Starting phenix.real_space_refine on Sat Sep 12 04:23:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zy5_11550/09_2026/6zy5_11550.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy5_11550/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6zy5_11550/09_2026/6zy5_11550.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zy5_11550/09_2026/6zy5_11550.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zy5_11550/09_2026/6zy5_11550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy5_11550/09_2026/6zy5_11550.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy5_11550/09_2026/6zy5_11550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy5_11550/09_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-2.2.1-6174/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: 3.09, per 1000 atoms: 0.23 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: 1.08 Conformation dependent library (CDL) restraints added in 628.3 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: 1.42 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: 2.59 Time building geometry restraints manager: 1.47 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: 0.03 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.130 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.540 ------------------------------------------------------------------------------- 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 1.16229 / 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 : 0.462 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: 0.8196 (t) REVERT: B 766 MET cc_start: 0.7497 (ttm) cc_final: 0.7252 (ttm) REVERT: B 774 ASN cc_start: 0.8606 (p0) cc_final: 0.8331 (p0) REVERT: B 805 TYR cc_start: 0.7935 (m-10) cc_final: 0.7620 (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: 0.6142 (ttp80) REVERT: A 498 HIS cc_start: 0.5993 (t70) cc_final: 0.5644 (t-170) REVERT: A 529 LYS cc_start: 0.7905 (tttt) cc_final: 0.7597 (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: 0.8148 (t) REVERT: A 766 MET cc_start: 0.7447 (ttm) cc_final: 0.7177 (ttm) REVERT: A 774 ASN cc_start: 0.8616 (p0) cc_final: 0.8342 (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: 0.6137 (ttp80) outliers start: 2 outliers final: 2 residues processed: 473 average time/residue: 0.1343 time to fit residues: 86.7027 Evaluate side-chains 225 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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: 20.0000 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 = 0.3944 r_free = 0.3944 target = 0.155012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133854 restraints weight = 20839.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.137305 restraints weight = 11948.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139668 restraints weight = 8060.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.141314 restraints weight = 6070.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142465 restraints weight = 4940.112| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13908 Z= 0.160 Angle : 0.606 9.088 19030 Z= 0.327 Chirality : 0.043 0.233 2094 Planarity : 0.005 0.056 2220 Dihedral : 18.388 137.321 2286 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.03 % Allowed : 11.30 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.22), residues: 1512 helix: 1.66 (0.20), residues: 680 sheet: -1.32 (0.38), residues: 196 loop : -2.19 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 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 0.00342 / 0.16 (13908) covalent geometry : angle 0.60573 / 0.33 (19030) hydrogen bonds : bond 0.04783 / 3.15 ( 591) hydrogen bonds : angle 4.14745 / 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 235 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 503 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 712 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7345 (mt-10) REVERT: B 774 ASN cc_start: 0.8474 (p0) cc_final: 0.8250 (p0) REVERT: B 1053 ARG cc_start: 0.6860 (mmm160) cc_final: 0.6365 (ttp80) REVERT: A 712 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7351 (mt-10) REVERT: A 774 ASN cc_start: 0.8488 (p0) cc_final: 0.8271 (p0) REVERT: A 1053 ARG cc_start: 0.6857 (mmm160) cc_final: 0.6364 (ttp80) outliers start: 27 outliers final: 18 residues processed: 232 average time/residue: 0.1159 time to fit residues: 38.5360 Evaluate side-chains 168 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 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 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: 0.9990 chunk 151 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 559 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN A 559 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.145137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123456 restraints weight = 21218.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126692 restraints weight = 12360.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128954 restraints weight = 8460.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130548 restraints weight = 6456.