Starting phenix.real_space_refine on Fri Jul 3 10:36:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zy5_11550/07_2026/6zy5_11550.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy5_11550/07_2026/6zy5_11550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2026/6zy5_11550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2026/6zy5_11550.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2026/6zy5_11550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2026/6zy5_11550.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2026/6zy5_11550.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2026/6zy5_11550.cif" } resolution = 3.6 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= 0.005 sd= 0.097 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: 5 Type Number sf(0) Gaussians P 56 5.49 5 S 52 5.16 5 C 8418 2.51 5 N 2312 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13504 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "F" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 337 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Chain: "C" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 272 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 6101 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.34, per 1000 atoms: 0.17 Number of scatterers: 13504 At special positions: 0 Unit cell: (103.983, 116.039, 119.053, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 56 15.00 O 2666 8.00 N 2312 7.00 C 8418 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: 1.23 Conformation dependent library (CDL) restraints added in 661.5 milliseconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2848 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 52.2% alpha, 6.4% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'B' and resid 463 through 477 removed outlier: 3.890A pdb=" N THR B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 504 through 515 removed outlier: 4.018A pdb=" N ASN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 531 removed outlier: 3.587A pdb=" N LEU B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 removed outlier: 3.507A pdb=" N SER B 547 " --> pdb=" O ASP B 543 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 removed outlier: 3.576A pdb=" N ARG B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS B 567 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 630 through 635 removed outlier: 3.678A pdb=" N HIS B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 653 removed outlier: 3.758A pdb=" N ALA B 647 " --> pdb=" O PRO B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 679 removed outlier: 3.595A pdb=" N PHE B 668 " --> pdb=" O TRP B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 702 Processing helix chain 'B' and resid 702 through 714 Processing helix chain 'B' and resid 723 through 736 removed outlier: 3.547A pdb=" N VAL B 729 " --> pdb=" O GLY B 725 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 755 Processing helix chain 'B' and resid 760 through 771 removed outlier: 3.775A pdb=" N MET B 766 " --> pdb=" O MET B 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 818 Processing helix chain 'B' and resid 819 through 823 removed outlier: 4.068A pdb=" N ASP B 823 " --> pdb=" O PRO B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 Processing helix chain 'B' and resid 847 through 852 Processing helix chain 'B' and resid 868 through 882 removed outlier: 3.726A pdb=" N ASP B 881 " --> pdb=" O ARG B 877 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 882 " --> pdb=" O ARG B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 945 removed outlier: 4.589A pdb=" N GLU B 941 " --> pdb=" O GLU B 937 " (cutoff:3.500A) Proline residue: B 942 - end of helix removed outlier: 3.778A pdb=" N ASN B 945 " --> pdb=" O GLU B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 984 Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 1014 through 1028 removed outlier: 3.649A pdb=" N ILE B1018 " --> pdb=" O THR B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1061 removed outlier: 4.800A pdb=" N GLY B1039 " --> pdb=" O GLU B1035 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET B1040 " --> pdb=" O TRP B1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY B1042 " --> pdb=" O LEU B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1080 removed outlier: 3.686A pdb=" N ARG B1080 " --> pdb=" O VAL B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1096 Processing helix chain 'B' and resid 1132 through 1136 Processing helix chain 'B' and resid 1137 through 1161 removed outlier: 3.998A pdb=" N GLU B1143 " --> pdb=" O GLU B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1193 removed outlier: 3.696A pdb=" N ALA B1180 " --> pdb=" O GLU B1176 