Starting phenix.real_space_refine on Thu Jul 31 17:54:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy5_11550/07_2025/6zy5_11550.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy5_11550/07_2025/6zy5_11550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2025/6zy5_11550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2025/6zy5_11550.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2025/6zy5_11550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy5_11550/07_2025/6zy5_11550.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.14, per 1000 atoms: 0.60 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: 3.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.63 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: 4.92 Time building geometry restraints manager: 3.55 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: 15357 1.53 - 3.05: 3411 3.05 - 4.58: 230 4.58 - 6.10: 30 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: 8028 28.12 - 56.24: 307 56.24 - 84.36: 45 84.36 - 112.48: 2 112.48 - 140.60: 2 Dihedral angle restraints: 8384 sinusoidal: 3964 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 8381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1060 0.058 - 0.115: 634 0.115 - 0.173: 308 0.173 - 0.230: 82 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: 0.07 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.690 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 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= 0.776 Angle : 1.165 7.628 19030 Z= 0.866 Chirality : 0.086 0.288 2094 Planarity : 0.007 0.039 2220 Dihedral : 13.851 140.604 5536 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (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 TRP 0.011 0.003 TRP B1090 HIS 0.004 0.001 HIS B 986 PHE 0.010 0.002 PHE A 818 TYR 0.022 0.002 TYR B 830 ARG 0.006 0.001 ARG A 804 Details of bonding type rmsd hydrogen bonds : bond 0.18509 ( 591) hydrogen bonds : angle 5.96383 ( 1628) covalent geometry : bond 0.01086 (13908) covalent geometry : angle 1.16511 (19030) *********************** 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 : 1.407 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: 0.8648 (m) cc_final: 0.8420 (p) REVERT: B 657 GLN cc_start: 0.7537 (mt0) cc_final: 0.7252 (mm-40) REVERT: B 714 SER cc_start: 0.8491 (m) cc_final: 0.8194 (t) REVERT: B 766 MET cc_start: 0.7498 (ttm) cc_final: 0.7254 (ttm) REVERT: B 774 ASN cc_start: 0.8606 (p0) cc_final: 0.8332 (p0) REVERT: B 805 TYR cc_start: 0.7935 (m-10) cc_final: 0.7621 (m-10) REVERT: B 856 ILE cc_start: 0.9163 (mt) cc_final: 0.8945 (mt) REVERT: B 916 LEU cc_start: 0.8902 (mt) cc_final: 0.7892 (tt) REVERT: B 1053 ARG cc_start: 0.6470 (mmm160) cc_final: 0.6143 (ttp80) REVERT: A 498 HIS cc_start: 0.5993 (t70) cc_final: 0.5645 (t-170) REVERT: A 529 LYS cc_start: 0.7905 (tttt) cc_final: 0.7598 (mtpt) REVERT: A 530 THR cc_start: 0.8655 (m) cc_final: 0.8421 (p) REVERT: A 657 GLN cc_start: 0.7518 (mt0) cc_final: 0.7242 (mm-40) REVERT: A 714 SER cc_start: 0.8492 (m) cc_final: 0.8146 (t) REVERT: A 766 MET cc_start: 0.7446 (ttm) cc_final: 0.7180 (ttm) REVERT: A 774 ASN cc_start: 0.8616 (p0) cc_final: 0.8343 (p0) REVERT: A 805 TYR cc_start: 0.7925 (m-10) cc_final: 0.7614 (m-10) REVERT: A 856 ILE cc_start: 0.9244 (mt) cc_final: 0.9040 (mt) REVERT: A 916 LEU cc_start: 0.8896 (mt) cc_final: 0.7880 (tt) REVERT: A 1053 ARG cc_start: 0.6472 (mmm160) cc_final: 0.6138 (ttp80) outliers start: 2 outliers final: 2 residues processed: 473 average time/residue: 0.3481 time to fit residues: 223.8763 Evaluate side-chains 223 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 131 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 HIS B 634 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 ASN A 634 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128911 restraints weight = 20814.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132313 restraints weight = 12081.