Starting phenix.real_space_refine on Thu Jul 2 16:50:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ovr_70906/07_2026/9ovr_70906.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ovr_70906/07_2026/9ovr_70906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ovr_70906/07_2026/9ovr_70906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ovr_70906/07_2026/9ovr_70906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ovr_70906/07_2026/9ovr_70906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ovr_70906/07_2026/9ovr_70906.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.043 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 S 66 5.16 5 Na 6 4.78 5 C 5948 2.51 5 N 1408 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8990 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 4414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4414 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 27, 'TRANS': 530} Chain: "A" Number of atoms: 4414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4414 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 27, 'TRANS': 530} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 22 Ad-hoc single atom residues: {' NA': 3} Unusual residues: {'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 22 Ad-hoc single atom residues: {' NA': 3} Unusual residues: {'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.94, per 1000 atoms: 0.22 Number of scatterers: 8990 At special positions: 0 Unit cell: (111.1, 106.7, 104.5, 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 66 16.00 Na 6 11.00 O 1562 8.00 N 1408 7.00 C 5948 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=1, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1306 " - " ASN A 786 " " NAG B1303 " - " ASN B 786 " " NAG C 1 " - " ASN B 796 " " NAG D 1 " - " ASN B 776 " " NAG E 1 " - " ASN A 776 " " NAG F 1 " - " ASN A 796 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 237.2 milliseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 67.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 582 through 593 Processing helix chain 'B' and resid 595 through 602 removed outlier: 3.656A pdb=" N PHE B 600 " --> pdb=" O PHE B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 removed outlier: 4.149A pdb=" N LEU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS B 617 " --> pdb=" O LEU B 613 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 618 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 621 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 622 - end of helix Processing helix chain 'B' and resid 639 through 657 removed outlier: 3.627A pdb=" N PHE B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 685 removed outlier: 3.972A pdb=" N LEU B 672 " --> pdb=" O THR B 668 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 673 " --> pdb=" O GLY B 669 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 674 " --> pdb=" O PRO B 670 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 677 " --> pdb=" O VAL B 673 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 680 " --> pdb=" O LYS B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 711 Processing helix chain 'B' and resid 712 through 719 Processing helix chain 'B' and resid 722 through 725 Processing helix chain 'B' and resid 726 through 745 removed outlier: 3.582A pdb=" N LEU B 743 " --> pdb=" O ALA B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 750 removed outlier: 4.165A pdb=" N THR B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 764 removed outlier: 3.832A pdb=" N TYR B 764 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 786 Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 824 through 843 Processing helix chain 'B' and resid 862 through 879 removed outlier: 3.623A pdb=" N THR B 867 " --> pdb=" O ALA B 863 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 868 " --> pdb=" O VAL B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 916 Processing helix chain 'B' and resid 916 through 939 removed outlier: 3.820A pdb=" N ALA B 920 " --> pdb=" O ALA B 916 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 