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B1189 " --> pdb=" O GLU B1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.890A pdb=" N THR A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 476 " --> pdb=" O GLY A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 515 removed outlier: 4.019A pdb=" N ASN A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 531 removed outlier: 3.588A pdb=" N LEU A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 removed outlier: 3.508A pdb=" N SER A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.576A pdb=" N ARG A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS A 567 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.678A pdb=" N HIS A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 653 removed outlier: 3.759A pdb=" N ALA A 647 " --> pdb=" O PRO A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 679 removed outlier: 3.596A pdb=" N PHE A 668 " --> pdb=" O TRP A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 702 Processing helix chain 'A' and resid 702 through 714 Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.547A pdb=" N VAL A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 755 Processing helix chain 'A' and resid 760 through 771 removed outlier: 3.773A pdb=" N MET A 766 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 767 " --> pdb=" O SER A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 819 through 823 removed outlier: 4.070A pdb=" N ASP A 823 " --> pdb=" O PRO A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 868 through 882 removed outlier: 3.726A pdb=" N ASP A 881 " --> pdb=" O ARG A 877 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 882 " --> pdb=" O ARG A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 945 removed outlier: 4.587A pdb=" N GLU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Proline residue: A 942 - end of helix removed outlier: 3.779A pdb=" N ASN A 945 " --> pdb=" O GLU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 984 Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 1014 through 1028 removed outlier: 3.649A pdb=" N ILE A1018 " --> pdb=" O THR A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1061 removed outlier: 4.798A pdb=" N GLY A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY A1042 " --> pdb=" O LEU A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1080 removed outlier: 3.686A pdb=" N ARG A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1096 Processing helix chain 'A' and resid 1132 through 1136 Processing helix chain 'A' and resid 1137 through 1161 removed outlier: 3.998A pdb=" N GLU A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1193 removed outlier: 3.696A pdb=" N ALA A1180 " --> pdb=" O GLU A1176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A1189 " --> pdb=" O GLU A1185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 483 through 485 removed outlier: 6.594A pdb=" N ILE B 458 " --> pdb=" O PHE B 484 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU B 459 " --> pdb=" O MET B 539 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 589 removed outlier: 3.551A pdb=" N VAL B 578 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 742 through 743 Processing sheet with id=AA4, first strand: chain 'B' and resid 853 through 856 Processing sheet with id=AA5, first strand: chain 'B' and resid 898 through 901 Processing sheet with id=AA6, first strand: chain 'B' and resid 956 through 959 removed outlier: 6.340A pdb=" N GLU B 912 " --> pdb=" O SER B 924 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS B1203 " --> pdb=" O ILE B 915 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1001 through 1002 removed outlier: 3.622A pdb=" N LEU B1002 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 483 through 485 removed outlier: 6.594A pdb=" N ILE A 458 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 459 " --> pdb=" O MET A 539 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 589 removed outlier: 3.551A pdb=" N VAL A 578 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 742 through 743 Processing sheet with id=AB2, first strand: chain 'A' and resid 853 through 856 Processing sheet with id=AB3, first strand: chain 'A' and resid 898 through 901 Processing sheet with id=AB4, first strand: chain 'A' and resid 956 through 959 removed outlier: 6.342A pdb=" N GLU A 912 " --> pdb=" O SER A 924 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS A1203 " --> pdb=" O ILE A 915 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1001 through 1002 removed outlier: 3.621A pdb=" N LEU A1002 " --> pdb=" O LYS A1010 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2331 1.32 - 1.44: 3733 1.44 - 1.57: 7640 1.57 - 1.69: 112 1.69 - 1.82: 92 Bond restraints: 