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134651 restraints weight = 8216.795| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13908 Z= 0.152 Angle : 0.563 5.927 19030 Z= 0.300 Chirality : 0.040 0.169 2094 Planarity : 0.004 0.037 2220 Dihedral : 17.712 136.177 2424 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.26 % Allowed : 11.37 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1512 helix: 1.99 (0.20), residues: 678 sheet: -1.33 (0.39), residues: 196 loop : -2.12 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 664 HIS 0.005 0.001 HIS B 605 PHE 0.014 0.001 PHE B 807 TYR 0.016 0.001 TYR A 957 ARG 0.007 0.001 ARG B1146 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 591) hydrogen bonds : angle 4.00386 ( 1628) covalent geometry : bond 0.00346 (13908) covalent geometry : angle 0.56290 (19030) *********************** 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 244 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 503 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 712 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7339 (mt-10) REVERT: B 737 ASN cc_start: 0.7846 (t0) cc_final: 0.7573 (t0) REVERT: B 774 ASN cc_start: 0.8556 (p0) cc_final: 0.8263 (p0) REVERT: B 1053 ARG cc_start: 0.7067 (mmm160) cc_final: 0.6397 (ttm170) REVERT: B 1153 GLN cc_start: 0.6596 (mm-40) cc_final: 0.6220 (mt0) REVERT: A 503 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 529 LYS cc_start: 0.7603 (tttt) cc_final: 0.7289 (mtpt) REVERT: A 712 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 737 ASN cc_start: 0.7870 (t0) cc_final: 0.7670 (t0) REVERT: A 774 ASN cc_start: 0.8569 (p0) cc_final: 0.8284 (p0) REVERT: A 1053 ARG cc_start: 0.7052 (mmm160) cc_final: 0.6392 (ttm170) REVERT: A 1153 GLN cc_start: 0.6584 (mm-40) cc_final: 0.6217 (mt0) outliers start: 30 outliers final: 20 residues processed: 242 average time/residue: 0.2847 time to fit residues: 99.2591 Evaluate side-chains 175 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 541 ASP Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 821 LYS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1145 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU 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 955 THR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1145 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 65 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 508 ASN B 558 HIS ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 558 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.122294 restraints weight = 20947.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125498 restraints weight = 12266.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127754 restraints weight = 8443.388| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13908 Z= 0.151 Angle : 0.537 5.563 19030 Z= 0.289 Chirality : 0.040 0.158 2094 Planarity : 0.004 0.032 2220 Dihedral : 17.703 135.327 2420 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.24 % Allowed : 12.58 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.23), residues: 1512 helix: 1.97 (0.20), residues: 688 sheet: -1.20 (0.40), residues: 196 loop : -1.97 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 840 HIS 0.006 0.001 HIS B 605 PHE 0.010 0.001 PHE A 706 TYR 0.016 0.001 TYR A 957 ARG 0.004 0.001 ARG B 478 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 591) hydrogen bonds : angle 3.80137 ( 1628) covalent geometry : bond 0.00344 (13908) covalent geometry : angle 0.53662 (19030) *********************** 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 197 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 751 VAL cc_start: 0.9117 (t) cc_final: 0.8901 (t) REVERT: B 755 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8624 (t) REVERT: B 774 ASN cc_start: 0.8482 (p0) cc_final: 0.8251 (p0) REVERT: B 883 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7465 (mt-10) REVERT: B 1153 GLN cc_start: 0.6635 (mm-40) cc_final: 0.6277 (mt0) REVERT: A 503 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7798 (mm-30) REVERT: A 751 VAL cc_start: 0.9113 (t) cc_final: 0.8897 (t) REVERT: A 755 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8632 (t) REVERT: A 774 ASN cc_start: 0.8493 (p0) cc_final: 0.8271 (p0) REVERT: A 883 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7484 (mt-10) REVERT: A 1153 GLN cc_start: 0.6577 (mm-40) cc_final: 0.6282 (mt0) outliers start: 43 outliers final: 19 residues processed: 187 average time/residue: 0.2260 time to fit residues: 64.3167 Evaluate side-chains 160 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 541 ASP Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 825 THR Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 920 THR 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 541 ASP Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 825 THR Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 920 THR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 559 HIS B 674 GLN ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 HIS ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.131874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107672 restraints weight = 23537.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111040 restraints weight = 12813.