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131656 restraints weight = 5307.205| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13908 Z= 0.183 Angle : 0.608 7.790 19030 Z= 0.326 Chirality : 0.043 0.184 2094 Planarity : 0.004 0.032 2220 Dihedral : 18.494 139.551 2282 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: -0.31 (0.22), residues: 1512 helix: 1.77 (0.20), residues: 680 sheet: -1.38 (0.38), residues: 196 loop : -2.11 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 982 TYR 0.019 0.002 TYR B1012 PHE 0.012 0.002 PHE A 706 TRP 0.012 0.002 TRP B 664 HIS 0.006 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (13908) covalent geometry : angle 0.60756 / 0.33 (19030) hydrogen bonds : bond 0.04618 / 3.03 ( 591) hydrogen bonds : angle 4.09422 / 2.88 ( 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 200 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 493 VAL cc_start: 0.9456 (m) cc_final: 0.9189 (p) REVERT: B 503 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7679 (mm-30) REVERT: B 774 ASN cc_start: 0.8596 (p0) cc_final: 0.8283 (p0) REVERT: B 922 GLU cc_start: 0.7024 (tt0) cc_final: 0.6817 (pt0) REVERT: B 1153 GLN cc_start: 0.6565 (mm-40) cc_final: 0.6122 (mt0) REVERT: A 493 VAL cc_start: 0.9475 (m) cc_final: 0.9250 (p) REVERT: A 503 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 774 ASN cc_start: 0.8604 (p0) cc_final: 0.8298 (p0) REVERT: A 1153 GLN cc_start: 0.6573 (mm-40) cc_final: 0.6330 (mt0) outliers start: 36 outliers final: 18 residues processed: 195 average time/residue: 0.0983 time to fit residues: 28.8088 Evaluate side-chains 146 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 821 LYS 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 B residue 1128 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 821 LYS Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 508 ASN ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121142 restraints weight = 20989.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124310 restraints weight = 12313.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126572 restraints weight = 8446.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127991 restraints weight = 6445.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129157 restraints weight = 5357.025| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13908 Z= 0.159 Angle : 0.563 7.309 19030 Z= 0.303 Chirality : 0.041 0.181 2094 Planarity : 0.004 0.035 2220 Dihedral : 18.454 137.678 2282 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.33 % Allowed : 14.53 % Favored : 83.13 % 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: -0.17 (0.22), residues: 1512 helix: 1.87 (0.20), residues: 676 sheet: -1.46 (0.38), residues: 198 loop : -1.93 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 982 TYR 0.016 0.002 TYR B1029 PHE 0.011 0.001 PHE B 706 TRP 0.013 0.002 TRP B 840 HIS 0.006 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (13908) covalent geometry : angle 0.56309 / 0.30 (19030) hydrogen bonds : bond 0.04088 / 2.73 ( 591) hydrogen bonds : angle 3.93888 / 2.78 ( 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 164 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.448 Fit side-chains REVERT: B 493 VAL cc_start: 0.9459 (m) cc_final: 0.9243 (p) REVERT: B 503 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7690 (mm-30) REVERT: B 751 VAL cc_start: 0.9142 (t) cc_final: 0.8894 (t) REVERT: B 774 ASN cc_start: 0.8575 (p0) cc_final: 0.8318 (p0) REVERT: A 503 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7696 (mm-30) REVERT: A 751 VAL cc_start: 0.9144 (t) cc_final: 0.8894 (t) REVERT: A 774 ASN cc_start: 0.8577 (p0) cc_final: 0.8329 (p0) outliers start: 31 outliers final: 20 residues processed: 160 average time/residue: 0.0901 time to fit residues: 22.7716 Evaluate side-chains 147 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 768 ILE 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 940 LEU 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 768 ILE Chi-restraints excluded: chain A residue 821 LYS 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=3.50 ------------------------------------------------------------------------------- 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: 2.9990 chunk 127 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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** A1153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.117821 restraints weight = 21128.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120892 restraints weight = 12447.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123103 restraints weight = 8623.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124605 restraints weight = 6626.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125507 restraints weight = 5495.501| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13908 Z= 0.173 Angle : 0.570 7.236 19030 Z= 0.308 Chirality : 0.042 0.175 2094 Planarity : 0.004 0.035 2220 Dihedral : 18.551 137.032 2282 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.48 % Allowed : 14.68 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.23), residues: 1512 helix: 1.98 (0.20), residues: 676 sheet: -1.51 (0.38), residues: 198 loop : -1.83 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 633 TYR 0.014 0.002 TYR B1012 PHE 0.012 0.001 PHE A 706 TRP 0.012 0.002 TRP A 931 HIS 0.005 0.001 HIS A 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (13908) covalent geometry : angle 0.57022 / 0.31 (19030) hydrogen bonds : bond 0.04198 / 2.78 ( 591) hydrogen bonds : angle 3.92671 / 2.76 ( 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 169 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.345 Fit side-chains REVERT: B 493 VAL cc_start: 0.9455 (m) cc_final: 0.9253 (p) REVERT: B 506 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6810 (pt0) REVERT: B 774 ASN cc_start: 0.8622 (p0) cc_final: 0.8409 (p0) REVERT: B 802 SER cc_start: 0.7790 (t) cc_final: 0.7576 (m) REVERT: B 1030 TYR cc_start: 0.6578 (OUTLIER) cc_final: 