13908 Sorted by residual: bond pdb=" C LYS B1071 " pdb=" O LYS B1071 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.16e-02 7.43e+03 1.89e+01 bond pdb=" C LYS A1071 " pdb=" O LYS A1071 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.16e-02 7.43e+03 1.88e+01 bond pdb=" C ILE B1074 " pdb=" O ILE B1074 " ideal model delta sigma weight residual 1.237 1.288 -0.051 1.17e-02 7.31e+03 1.87e+01 bond pdb=" C ILE A1074 " pdb=" O ILE A1074 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.17e-02 7.31e+03 1.80e+01 bond pdb=" CA SER B 861 " pdb=" CB SER B 861 " ideal model delta sigma weight residual 1.534 1.469 0.066 1.77e-02 3.19e+03 1.38e+01 ... (remaining 13903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 15370 1.53 - 3.05: 3396 3.05 - 4.58: 230 4.58 - 6.10: 32 6.10 - 7.63: 2 Bond angle restraints: 19030 Sorted by residual: angle pdb=" CA SER A 861 " pdb=" C SER A 861 " pdb=" O SER A 861 " ideal model delta sigma weight residual 121.51 116.15 5.36 1.12e+00 7.97e-01 2.29e+01 angle pdb=" CA SER B 861 " pdb=" C SER B 861 " pdb=" O SER B 861 " ideal model delta sigma weight residual 121.51 116.29 5.22 1.12e+00 7.97e-01 2.17e+01 angle pdb=" N LEU B1166 " pdb=" CA LEU B1166 " pdb=" C LEU B1166 " ideal model delta sigma weight residual 112.23 106.62 5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N LEU A1166 " pdb=" CA LEU A1166 " pdb=" C LEU A1166 " ideal model delta sigma weight residual 112.23 106.63 5.60 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N ILE B1065 " pdb=" CA ILE B1065 " pdb=" C ILE B1065 " ideal model delta sigma weight residual 112.43 108.58 3.85 9.20e-01 1.18e+00 1.75e+01 ... (remaining 19025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.12: 7890 28.12 - 56.24: 307 56.24 - 84.36: 45 84.36 - 112.48: 2 112.48 - 140.60: 2 Dihedral angle restraints: 8246 sinusoidal: 3826 harmonic: 4420 Sorted by residual: dihedral pdb=" C4' DC E 9 " pdb=" C3' DC E 9 " pdb=" O3' DC E 9 " pdb=" P DG E 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.40 140.60 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DC C 9 " pdb=" C3' DC C 9 " pdb=" O3' DC C 9 " pdb=" P DG C 10 " ideal model delta sinusoidal sigma weight residual 220.00 79.49 140.51 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C TYR A 830 " pdb=" N TYR A 830 " pdb=" CA TYR A 830 " pdb=" CB TYR A 830 " ideal model delta harmonic sigma weight residual -122.60 -131.77 9.17 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 8243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1057 0.058 - 0.115: 635 0.115 - 0.173: 308 0.173 - 0.230: 84 0.230 - 0.288: 10 Chirality restraints: 2094 Sorted by residual: chirality pdb=" CA ILE B 915 " pdb=" N ILE B 915 " pdb=" C ILE B 915 " pdb=" CB ILE B 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA ILE A 915 " pdb=" N ILE A 915 " pdb=" C ILE A 915 " pdb=" CB ILE A 915 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ILE A 864 " pdb=" N ILE A 864 " pdb=" C ILE A 864 " pdb=" CB ILE A 864 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2091 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 824 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C HIS B 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS B 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR B 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 824 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C HIS A 824 " 0.040 2.00e-02 2.50e+03 pdb=" O HIS A 824 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 825 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 936 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C LYS A 936 " 0.040 2.00e-02 2.50e+03 pdb=" O LYS A 936 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 937 " -0.014 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1615 2.76 - 3.29: 13178 3.29 - 3.83: 20913 3.83 - 4.36: 25193 4.36 - 4.90: 41052 Nonbonded interactions: 101951 Sorted by model distance: nonbonded pdb=" O6 DG E 13 " pdb=" O13 EVP F 101 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLN B1094 " pdb=" NE2 GLN B1095 " model vdw 2.348 3.120 nonbonded pdb=" OE1 GLN A1094 " pdb=" NE2 GLN A1095 " model vdw 2.348 3.120 nonbonded pdb=" NH2 ARG A 870 " pdb=" OE1 GLU A1182 " model vdw 2.348 3.120 nonbonded pdb=" NH2 ARG B 870 " pdb=" OE1 GLU B1182 " model vdw 2.349 3.120 ... (remaining 101946 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'C' } 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 group one per residue 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: 0.630 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.520 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.011 0.066 13908 Z= 0.779 Angle : 1.162 7.628 19030 Z= 0.871 Chirality : 0.086 0.288 2094 Planarity : 0.007 