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113354 restraints weight = 8572.989| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13908 Z= 0.239 Angle : 0.659 7.313 19030 Z= 0.349 Chirality : 0.045 0.147 2094 Planarity : 0.004 0.037 2220 Dihedral : 18.175 133.673 2420 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.33 % Allowed : 14.68 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.22), residues: 1512 helix: 1.48 (0.19), residues: 712 sheet: -1.60 (0.37), residues: 216 loop : -1.88 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 931 HIS 0.006 0.001 HIS B 605 PHE 0.018 0.002 PHE B 790 TYR 0.014 0.002 TYR A 957 ARG 0.004 0.001 ARG B 727 Details of bonding type rmsd hydrogen bonds : bond 0.05309 ( 591) hydrogen bonds : angle 4.29327 ( 1628) covalent geometry : bond 0.00558 (13908) covalent geometry : angle 0.65901 (19030) *********************** 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 185 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.485 Fit side-chains REVERT: B 669 MET cc_start: 0.8656 (mtp) cc_final: 0.8212 (mtp) REVERT: B 751 VAL cc_start: 0.8775 (t) cc_final: 0.8412 (t) REVERT: B 1030 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7693 (m-10) REVERT: B 1153 GLN cc_start: 0.6679 (mm-40) cc_final: 0.6249 (mt0) REVERT: A 526 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5595 (m-30) REVERT: A 529 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7528 (mttp) REVERT: A 669 MET cc_start: 0.8682 (mtp) cc_final: 0.8255 (mtp) REVERT: A 751 VAL cc_start: 0.8782 (t) cc_final: 0.8419 (t) REVERT: A 1030 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: A 1153 GLN cc_start: 0.6684 (mm-40) cc_final: 0.6259 (mt0) outliers start: 31 outliers final: 19 residues processed: 179 average time/residue: 0.2452 time to fit residues: 66.5392 Evaluate side-chains 147 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 541 ASP Chi-restraints excluded: chain B residue 768 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 455 CYS Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1056 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110746 restraints weight = 23319.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114200 restraints weight = 12648.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116570 restraints weight = 8415.047| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13908 Z= 0.132 Angle : 0.535 7.028 19030 Z= 0.285 Chirality : 0.039 0.149 2094 Planarity : 0.004 0.033 2220 Dihedral : 17.985 135.473 2420 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.18 % Allowed : 16.79 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.23), residues: 1512 helix: 1.89 (0.20), residues: 708 sheet: -1.15 (0.39), residues: 184 loop : -1.83 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 931 HIS 0.005 0.001 HIS B 605 PHE 0.011 0.001 PHE B 706 TYR 0.011 0.001 TYR A 957 ARG 0.004 0.000 ARG B1146 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 591) hydrogen bonds : angle 3.84409 ( 1628) covalent geometry : bond 0.00299 (13908) covalent geometry : angle 0.53459 (19030) *********************** 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 188 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.385 Fit side-chains REVERT: B 503 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8111 (mm-30) REVERT: B 506 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: B 572 GLU cc_start: 0.7524 (tt0) cc_final: 0.7063 (tt0) REVERT: B 751 VAL cc_start: 0.8948 (t) cc_final: 0.8674 (t) REVERT: B 1030 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7200 (m-10) REVERT: B 1033 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6588 (tpp80) REVERT: B 1153 GLN cc_start: 0.6511 (mm-40) cc_final: 0.6062 (mt0) REVERT: A 487 ARG cc_start: 0.7017 (tpt170) cc_final: 0.6528 (tpp80) REVERT: A 506 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: A 572 GLU cc_start: 0.7524 (tt0) cc_final: 0.7029 (tt0) REVERT: A 751 VAL cc_start: 0.8960 (t) cc_final: 0.8683 (t) REVERT: A 864 ILE cc_start: 0.8345 (mm) cc_final: 0.8138 (mt) REVERT: A 1030 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7321 (m-10) REVERT: A 1033 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6567 (tpp80) REVERT: A 1153 GLN cc_start: 0.6519 (mm-40) cc_final: 0.6075 (mt0) outliers start: 29 outliers final: 15 residues processed: 181 average time/residue: 0.2257 time to fit residues: 61.9861 Evaluate side-chains 161 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 455 CYS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 845 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1033 ARG 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 70 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 57 optimal weight: 0.0060 chunk 133 optimal weight: 0.0370 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN ** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.137612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113081 restraints weight = 23302.