0.004 0.042 1748 Dihedral : 12.927 147.180 1731 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.47 % Favored : 93.37 % Rotamer: Outliers : 2.28 % Allowed : 15.20 % Favored : 82.52 % 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: -0.21 (0.24), residues: 1221 helix: 1.51 (0.29), residues: 316 sheet: -0.14 (0.39), residues: 177 loop : -0.91 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 106 TYR 0.018 0.002 TYR A1436 PHE 0.014 0.001 PHE A1520 TRP 0.026 0.001 TRP A 113 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (10577) covalent geometry : angle 0.73258 / 0.34 (14474) hydrogen bonds : bond 0.03590 / 2.36 ( 325) hydrogen bonds : angle 4.64573 / 3.21 ( 978) metal coordination : bond 0.00775 / 0.48 ( 16) metal coordination : angle 4.32979 / 2.27 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8884 (tpp) cc_final: 0.8377 (tpp) REVERT: A 374 THR cc_start: 0.7219 (OUTLIER) cc_final: 0.6923 (p) REVERT: A 622 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8474 (mp) REVERT: A 637 MET cc_start: 0.7345 (ppp) cc_final: 0.6257 (ppp) REVERT: A 788 ASP cc_start: 0.8386 (p0) cc_final: 0.8146 (p0) REVERT: A 939 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.7750 (pt) REVERT: A 1002 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8482 (tp30) outliers start: 22 outliers final: 18 residues processed: 91 average time/residue: 0.0769 time to fit residues: 10.9961 Evaluate side-chains 93 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 939 ILE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1419 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 0.0270 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 1 optimal weight: 0.0870 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 ASN A 112 GLN ** A1449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111243 restraints weight = 12707.218| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.87 r_work: 0.3180 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 10593 Z= 0.195 Angle : 1.003 59.199 14495 Z= 0.523 Chirality : 0.066 0.596 1608 Planarity : 0.004 0.041 1748 Dihedral : 12.927 147.201 1731 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.39 % Favored : 93.45 % Rotamer: Outliers : 2.38 % Allowed : 14.99 % Favored : 82.63 % Cbeta Deviations : 0.09 % 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: -0.21 (0.24), residues: 1221 helix: 1.53 (0.29), residues: 316 sheet: -0.14 (0.39), residues: 177 loop : -0.92 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 476 TYR 0.016 0.001 TYR A1436 PHE 0.014 0.001 PHE A1520 TRP 0.018 0.001 TRP A 113 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (10577) covalent geometry : angle 0.99062 / 0.52 (14474) hydrogen bonds : bond 0.03543 / 2.33 ( 325) hydrogen bonds : angle 4.64598 / 3.21 ( 978) metal coordination : bond 0.00686 / 0.43 ( 16) metal coordination : angle 4.31894 / 2.27 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2405.04 seconds wall clock time: 42 minutes 6.48 seconds (2526.48 seconds total)