0.6370 (m-80) REVERT: B 1134 TRP cc_start: 0.7635 (m100) cc_final: 0.7188 (m100) REVERT: A 506 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6861 (pt0) REVERT: A 751 VAL cc_start: 0.9026 (t) cc_final: 0.8791 (t) REVERT: A 774 ASN cc_start: 0.8615 (p0) cc_final: 0.8414 (p0) REVERT: A 802 SER cc_start: 0.7842 (t) cc_final: 0.7639 (m) REVERT: A 864 ILE cc_start: 0.8608 (mm) cc_final: 0.8322 (mt) REVERT: A 1134 TRP cc_start: 0.7644 (m100) cc_final: 0.7188 (m100) outliers start: 33 outliers final: 21 residues processed: 162 average time/residue: 0.0802 time to fit residues: 20.9604 Evaluate side-chains 145 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 541 ASP Chi-restraints excluded: chain B residue 821 LYS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1040 MET Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 455 CYS 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 541 ASP Chi-restraints excluded: chain A residue 821 LYS 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: 5.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 102 optimal weight: 0.7980 chunk 14 optimal weight: 0.0020 chunk 116 optimal weight: 0.4980 chunk 68 optimal weight: 0.2980 chunk 123 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.3204 ------------------------------------------------------------------------------- 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 906 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.142586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120797 restraints weight = 20944.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123943 restraints weight = 12367.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.126206 restraints weight = 8520.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127775 restraints weight = 6516.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.128850 restraints weight = 5374.051| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13908 Z= 0.101 Angle : 0.498 7.164 19030 Z= 0.272 Chirality : 0.039 0.155 2094 Planarity : 0.003 0.031 2220 Dihedral : 18.458 137.233 2282 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.51 % Allowed : 16.19 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1512 helix: 2.25 (0.20), residues: 676 sheet: -1.43 (0.38), residues: 198 loop : -1.69 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1026 TYR 0.011 0.001 TYR A 957 PHE 0.013 0.001 PHE B 706 TRP 0.013 0.001 TRP B 931 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (13908) covalent geometry : angle 0.49793 / 0.27 (19030) hydrogen bonds : bond 0.03421 / 2.30 ( 591) hydrogen bonds : angle 3.68776 / 2.61 ( 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 153 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.487 Fit side-chains REVERT: B 493 VAL cc_start: 0.9463 (m) cc_final: 0.9246 (p) REVERT: B 503 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7954 (mm-30) REVERT: B 774 ASN cc_start: 0.8610 (p0) cc_final: 0.8375 (p0) REVERT: B 864 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8148 (mt) REVERT: B 917 ASN cc_start: 0.7423 (m-40) cc_final: 0.6384 (p0) REVERT: B 1134 TRP cc_start: 0.7523 (m100) cc_final: 0.7117 (m100) REVERT: A 751 VAL cc_start: 0.9010 (t) cc_final: 0.8742 (t) REVERT: A 774 ASN cc_start: 0.8606 (p0) cc_final: 0.8380 (p0) REVERT: A 864 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8160 (mt) REVERT: A 917 ASN cc_start: 0.7449 (m-40) cc_final: 0.6384 (p0) REVERT: A 985 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7728 (mp) REVERT: A 1134 TRP cc_start: 0.7538 (m100) cc_final: 0.7119 (m100) outliers start: 20 outliers final: 12 residues processed: 150 average time/residue: 0.0738 time to fit residues: 18.2671 Evaluate side-chains 133 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER 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 528 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 985 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: 0.9990 chunk 59 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 146 optimal weight: 0.0370 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 153 optimal weight: 0.0070 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.141826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.119944 restraints weight = 21109.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.123067 restraints weight = 12549.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125281 restraints weight = 8661.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.126845 restraints weight = 6667.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.127845 restraints weight = 5505.869| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5050 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= 0.107 Angle : 0.496 7.746 19030 Z= 0.270 Chirality : 0.039 0.152 2094 Planarity : 0.004 0.037 2220 Dihedral : 18.456 137.251 2282 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.66 % Allowed : 17.02 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.23), residues: 1512 helix: 2.16 (0.20), residues: 688 sheet: -1.45 (0.38), residues: 200 loop : -1.65 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1026 TYR 0.014 0.001 TYR A1030 PHE 0.012 0.001 PHE A 706 TRP 0.014 0.001 TRP B 931 HIS 0.005 0.000 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (13908) covalent geometry : angle 0.49585 / 0.27 (19030) hydrogen bonds : bond 0.03344 / 2.24 ( 591) hydrogen bonds : angle 3.65058 / 2.57 ( 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 141 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.472 