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116603 restraints weight = 12561.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119027 restraints weight = 8282.902| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13908 Z= 0.104 Angle : 0.494 8.359 19030 Z= 0.262 Chirality : 0.037 0.168 2094 Planarity : 0.003 0.033 2220 Dihedral : 17.827 136.716 2420 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.58 % Allowed : 18.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1512 helix: 2.32 (0.20), residues: 688 sheet: -1.12 (0.42), residues: 178 loop : -1.64 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 931 HIS 0.005 0.000 HIS B 605 PHE 0.009 0.001 PHE B 706 TYR 0.009 0.001 TYR A 957 ARG 0.003 0.000 ARG B 568 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 591) hydrogen bonds : angle 3.59362 ( 1628) covalent geometry : bond 0.00226 (13908) covalent geometry : angle 0.49408 (19030) *********************** 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 177 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.384 Fit side-chains REVERT: B 502 MET cc_start: 0.8110 (mmm) cc_final: 0.7900 (mmm) REVERT: B 506 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6715 (pm20) REVERT: B 669 MET cc_start: 0.8695 (mtp) cc_final: 0.8329 (mtp) REVERT: B 751 VAL cc_start: 0.8977 (t) cc_final: 0.8702 (t) REVERT: B 1033 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6684 (tpp80) REVERT: B 1153 GLN cc_start: 0.6683 (mm-40) cc_final: 0.6256 (mt0) REVERT: A 669 MET cc_start: 0.8628 (mtp) cc_final: 0.8229 (mtp) REVERT: A 751 VAL cc_start: 0.8984 (t) cc_final: 0.8710 (t) REVERT: A 1033 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6663 (tpp80) REVERT: A 1153 GLN cc_start: 0.6689 (mm-40) cc_final: 0.6265 (mt0) outliers start: 21 outliers final: 13 residues processed: 174 average time/residue: 0.2443 time to fit residues: 63.0669 Evaluate side-chains 150 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 1033 ARG 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 491 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1033 ARG 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 6 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 40 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3782 r_free = 0.3782 target = 0.136471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112020 restraints weight = 23330.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115467 restraints weight = 12606.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.117816 restraints weight = 8359.376| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13908 Z= 0.121 Angle : 0.508 7.240 19030 Z= 0.270 Chirality : 0.038 0.169 2094 Planarity : 0.003 0.030 2220 Dihedral : 17.841 136.633 2420 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.96 % Allowed : 18.15 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1512 helix: 2.31 (0.20), residues: 698 sheet: -1.08 (0.43), residues: 178 loop : -1.62 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 931 HIS 0.005 0.001 HIS B 605 PHE 0.008 0.001 PHE A 653 TYR 0.009 0.001 TYR B1012 ARG 0.003 0.000 ARG B1026 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 591) hydrogen bonds : angle 3.62167 ( 1628) covalent geometry : bond 0.00276 (13908) covalent geometry : angle 0.50843 (19030) *********************** 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 152 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.504 Fit side-chains REVERT: B 506 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6857 (pm20) REVERT: B 751 VAL cc_start: 0.8998 (t) cc_final: 0.8712 (t) REVERT: B 755 SER cc_start: 0.8724 (OUTLIER) cc_final: 0.8205 (t) REVERT: B 1033 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6986 (tpp80) REVERT: B 1153 GLN cc_start: 0.6704 (mm-40) cc_final: 0.6273 (mt0) REVERT: A 506 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6787 (pm20) REVERT: A 669 MET cc_start: 0.8625 (mtp) cc_final: 0.8193 (mtp) REVERT: A 755 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8193 (t) REVERT: A 1033 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6974 (tpp80) REVERT: A 1153 GLN cc_start: 0.6568 (mm-40) cc_final: 0.6150 (mt0) outliers start: 26 outliers final: 19 residues processed: 150 average time/residue: 0.2169 time to fit residues: 51.0017 Evaluate side-chains 149 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 703 LEU Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1033 ARG 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 755 SER Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1033 ARG 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 19 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 12 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 41 optimal weight: 0.0010 chunk 43 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3807 r_free = 0.3807 target = 0.138483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113814 restraints weight = 23037.