921 " --> pdb=" O ALA B 917 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 922 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 944 Processing helix chain 'B' and resid 951 through 969 Processing helix chain 'B' and resid 976 through 986 Processing helix chain 'B' and resid 1009 through 1021 removed outlier: 3.701A pdb=" N LEU B1013 " --> pdb=" O ARG B1009 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B1020 " --> pdb=" O PHE B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1030 Processing helix chain 'B' and resid 1033 through 1048 removed outlier: 3.811A pdb=" N LEU B1037 " --> pdb=" O PRO B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1059 removed outlier: 4.088A pdb=" N ASP B1056 " --> pdb=" O ILE B1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1077 Processing helix chain 'B' and resid 1078 through 1102 removed outlier: 3.534A pdb=" N VAL B1082 " --> pdb=" O PRO B1078 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL B1101 " --> pdb=" O TRP B1097 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B1102 " --> pdb=" O VAL B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1110 removed outlier: 3.559A pdb=" N PHE B1108 " --> pdb=" O ALA B1105 " (cutoff:3.500A) Proline residue: B1109 - end of helix Processing helix chain 'B' and resid 1111 through 1121 removed outlier: 3.854A pdb=" N VAL B1116 " --> pdb=" O VAL B1112 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1135 Processing helix chain 'A' and resid 582 through 593 Processing helix chain 'A' and resid 595 through 602 removed outlier: 3.655A pdb=" N PHE A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 removed outlier: 4.148A pdb=" N LEU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N CYS A 617 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 618 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 621 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Proline residue: A 622 - end of helix Processing helix chain 'A' and resid 639 through 657 removed outlier: 3.627A pdb=" N PHE A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 685 removed outlier: 4.091A pdb=" N PHE A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TYR A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 711 Processing helix chain 'A' and resid 712 through 719 Processing helix chain 'A' and resid 722 through 726 Processing helix chain 'A' and resid 728 through 745 removed outlier: 3.582A pdb=" N LEU A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 removed outlier: 4.165A pdb=" N THR A 749 " --> pdb=" O ASP A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 764 removed outlier: 3.832A pdb=" N TYR A 764 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 824 through 843 Processing helix chain 'A' and resid 862 through 879 removed outlier: 3.623A pdb=" N THR A 867 " --> pdb=" O ALA A 863 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 868 " --> pdb=" O VAL A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 916 through 939 removed outlier: 3.821A pdb=" N ALA A 920 " --> pdb=" O ALA A 916 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 921 " --> pdb=" O ALA A 917 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 922 " --> pdb=" O ILE A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 951 through 969 Processing helix chain 'A' and resid 976 through 986 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.701A pdb=" N LEU A1013 " --> pdb=" O ARG A1009 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'A' and resid 1033 through 1048 removed outlier: 3.812A pdb=" N LEU A1037 " --> pdb=" O PRO A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1059 removed outlier: 4.088A pdb=" N ASP A1056 " --> pdb=" O ILE A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1077 Processing helix chain 'A' and resid 1078 through 1102 removed outlier: 4.141A pdb=" N VAL A1101 " --> pdb=" O TRP A1097 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A1102 " --> pdb=" O VAL A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1110 removed outlier: 3.559A pdb=" N PHE A1108 " --> pdb=" O ALA A1105 " (cutoff:3.500A) Proline residue: A1109 - end of helix Processing helix chain 'A' and resid 1111 through 1121 removed outlier: 3.854A pdb=" N VAL A1116 " --> pdb=" O VAL A1112 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1135 Processing sheet with id=AA1, first strand: chain 'B' and resid 665 through 666 removed outlier: 3.827A pdb=" N VAL B 974 " --> pdb=" O GLY B 666 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 768 through 769 Processing sheet with id=AA3, first strand: chain 'B' and resid 988 through 990 removed outlier: 3.706A pdb=" N GLY B1004 " --> pdb=" O VAL B 989 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 665 through 666 removed outlier: 3.837A pdb=" N VAL A 974 " --> pdb=" O GLY A 666 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 768 through 769 Processing sheet with id=AA6, first strand: chain 'A' and resid 988 through 990 removed outlier: 3.706A pdb=" N GLY A1004 " --> pdb=" O VAL A 989 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1346 1.31 - 1.43: 2464 1.43 - 1.56: 5306 1.56 - 1.68: 0 1.68 - 1.81: 98 Bond restraints: 9214 Sorted by residual: bond pdb=" CA SER B 667 " pdb=" C SER B 667 " ideal model delta sigma weight residual 1.524 1.410 0.114 1.35e-02 5.49e+03 7.09e+01 bond pdb=" CA SER A 667 " pdb=" C SER A 667 " ideal model delta sigma weight residual 1.524 1.417 0.107 1.29e-02 6.01e+03 6.89e+01 bond pdb=" CA VAL B 671 " pdb=" C VAL B 671 " ideal model delta sigma weight residual 1.524 1.455 0.068 1.22e-02 6.72e+03 3.12e+01 bond pdb=" CA ALA A 726 " pdb=" CB ALA A 726 " ideal model delta sigma weight residual 1.530 1.466 0.064 1.24e-02 6.50e+03 2.66e+01 bond pdb=" C GLY B 666 " pdb=" O GLY B 666 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.02e-02 9.61e+03 2.18e+01 ... (remaining 9209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 12319 3.37 - 6.74: 176 6.74 - 10.11: 19 10.11 - 13.48: 3 13.48 - 16.85: 1 Bond angle restraints: 12518 Sorted by residual: angle pdb=" C GLU B 724 " pdb=" CA GLU B 724 " pdb=" CB GLU B 724 " ideal model delta sigma weight residual 110.42 93.57 16.85 1.99e+00 2.53e-01 7.17e+01 angle pdb=" N ALA A 726 " pdb=" CA ALA A 726 " pdb=" C ALA A 726 " ideal model delta sigma weight residual 111.34 99.31 12.03 1.49e+00 4.50e-01 6.52e+01 angle pdb=" N VAL A 855 " pdb=" CA VAL A 855 " pdb=" C VAL A 855 " ideal model delta sigma weight residual 113.53 107.37 6.16 9.80e-01 1.04e+00 3.96e+01 angle pdb=" N VAL B 855 " pdb=" CA VAL B 855 " pdb=" C VAL B 855 " ideal model delta sigma weight residual 113.53 107.37 6.16 9.80e-01 1.04e+00 3.95e+01 angle pdb=" C LEU B 665 " pdb=" CA LEU B 665 " pdb=" CB LEU B 665 " ideal model delta sigma weight residual 109.53 118.79 -9.26 1.69e+00 3.50e-01 3.00e+01 ... (remaining 12513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.60: 5071 21.60 - 43.19: 344 43.19 - 64.79: 63 64.79 - 86.38: 23 86.38 - 107.98: 43 Dihedral angle restraints: 5544 sinusoidal: 2296 harmonic: 3248 Sorted by residual: dihedral pdb=" C GLU B 724 " pdb=" N GLU B 724 " pdb=" CA GLU B 724 " pdb=" CB GLU B 724 " ideal model delta harmonic sigma weight residual -122.60 -106.60 -16.00 0 2.50e+00 1.60e-01 4.09e+01 dihedral pdb=" CA MET A1063 " pdb=" C MET A1063 " pdb=" N PRO A1064 " pdb=" CA PRO A1064 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA MET B1063 " pdb=" C MET B1063 " pdb=" N PRO B1064 " pdb=" CA PRO B1064 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 5541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1348 0.076 - 0.152: 131 0.152 - 0.228: 14 0.228 - 0.305: 6 0.305 - 0.381: 3 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA PHE A 727 " pdb=" N PHE A 727 " pdb=" C PHE A 727 " pdb=" CB PHE A 727 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 776 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 776 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1499 not shown) Planarity restraints: 1510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 999 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO B1000 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO B1000 