Fit side-chains REVERT: B 493 VAL cc_start: 0.9458 (m) cc_final: 0.9242 (p) REVERT: B 503 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7970 (mm-30) REVERT: B 754 MET cc_start: 0.7408 (ttm) cc_final: 0.7107 (mtp) REVERT: B 864 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 917 ASN cc_start: 0.7479 (m-40) cc_final: 0.6344 (p0) REVERT: B 1030 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.6417 (m-80) REVERT: B 1134 TRP cc_start: 0.7532 (m100) cc_final: 0.7140 (m100) REVERT: A 503 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 864 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8169 (mt) REVERT: A 917 ASN cc_start: 0.7479 (m-40) cc_final: 0.6357 (p0) REVERT: A 985 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7689 (mp) REVERT: A 1134 TRP cc_start: 0.7546 (m100) cc_final: 0.7146 (m100) outliers start: 22 outliers final: 15 residues processed: 139 average time/residue: 0.0851 time to fit residues: 19.4531 Evaluate side-chains 134 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER 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 1030 TYR Chi-restraints excluded: chain B residue 1040 MET 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 493 VAL Chi-restraints excluded: chain A residue 528 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 985 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: 4.9990 chunk 78 optimal weight: 10.0000 chunk 24 optimal weight: 0.2980 chunk 128 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 153 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 779 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110994 restraints weight = 23464.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114399 restraints weight = 12825.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116768 restraints weight = 8547.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118377 restraints weight = 6452.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119432 restraints weight = 5316.784| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13908 Z= 0.165 Angle : 0.579 9.265 19030 Z= 0.307 Chirality : 0.042 0.184 2094 Planarity : 0.004 0.032 2220 Dihedral : 18.533 136.667 2282 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.88 % Allowed : 17.77 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.23), residues: 1512 helix: 2.00 (0.20), residues: 698 sheet: -1.53 (0.38), residues: 210 loop : -1.72 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 487 TYR 0.015 0.001 TYR A1030 PHE 0.010 0.002 PHE B 706 TRP 0.027 0.002 TRP A 931 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (13908) covalent geometry : angle 0.57878 / 0.31 (19030) hydrogen bonds : bond 0.04140 / 2.74 ( 591) hydrogen bonds : angle 3.84480 / 2.70 ( 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 144 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.415 Fit side-chains REVERT: B 506 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6831 (pm20) REVERT: B 864 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8394 (mt) REVERT: B 1030 TYR cc_start: 0.7695 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: B 1134 TRP cc_start: 0.7645 (m100) cc_final: 0.7125 (m100) REVERT: A 503 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7918 (mm-30) REVERT: A 506 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: A 753 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 864 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8379 (mt) REVERT: A 985 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 1134 TRP cc_start: 0.7651 (m100) cc_final: 0.7127 (m100) outliers start: 25 outliers final: 16 residues processed: 142 average time/residue: 0.0881 time to fit residues: 20.2301 Evaluate side-chains 134 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 940 LEU 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 493 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 528 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 985 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: 0.8980 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 77 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.136452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112116 restraints weight = 23372.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115594 restraints weight = 12628.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.117978 restraints weight = 8383.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119600 restraints weight = 6318.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120591 restraints weight = 5198.861| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13908 Z= 0.116 Angle : 0.526 10.064 19030 Z= 0.281 Chirality : 0.039 0.164 2094 Planarity : 0.004 0.031 2220 Dihedral : 18.500 136.960 2282 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.51 % Allowed : 18.45 % Favored : 80.05 % 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: 2.24 (0.20), residues: 686 sheet: -1.47 (0.38), residues: 208 loop : -1.62 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1026 TYR 0.010 0.001 TYR A 957 PHE 0.012 0.001 PHE A 706 TRP 0.023 0.001 TRP B 931 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (13908) covalent geometry : angle 0.52580 / 0.28 (19030) hydrogen bonds : bond 0.03690 / 2.46 ( 591) hydrogen bonds : angle 3.69564 / 2.60 ( 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 145 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.570 Fit side-chains REVERT: B 753 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8204 (tm-30) REVERT: B 864 