0.039 2220 Dihedral : 13.991 140.604 5398 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.15 % Allowed : 0.90 % Favored : 98.95 % 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: -0.64 (0.21), residues: 1512 helix: 1.50 (0.19), residues: 678 sheet: -1.37 (0.37), residues: 198 loop : -2.35 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 804 TYR 0.022 0.002 TYR B 830 PHE 0.010 0.002 PHE A 818 TRP 0.011 0.003 TRP B1090 HIS 0.004 0.001 HIS B 986 Details of bonding type rmsd/Z covalent geometry : bond 0.01081 / 0.78 (13908) covalent geometry : angle 1.16181 / 0.87 (19030) hydrogen bonds : bond 0.18509 / 12.78 ( 591) hydrogen bonds : angle 5.96383 / 4.16 ( 1628) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 471 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 498 HIS cc_start: 0.5973 (t70) cc_final: 0.5327 (t-170) REVERT: B 530 THR cc_start: 0.8649 (m) cc_final: 0.8420 (p) REVERT: B 657 GLN cc_start: 0.7537 (mt0) cc_final: 0.7252 (mm-40) REVERT: B 714 SER cc_start: 0.8491 (m) cc_final: 0.8194 (t) REVERT: B 766 MET cc_start: 0.7497 (ttm) cc_final: 0.7254 (ttm) REVERT: B 774 ASN cc_start: 0.8606 (p0) cc_final: 0.8332 (p0) REVERT: B 805 TYR cc_start: 0.7935 (m-10) cc_final: 0.7621 (m-10) REVERT: B 856 ILE cc_start: 0.9163 (mt) cc_final: 0.8945 (mt) REVERT: B 916 LEU cc_start: 0.8902 (mt) cc_final: 0.7892 (tt) REVERT: B 1053 ARG cc_start: 0.6470 (mmm160) cc_final: 0.6143 (ttp80) REVERT: A 498 HIS cc_start: 0.5993 (t70) cc_final: 0.5645 (t-170) REVERT: A 529 LYS cc_start: 0.7905 (tttt) cc_final: 0.7598 (mtpt) REVERT: A 530 THR cc_start: 0.8655 (m) cc_final: 0.8421 (p) REVERT: A 657 GLN cc_start: 0.7518 (mt0) cc_final: 0.7242 (mm-40) REVERT: A 714 SER cc_start: 0.8492 (m) cc_final: 0.8146 (t) REVERT: A 766 MET cc_start: 0.7447 (ttm) cc_final: 0.7180 (ttm) REVERT: A 774 ASN cc_start: 0.8616 (p0) cc_final: 0.8343 (p0) REVERT: A 805 TYR cc_start: 0.7925 (m-10) cc_final: 0.7614 (m-10) REVERT: A 856 ILE cc_start: 0.9244 (mt) cc_final: 0.9040 (mt) REVERT: A 916 LEU cc_start: 0.8896 (mt) cc_final: 0.7880 (tt) REVERT: A 1053 ARG cc_start: 0.6472 (mmm160) cc_final: 0.6138 (ttp80) outliers start: 2 outliers final: 2 residues processed: 473 average time/residue: 0.1257 time to fit residues: 81.5402 Evaluate side-chains 223 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain A residue 1078 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 558 HIS B 634 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 ASN A 558 HIS A 634 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.154509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.133323 restraints weight = 20811.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.136722 restraints weight = 11934.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.139133 restraints weight = 8085.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.140795 restraints weight = 6078.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141801 restraints weight = 4940.064| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13908 Z= 0.165 Angle : 0.609 8.773 19030 Z= 0.332 Chirality : 0.043 0.232 2094 Planarity : 0.005 0.056 2220 Dihedral : 18.394 137.959 2286 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.26 % Allowed : 11.14 % 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: -0.42 (0.22), residues: 1512 helix: 1.64 (0.20), residues: 682 sheet: -1.29 (0.38), residues: 196 loop : -2.19 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1146 TYR 0.015 0.002 TYR A 957 PHE 0.021 0.002 PHE B 807 TRP 0.013 0.002 TRP B1036 HIS 0.008 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (13908) covalent geometry : angle 0.60911 / 0.33 (19030) hydrogen bonds : bond 0.04608 / 3.04 ( 591) hydrogen bonds : angle 4.14401 / 2.92 ( 1628) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 503 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 712 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 774 ASN cc_start: 0.8477 (p0) cc_final: 0.8251 (p0) REVERT: B 1053 ARG cc_start: 0.6871 (mmm160) cc_final: 0.6356 (ttp80) REVERT: A 712 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7348 (mt-10) REVERT: A 774 ASN cc_start: 0.8492 (p0) cc_final: 0.8276 (p0) REVERT: A 1053 ARG cc_start: 0.6868 (mmm160) cc_final: 0.6356 (ttp80) outliers start: 30 outliers final: 21 residues processed: 235 average time/residue: 0.1143 time to fit residues: 38.3936 Evaluate side-chains 170 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 608 TRP Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 821 LYS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1173 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 105 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 116 optimal weight: 0.0030 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129761 restraints weight = 21056.