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B1000 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 722 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C PHE B 722 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE B 722 " -0.021 2.00e-02 2.50e+03 pdb=" N THR B 723 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 903 " -0.048 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO B 904 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 904 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 904 " -0.040 5.00e-02 4.00e+02 ... (remaining 1507 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 3 1.95 - 2.69: 262 2.69 - 3.43: 12707 3.43 - 4.16: 19543 4.16 - 4.90: 35669 Nonbonded interactions: 68184 Sorted by model distance: nonbonded pdb=" CZ PHE A1085 " pdb=" OD1 ASP A1135 " model vdw 1.213 3.340 nonbonded pdb=" NE ARG A 721 " pdb=" CD1 LEU A1137 " model vdw 1.542 2.832 nonbonded pdb=" CE2 PHE A1085 " pdb=" OD1 ASP A1135 " model vdw 1.690 3.340 nonbonded pdb=" CD ARG A 721 " pdb=" CD1 LEU A1137 " model vdw 2.023 3.860 nonbonded pdb=" NH1 ARG A 721 " pdb=" CD2 LEU A1137 " model vdw 2.030 2.832 ... (remaining 68179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 580 through 1137) selection = (chain 'B' and resid 580 through 1137) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.140 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 : 0.007 0.361 9225 Z= 0.527 Angle : 1.010 16.854 12548 Z= 0.602 Chirality : 0.051 0.381 1502 Planarity : 0.006 0.108 1504 Dihedral : 18.748 107.977 3444 Min Nonbonded Distance : 1.213 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 1.35 % Allowed : 7.64 % Favored : 91.01 % Rotamer: Outliers : 1.12 % Allowed : 1.12 % Favored : 97.76 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 1112 helix: 0.91 (0.21), residues: 676 sheet: 0.47 (0.86), residues: 20 loop : -1.99 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 898 TYR 0.016 0.001 TYR B1076 PHE 0.014 0.001 PHE A 674 TRP 0.013 0.001 TRP A 911 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.37 ( 9214) covalent geometry : angle 0.97668 / 0.60 (12518) hydrogen bonds : bond 0.16228 / 10.95 ( 471) hydrogen bonds : angle 4.98732 / 3.56 ( 1332) Misc. bond : bond 0.36058 / 18.98 ( 1) link_BETA1-4 : bond 0.01106 / 0.54 ( 4) link_BETA1-4 : angle 2.02606 / 1.20 ( 12) link_NAG-ASN : bond 0.01504 / 0.77 ( 6) link_NAG-ASN : angle 6.65850 / 3.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 597 LEU cc_start: 0.7922 (tp) cc_final: 0.7655 (mt) REVERT: B 602 ASP cc_start: 0.7975 (t0) cc_final: 0.7598 (t0) REVERT: B 745 ASP cc_start: 0.7432 (t0) cc_final: 0.6762 (m-30) REVERT: B 754 MET cc_start: 0.8982 (mtt) cc_final: 0.8641 (mtt) REVERT: B 844 GLN cc_start: 0.7992 (tp40) cc_final: 0.7709 (mm-40) REVERT: B 846 LYS cc_start: 0.7622 (pttm) cc_final: 0.7006 (ttmm) REVERT: B 875 ASP cc_start: 0.7800 (t0) cc_final: 0.7565 (t0) REVERT: B 907 ASP cc_start: 0.8523 (t0) cc_final: 0.8311 (t0) REVERT: B 1014 MET cc_start: 0.7168 (tpp) cc_final: 0.6894 (mmm) REVERT: B 1122 MET cc_start: 0.6677 (mtp) cc_final: 0.6462 (mtp) REVERT: A 601 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7395 (ttmt) REVERT: A 602 ASP cc_start: 0.7581 (t0) cc_final: 0.7363 (t0) REVERT: A 745 ASP cc_start: 0.7335 (t0) cc_final: 0.6542 (m-30) REVERT: A 748 GLU cc_start: 0.7254 (tt0) cc_final: 0.6876 (mt-10) REVERT: A 875 ASP cc_start: 0.7811 (t0) cc_final: 0.7560 (t0) REVERT: A 900 TRP cc_start: 0.6406 (m-10) cc_final: 0.5954 (m-10) REVERT: A 907 ASP cc_start: 0.8553 (t0) cc_final: 0.8302 (t0) REVERT: A 1014 MET cc_start: 0.7333 (tpp) cc_final: 0.7036 (mmm) REVERT: A 1050 LYS cc_start: 0.6091 (mptt) cc_final: 0.5806 (mmtp) REVERT: A 1111 MET cc_start: 0.5882 (tpp) cc_final: 0.5334 (ppp) outliers start: 11 outliers final: 6 residues processed: 163 average time/residue: 0.0721 time to fit residues: 16.8378 Evaluate side-chains 112 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 670 PRO Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1077 VAL Chi-restraints excluded: chain B residue 1135 ASP Chi-restraints excluded: chain A residue 670 PRO Chi-restraints