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8228 (mt) REVERT: B 915 ILE cc_start: 0.7377 (mt) cc_final: 0.7176 (pt) REVERT: B 1030 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: B 1134 TRP cc_start: 0.7607 (m100) cc_final: 0.7106 (m100) REVERT: A 503 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7886 (mm-30) REVERT: A 506 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6828 (pm20) REVERT: A 572 GLU cc_start: 0.7417 (tt0) cc_final: 0.6779 (tt0) REVERT: A 915 ILE cc_start: 0.7197 (mt) cc_final: 0.6983 (pt) REVERT: A 985 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7421 (mp) REVERT: A 1134 TRP cc_start: 0.7612 (m100) cc_final: 0.7104 (m100) outliers start: 20 outliers final: 16 residues processed: 144 average time/residue: 0.0789 time to fit residues: 18.9422 Evaluate side-chains 140 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 471 SER 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 940 LEU 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 493 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 985 LEU 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: 0.9990 chunk 95 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.136041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111867 restraints weight = 23404.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115314 restraints weight = 12753.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.117647 restraints weight = 8467.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.119226 restraints weight = 6402.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120286 restraints weight = 5296.054| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5532 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= 0.131 Angle : 0.541 9.950 19030 Z= 0.289 Chirality : 0.040 0.161 2094 Planarity : 0.004 0.034 2220 Dihedral : 18.503 137.032 2282 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.73 % Allowed : 18.15 % Favored : 80.12 % 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: 0.27 (0.23), residues: 1512 helix: 2.13 (0.20), residues: 698 sheet: -1.42 (0.38), residues: 208 loop : -1.62 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1026 TYR 0.012 0.001 TYR A1030 PHE 0.010 0.001 PHE A 706 TRP 0.027 0.002 TRP A 931 HIS 0.005 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13908) covalent geometry : angle 0.54053 / 0.29 (19030) hydrogen bonds : bond 0.03764 / 2.50 ( 591) hydrogen bonds : angle 3.70701 / 2.61 ( 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 142 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.481 Fit side-chains REVERT: B 506 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: B 572 GLU cc_start: 0.7515 (tt0) cc_final: 0.6912 (tt0) REVERT: B 753 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8341 (tm-30) REVERT: B 864 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 1030 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.6742 (m-80) REVERT: B 1134 TRP cc_start: 0.7623 (m100) cc_final: 0.7137 (m100) REVERT: A 503 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7900 (mm-30) REVERT: A 506 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: A 572 GLU cc_start: 0.7517 (tt0) cc_final: 0.6876 (tt0) REVERT: A 669 MET cc_start: 0.8710 (mtp) cc_final: 0.8349 (mtp) REVERT: A 864 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8233 (mt) REVERT: A 880 MET cc_start: 0.7974 (ttm) cc_final: 0.7351 (mtt) REVERT: A 985 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7438 (mp) REVERT: A 1134 TRP cc_start: 0.7638 (m100) cc_final: 0.7145 (m100) outliers start: 23 outliers final: 16 residues processed: 141 average time/residue: 0.0824 time to fit residues: 19.0908 Evaluate side-chains 139 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 940 LEU 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 493 VAL Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 528 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 985 LEU 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: 0.3980 chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 75 optimal weight: 0.0040 chunk 86 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.137199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112881 restraints weight = 23376.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116380 restraints weight = 12617.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.118738 restraints weight = 8363.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120372 restraints weight = 6313.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121464 restraints weight = 5188.007| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5603 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= 0.109 Angle : 0.514 9.968 19030 Z= 0.276 Chirality : 0.039 0.159 2094 Planarity : 0.003 0.036 2220 Dihedral : 18.462 137.553 2282 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.58 % Allowed : 18.83 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.23), residues: 1512 helix: 2.38 (0.20), residues: 686 sheet: -1.34 (0.39), residues: 206 loop : -1.52 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1026 TYR 0.011 0.001 TYR A 957 PHE 0.011 0.001 PHE B 706 TRP 0.022 0.001 TRP A 931 HIS 0.004 0.001 HIS B 605 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (13908) covalent geometry : angle 0.51376 / 0.28 (19030) hydrogen bonds : bond 0.03463 / 2.32 ( 591) hydrogen bonds : angle 3.62084 / 2.55 ( 1628) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1859.41 seconds wall clock time: 33 minutes 2.98 seconds (1982.98 seconds total)