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.133109 restraints weight = 12205.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.135475 restraints weight = 8308.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137171 restraints weight = 6297.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138341 restraints weight = 5135.753| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13908 Z= 0.129 Angle : 0.531 5.863 19030 Z= 0.289 Chirality : 0.040 0.162 2094 Planarity : 0.004 0.035 2220 Dihedral : 18.366 139.526 2282 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.66 % Allowed : 13.55 % Favored : 84.79 % 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 (0.23), residues: 1512 helix: 1.91 (0.20), residues: 678 sheet: -1.25 (0.39), residues: 196 loop : -2.07 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 982 TYR 0.014 0.001 TYR A 957 PHE 0.010 0.001 PHE A 706 TRP 0.010 0.002 TRP B 664 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (13908) covalent geometry : angle 0.53135 / 0.29 (19030) hydrogen bonds : bond 0.04015 / 2.63 ( 591) hydrogen bonds : angle 3.93557 / 2.77 ( 1628) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 503 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 774 ASN cc_start: 0.8548 (p0) cc_final: 0.8251 (p0) REVERT: B 1053 ARG cc_start: 0.6997 (mmm160) cc_final: 0.6355 (ttp80) REVERT: B 1153 GLN cc_start: 0.6575 (mm-40) cc_final: 0.6192 (mt0) REVERT: A 503 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7754 (mm-30) REVERT: A 712 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7268 (mt-10) REVERT: A 774 ASN cc_start: 0.8565 (p0) cc_final: 0.8271 (p0) REVERT: A 1053 ARG cc_start: 0.6994 (mmm160) cc_final: 0.6345 (ttp80) REVERT: A 1153 GLN cc_start: 0.6579 (mm-40) cc_final: 0.6209 (mt0) outliers start: 22 outliers final: 12 residues processed: 183 average time/residue: 0.1001 time to fit residues: 27.4839 Evaluate side-chains 148 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 992 GLN Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 0.0370 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 559 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.145466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123358 restraints weight = 20977.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126646 restraints weight = 12156.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.129002 restraints weight = 8318.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130618 restraints weight = 6314.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131744 restraints weight = 5191.480| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13908 Z= 0.145 Angle : 0.552 6.656 19030 Z= 0.299 Chirality : 0.042 0.173 2094 Planarity : 0.004 0.055 2220 Dihedral : 18.412 138.572 2282 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.71 % Allowed : 13.55 % Favored : 83.73 % 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: -0.07 (0.23), residues: 1512 helix: 1.92 (0.20), residues: 680 sheet: -1.43 (0.39), residues: 200 loop : -1.85 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1026 TYR 0.018 0.002 TYR B1029 PHE 0.011 0.001 PHE A 706 TRP 0.010 0.002 TRP B 840 HIS 0.006 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13908) covalent geometry : angle 0.55174 / 0.30 (19030) hydrogen bonds : bond 0.03839 / 2.55 ( 591) hydrogen bonds : angle 3.82685 / 2.71 ( 1628) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: B 503 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7692 (mm-30) REVERT: B 755 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8514 (t) REVERT: B 774 ASN cc_start: 0.8405 (p0) cc_final: 0.8145 (p0) REVERT: B 1153 GLN cc_start: 0.6411 (mm-40) cc_final: 0.6207 (mt0) REVERT: A 493 VAL cc_start: 0.9497 (m) cc_final: 0.9222 (p) REVERT: A 503 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 755 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8518 (t) REVERT: A 774 ASN cc_start: 0.8420 (p0) cc_final: 0.8162 (p0) outliers start: 36 outliers final: 22 residues processed: 176 average time/residue: 0.0866 time to fit residues: 23.6552 Evaluate side-chains 146 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 821 LYS Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 508 ASN ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN A 508 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123588 restraints weight = 20895.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126802 restraints weight = 12249.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.129099 restraints weight = 8400.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.130646 restraints weight = 6387.