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117317 restraints weight = 12385.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.119724 restraints weight = 8204.281| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13908 Z= 0.100 Angle : 0.489 9.443 19030 Z= 0.259 Chirality : 0.037 0.174 2094 Planarity : 0.003 0.032 2220 Dihedral : 17.780 137.018 2420 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.66 % Allowed : 18.52 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1512 helix: 2.31 (0.20), residues: 706 sheet: -1.06 (0.42), residues: 178 loop : -1.50 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 931 HIS 0.004 0.000 HIS B 605 PHE 0.008 0.001 PHE A 706 TYR 0.024 0.001 TYR A1127 ARG 0.003 0.000 ARG A1026 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 591) hydrogen bonds : angle 3.49103 ( 1628) covalent geometry : bond 0.00222 (13908) covalent geometry : angle 0.48940 (19030) *********************** 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 166 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.611 Fit side-chains REVERT: B 572 GLU cc_start: 0.7474 (tt0) cc_final: 0.6957 (tt0) REVERT: B 669 MET cc_start: 0.8440 (mtp) cc_final: 0.8088 (mtp) REVERT: B 751 VAL cc_start: 0.8951 (t) cc_final: 0.8639 (t) REVERT: B 753 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8432 (tm-30) REVERT: B 1033 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6647 (tpp80) REVERT: B 1153 GLN cc_start: 0.6641 (mm-40) cc_final: 0.6213 (mt0) REVERT: A 506 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6568 (pm20) REVERT: A 572 GLU cc_start: 0.7482 (tt0) cc_final: 0.6928 (tt0) REVERT: A 669 MET cc_start: 0.8684 (mtp) cc_final: 0.8307 (mtp) REVERT: A 1033 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6548 (tpp80) REVERT: A 1153 GLN cc_start: 0.6644 (mm-40) cc_final: 0.6217 (mt0) outliers start: 22 outliers final: 18 residues processed: 164 average time/residue: 0.2121 time to fit residues: 54.9122 Evaluate side-chains 154 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 913 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1033 ARG 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 491 LEU Chi-restraints excluded: chain A residue 506 GLU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1033 ARG 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 129 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 0.0050 chunk 54 optimal weight: 4.9990 chunk 130 optimal weight: 0.0170 chunk 59 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.0270 chunk 67 optimal weight: 0.3980 overall best weight: 0.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3745 r_free = 0.3745 target = 0.137747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112002 restraints weight = 22040.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116006 restraints weight = 11247.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118722 restraints weight = 7162.910| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.6116 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= 0.095 Angle : 0.478 8.749 19030 Z= 0.255 Chirality : 0.037 0.180 2094 Planarity : 0.003 0.033 2220 Dihedral : 17.728 137.319 2420 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.51 % Allowed : 19.05 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1512 helix: 2.40 (0.20), residues: 706 sheet: -0.89 (0.40), residues: 184 loop : -1.49 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 931 HIS 0.004 0.000 HIS B 605 PHE 0.009 0.001 PHE B 775 TYR 0.008 0.001 TYR B1012 ARG 0.002 0.000 ARG A 568 Details of bonding type rmsd hydrogen bonds : bond 0.02788 ( 591) hydrogen bonds : angle 3.51003 ( 1628) covalent geometry : bond 0.00207 (13908) covalent geometry : angle 0.47762 (19030) *********************** 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 174 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.331 Fit side-chains REVERT: B 572 GLU cc_start: 0.7681 (tt0) cc_final: 0.7056 (tt0) REVERT: B 669 MET cc_start: 0.8129 (mtp) cc_final: 0.7782 (mtp) REVERT: B 753 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8408 (tm-30) REVERT: B 900 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7740 (mt-10) REVERT: B 917 ASN cc_start: 0.7817 (m110) cc_final: 0.6873 (p0) REVERT: B 1033 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6142 (tpp80) REVERT: B 1153 GLN cc_start: 0.6563 (mm-40) cc_final: 0.6109 (mt0) REVERT: A 461 GLU cc_start: 0.7915 (pt0) cc_final: 0.7549 (pt0) REVERT: A 669 MET cc_start: 0.8480 (mtp) cc_final: 0.8118 (mtp) REVERT: A 900 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 1033 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6197 (tpp80) REVERT: A 1153 GLN cc_start: 0.6482 (mm-40) cc_final: 0.6015 (mt0) outliers start: 20 outliers final: 14 residues processed: 173 average time/residue: 0.2241 time to fit residues: 59.9994 Evaluate side-chains 161 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1033 ARG Chi-restraints excluded: chain B residue 1044 GLU Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1033 ARG 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 65 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3748 r_free = 0.3748 target = 0.133474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109094 restraints weight = 23052.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112448 restraints weight = 12564.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.114728 restraints weight = 8402.006| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13908 Z= 0.170 Angle : 0.567 8.877 19030 Z= 0.300 Chirality : 0.041 0.160 2094 Planarity : 0.004 0.032 2220 Dihedral : 17.943 136.223 2420 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.36 % Allowed : 19.65 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1512 helix: 2.16 (0.20), residues: 714 sheet: -1.15 (0.42), residues: 178 loop : -1.54 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 931 HIS 0.005 0.001 HIS B 605 PHE 0.010 0.002 PHE B 790 TYR 0.024 0.002 TYR A1127 ARG 0.003 0.000 ARG B1026 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 591) hydrogen bonds : angle 3.85675 ( 1628) covalent geometry : bond 0.00402 (13908) covalent geometry : angle 0.56684 (19030) ********************** 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 150 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 1.354 Fit side-chains REVERT: B 669 MET cc_start: 0.8474 (mtp) cc_final: 0.8079 (mtp) REVERT: B 753 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 1033 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7073 (tpp80) REVERT: B 1153 GLN cc_start: 0.6606 (mm-40) cc_final: 0.6189 (mt0) REVERT: A 1033 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7047 (tpp80) REVERT: A 1153 GLN cc_start: 0.6610 (mm-40) cc_final: 0.6193 (mt0) outliers start: 18 outliers final: 16 residues processed: 150 average time/residue: 0.2231 time to fit residues: 51.4742 Evaluate side-chains 145 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 768 ILE Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 1033 ARG 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 703 LEU Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1033 ARG 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 26 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 147 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3779 r_free = 0.3779 target = 0.136128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111642 restraints weight = 23231.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115085 restraints weight = 12627.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117445 restraints weight = 8397.793| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.6397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13908 Z= 0.118 Angle : 0.510 8.559 19030 Z= 0.272 Chirality : 0.039 0.165 2094 Planarity : 0.004 0.033 2220 Dihedral : 17.891 136.511 2420 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.66 % Allowed : 19.43 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1512 helix: 2.28 (0.20), residues: 704 sheet: -1.12 (0.42), residues: 178 loop : -1.46 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 931 HIS 0.004 0.001 HIS B 605 PHE 0.009 0.001 PHE B 790 TYR 0.008 0.001 TYR A 957 ARG 0.003 0.000 ARG A1026 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 591) hydrogen bonds : angle 3.68015 ( 1628) covalent geometry : bond 0.00273 (13908) covalent geometry : angle 0.51043 (19030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3970.30 seconds wall clock time: 69 minutes 48.38 seconds (4188.38 seconds total)