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131697 restraints weight = 5271.484| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13908 Z= 0.123 Angle : 0.507 6.486 19030 Z= 0.276 Chirality : 0.039 0.148 2094 Planarity : 0.003 0.031 2220 Dihedral : 18.411 137.960 2282 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.73 % Allowed : 14.61 % Favored : 83.66 % 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: 0.15 (0.23), residues: 1512 helix: 2.16 (0.20), residues: 676 sheet: -1.39 (0.39), residues: 200 loop : -1.76 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 568 TYR 0.012 0.001 TYR A 957 PHE 0.012 0.001 PHE B 706 TRP 0.011 0.001 TRP B 840 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (13908) covalent geometry : angle 0.50697 / 0.28 (19030) hydrogen bonds : bond 0.03482 / 2.32 ( 591) hydrogen bonds : angle 3.74552 / 2.64 ( 1628) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 493 VAL cc_start: 0.9434 (m) cc_final: 0.9138 (p) REVERT: B 503 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 774 ASN cc_start: 0.8404 (p0) cc_final: 0.8142 (p0) REVERT: A 493 VAL cc_start: 0.9478 (m) cc_final: 0.9226 (p) REVERT: A 503 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7671 (mm-30) REVERT: A 774 ASN cc_start: 0.8407 (p0) cc_final: 0.8145 (p0) outliers start: 23 outliers final: 14 residues processed: 152 average time/residue: 0.0872 time to fit residues: 20.8252 Evaluate side-chains 139 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 116 optimal weight: 0.0970 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1153 GLN ** A 746 GLN ** 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 = 0.3805 r_free = 0.3805 target = 0.143135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121410 restraints weight = 20871.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124562 restraints weight = 12321.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126766 restraints weight = 8488.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128304 restraints weight = 6507.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.129357 restraints weight = 5377.796| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13908 Z= 0.128 Angle : 0.502 5.588 19030 Z= 0.274 Chirality : 0.040 0.162 2094 Planarity : 0.003 0.029 2220 Dihedral : 18.452 137.337 2282 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.88 % Allowed : 15.06 % Favored : 83.06 % 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: 0.30 (0.23), residues: 1512 helix: 2.22 (0.20), residues: 676 sheet: -1.14 (0.43), residues: 166 loop : -1.65 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 568 TYR 0.012 0.001 TYR A 957 PHE 0.010 0.001 PHE A 706 TRP 0.011 0.001 TRP A 931 HIS 0.006 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (13908) covalent geometry : angle 0.50159 / 0.27 (19030) hydrogen bonds : bond 0.03519 / 2.36 ( 591) hydrogen bonds : angle 3.72894 / 2.63 ( 1628) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.350 Fit side-chains REVERT: B 493 VAL cc_start: 0.9465 (m) cc_final: 0.9191 (p) REVERT: B 774 ASN cc_start: 0.8525 (p0) cc_final: 0.8293 (p0) REVERT: B 864 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8216 (mt) REVERT: B 917 ASN cc_start: 0.7428 (m-40) cc_final: 0.6520 (p0) REVERT: B 1134 TRP cc_start: 0.7463 (m100) cc_final: 0.7053 (m100) REVERT: A 493 VAL cc_start: 0.9536 (m) cc_final: 0.9298 (p) REVERT: A 503 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7991 (mm-30) REVERT: A 774 ASN cc_start: 0.8533 (p0) cc_final: 0.8305 (p0) REVERT: A 864 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8214 (mt) REVERT: A 1134 TRP cc_start: 0.7547 (m100) cc_final: 0.7107 (m100) outliers start: 25 outliers final: 18 residues processed: 153 average time/residue: 0.0724 time to fit residues: 17.8523 Evaluate side-chains 138 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 CYS Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 34 optimal weight: 0.0040 chunk 146 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 153 optimal weight: 0.7980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.121952 restraints weight = 20779.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.125151 restraints weight = 12241.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127406 restraints weight = 8412.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.128951 restraints weight = 6455.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.130089 restraints weight = 5331.169| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13908 Z= 0.111 Angle : 0.497 8.782 19030 Z= 0.270 Chirality : 0.039 0.149 2094 Planarity : 0.003 0.029 2220 Dihedral : 18.445 137.342 2282 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.20 % Allowed : 16.64 % Favored : 82.15 % 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: 0.40 (0.23), residues: 1512 helix: 2.32 (0.20), residues: 676 sheet: -1.15 (0.43), residues: 166 loop : -1.62 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1026 TYR 0.013 0.001 TYR A 695 PHE 0.011 0.001 PHE B 706 TRP 0.013 0.001 TRP A 931 HIS 0.004 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (13908) covalent geometry : angle 0.49682 / 0.27 (19030) hydrogen bonds : bond 0.03341 / 2.23 ( 591) hydrogen bonds : angle 3.66465 / 2.58 ( 1628) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: B 493 VAL cc_start: 0.9457 (m) cc_final: 0.9194 (p) REVERT: B 503 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7903 (mm-30) REVERT: B 774 ASN cc_start: 0.8505 (p0) cc_final: 0.8291 (p0) REVERT: B 864 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8123 (mt) REVERT: B 917 ASN cc_start: 0.7214 (m-40) cc_final: 0.6461 (p0) REVERT: B 1134 TRP cc_start: 0.7490 (m100) cc_final: 0.7096 (m100) REVERT: A 493 VAL cc_start: 0.9506 (m) cc_final: 0.9290 (p) REVERT: A 774 ASN cc_start: 0.8504 (p0) cc_final: 0.8293 (p0) REVERT: A 864 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8182 (mt) REVERT: A 1134 TRP cc_start: 0.7512 (m100) cc_final: 0.7101 (m100) outliers start: 16 outliers final: 12 residues processed: 146 average time/residue: 0.0775 time to fit residues: 18.3408 Evaluate side-chains 135 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1145 CYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 153 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.111011 restraints weight = 23376.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114539 restraints weight = 12778.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.116906 restraints weight = 8470.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118569 restraints weight = 6387.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119670 restraints weight = 5237.697| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13908 Z= 0.177 Angle : 0.597 6.815 19030 Z= 0.317 Chirality : 0.043 0.186 2094 Planarity : 0.004 0.036 2220 Dihedral : 18.576 136.624 2282 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.73 % Allowed : 16.87 % Favored : 81.40 % 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: 0.11 (0.23), residues: 1512 helix: 2.05 (0.20), residues: 688 sheet: -1.62 (0.36), residues: 220 loop : -1.65 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 487 TYR 0.015 0.002 TYR A1029 PHE 0.014 0.002 PHE B 790 TRP 0.027 0.002 TRP A 931 HIS 0.006 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (13908) covalent geometry : angle 0.59725 / 0.32 (19030) hydrogen bonds : bond 0.04343 / 2.86 ( 591) hydrogen bonds : angle 3.89681 / 2.73 ( 1628) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.377 Fit side-chains REVERT: B 506 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: B 774 ASN cc_start: 0.8821 (p0) cc_final: 0.8585 (p0) REVERT: B 864 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8197 (mt) REVERT: B 1134 TRP cc_start: 0.7646 (m100) cc_final: 0.7090 (m100) REVERT: A 506 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6732 (pm20) REVERT: A 774 ASN cc_start: 0.8829 (p0) cc_final: 0.8596 (p0) REVERT: A 864 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8187 (mt) REVERT: A 1134 TRP cc_start: 0.7661 (m100) cc_final: 0.7104 (m100) outliers start: 23 outliers final: 12 residues processed: 147 average time/residue: 0.0803 time to fit residues: 18.8761 Evaluate side-chains 131 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 CYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112255 restraints weight = 23351.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115789 restraints weight = 12710.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118177 restraints weight = 8386.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119763 restraints weight = 6307.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120883 restraints weight = 5204.857| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13908 Z= 0.132 Angle : 0.538 8.873 19030 Z= 0.290 Chirality : 0.040 0.196 2094 Planarity : 0.004 0.045 2220 Dihedral : 18.560 136.590 2282 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.51 % Allowed : 17.77 % Favored : 80.72 % 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 (0.23), residues: 1512 helix: 2.12 (0.20), residues: 688 sheet: -1.63 (0.36), residues: 220 loop : -1.65 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 568 TYR 0.011 0.001 TYR A 957 PHE 0.011 0.001 PHE B 706 TRP 0.026 0.001 TRP A 931 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13908) covalent geometry : angle 0.53756 / 0.29 (19030) hydrogen bonds : bond 0.03815 / 2.54 ( 591) hydrogen bonds : angle 3.75690 / 2.64 ( 1628) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.497 Fit side-chains REVERT: B 506 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: B 774 ASN cc_start: 0.8823 (p0) cc_final: 0.8593 (p0) REVERT: B 864 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8212 (mt) REVERT: B 1134 TRP cc_start: 0.7595 (m100) cc_final: 0.7092 (m100) REVERT: A 503 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 506 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: A 774 ASN cc_start: 0.8822 (p0) cc_final: 0.8600 (p0) REVERT: A 864 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8202 (mt) REVERT: A 1134 TRP cc_start: 0.7608 (m100) cc_final: 0.7099 (m100) outliers start: 20 outliers final: 14 residues processed: 140 average time/residue: 0.0807 time to fit residues: 18.8010 Evaluate side-chains 135 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 CYS Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 125 optimal weight: 0.0470 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113169 restraints weight = 23242.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116688 restraints weight = 12613.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119012 restraints weight = 8347.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.120562 restraints weight = 6328.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121722 restraints weight = 5231.796| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13908 Z= 0.116 Angle : 0.506 9.619 19030 Z= 0.274 Chirality : 0.039 0.157 2094 Planarity : 0.004 0.035 2220 Dihedral : 18.521 136.688 2282 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.36 % Allowed : 17.92 % Favored : 80.72 % 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: 0.36 (0.23), residues: 1512 helix: 2.25 (0.20), residues: 686 sheet: -1.43 (0.38), residues: 210 loop : -1.54 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 736 TYR 0.010 0.001 TYR A 957 PHE 0.011 0.001 PHE A 706 TRP 0.026 0.001 TRP A 931 HIS 0.005 0.000 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (13908) covalent geometry : angle 0.50617 / 0.27 (19030) hydrogen bonds : bond 0.03544 / 2.37 ( 591) hydrogen bonds : angle 3.66685 / 2.58 ( 1628) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.506 Fit side-chains REVERT: B 506 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6835 (pm20) REVERT: B 864 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 880 MET cc_start: 0.7940 (ttm) cc_final: 0.7335 (mtt) REVERT: B 917 ASN cc_start: 0.7620 (m-40) cc_final: 0.6469 (p0) REVERT: B 1134 TRP cc_start: 0.7580 (m100) cc_final: 0.7081 (m100) REVERT: A 503 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7989 (mm-30) REVERT: A 506 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: A 669 MET cc_start: 0.8584 (mtp) cc_final: 0.8221 (mtp) REVERT: A 864 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8052 (mt) REVERT: A 880 MET cc_start: 0.7946 (ttm) cc_final: 0.7340 (mtt) REVERT: A 1134 TRP cc_start: 0.7598 (m100) cc_final: 0.7095 (m100) outliers start: 18 outliers final: 14 residues processed: 140 average time/residue: 0.0756 time to fit residues: 17.7051 Evaluate side-chains 134 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 CYS Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 93 optimal weight: 4.9990 chunk 131 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.136513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112243 restraints weight = 23341.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115734 restraints weight = 12662.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118088 restraints weight = 8354.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119674 restraints weight = 6300.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120760 restraints weight = 5188.223| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13908 Z= 0.131 Angle : 0.527 9.812 19030 Z= 0.284 Chirality : 0.040 0.158 2094 Planarity : 0.004 0.038 2220 Dihedral : 18.536 136.525 2282 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.73 % Allowed : 18.00 % Favored : 80.27 % 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: 0.37 (0.23), residues: 1512 helix: 2.25 (0.20), residues: 686 sheet: -1.37 (0.38), residues: 208 loop : -1.55 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1026 TYR 0.010 0.001 TYR A1012 PHE 0.010 0.001 PHE B 653 TRP 0.028 0.001 TRP B 931 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (13908) covalent geometry : angle 0.52730 / 0.28 (19030) hydrogen bonds : bond 0.03681 / 2.45 ( 591) hydrogen bonds : angle 3.69026 / 2.60 ( 1628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1770.71 seconds wall clock time: 31 minutes 20.81 seconds (1880.81 seconds total)