excluded: chain A residue 1077 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 753 ASN B 908 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 ASN A 908 ASN ** A1083 HIS ** 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 = 0.4170 r_free = 0.4170 target = 0.200315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146007 restraints weight = 9044.065| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.24 r_work: 0.3092 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9225 Z= 0.175 Angle : 0.751 12.528 12548 Z= 0.372 Chirality : 0.048 0.399 1502 Planarity : 0.006 0.061 1504 Dihedral : 16.714 93.981 1405 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.01 % Favored : 92.72 % Rotamer: Outliers : 1.32 % Allowed : 6.61 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.27), residues: 1112 helix: 0.94 (0.21), residues: 696 sheet: 0.65 (0.83), residues: 20 loop : -2.00 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 898 TYR 0.015 0.001 TYR A 764 PHE 0.021 0.002 PHE A1085 TRP 0.010 0.001 TRP B 911 HIS 0.005 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 9214) covalent geometry : angle 0.71415 / 0.36 (12518) hydrogen bonds : bond 0.05289 / 3.60 ( 471) hydrogen bonds : angle 4.04604 / 2.95 ( 1332) Misc. bond : bond 0.00271 / 0.14 ( 1) link_BETA1-4 : bond 0.00760 / 0.37 ( 4) link_BETA1-4 : angle 2.77097 / 1.66 ( 12) link_NAG-ASN : bond 0.01205 / 0.63 ( 6) link_NAG-ASN : angle 5.75352 / 3.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 597 LEU cc_start: 0.8110 (tp) cc_final: 0.7804 (mt) REVERT: B 745 ASP cc_start: 0.8115 (t0) cc_final: 0.7397 (m-30) REVERT: B 754 MET cc_start: 0.9088 (mtt) cc_final: 0.8677 (mtt) REVERT: B 846 LYS cc_start: 0.7757 (pttm) cc_final: 0.7152 (ttmm) REVERT: B 875 ASP cc_start: 0.8306 (t0) cc_final: 0.8086 (t0) REVERT: B 966 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8435 (t) REVERT: B 1014 MET cc_start: 0.8049 (tpp) cc_final: 0.7813 (mmm) REVERT: B 1044 MET cc_start: 0.8522 (mtm) cc_final: 0.8080 (mtm) REVERT: A 601 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7752 (ttmt) REVERT: A 602 ASP cc_start: 0.8202 (t0) cc_final: 0.7922 (t0) REVERT: A 635 GLU cc_start: 0.7924 (tt0) cc_final: 0.7389 (mm-30) REVERT: A 680 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.8017 (mmmt) REVERT: A 745 ASP cc_start: 0.7977 (t0) cc_final: 0.7269 (m-30) REVERT: A 748 GLU cc_start: 0.8248 (tt0) cc_final: 0.7692 (mt-10) REVERT: A 875 ASP cc_start: 0.8364 (t0) cc_final: 0.8124 (t0) REVERT: A 900 TRP cc_start: 0.6765 (m-10) cc_final: 0.6230 (m-10) REVERT: A 907 ASP cc_start: 0.8519 (t0) cc_final: 0.8214 (t0) REVERT: A 1014 MET cc_start: 0.8070 (tpp) cc_final: 0.7815 (mmm) REVERT: A 1044 MET cc_start: 0.8560 (mtm) cc_final: 0.8111 (mtm) REVERT: A 1111 MET cc_start: 0.5715 (tpp) cc_final: 0.4933 (ppp) outliers start: 13 outliers final: 7 residues processed: 116 average time/residue: 0.0624 time to fit residues: 10.7496 Evaluate side-chains 111 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 1077 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 85 optimal weight: 0.0070 chunk 89 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1083 HIS ** 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 = 0.4106 r_free = 0.4106 target = 0.193579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138992 restraints weight = 9006.232| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.91 r_work: 0.2970 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9225 Z= 0.182 Angle : 0.729 11.621 12548 Z= 0.356 Chirality : 0.047 0.357 1502 Planarity : 0.006 0.055 1504 Dihedral : 13.064 88.821 1396 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.47 % Favored : 93.26 % Rotamer: Outliers : 2.34 % Allowed : 8.03 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.27), residues: 1112 helix: 0.92 (0.21), residues: 696 sheet: 0.06 (0.98), residues: 20 loop : -1.83 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 898 TYR 0.021 0.001 TYR A 764 PHE 0.024 0.002 PHE B 614 TRP 0.012 0.001 TRP B 911 HIS 0.009 0.002 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 ( 9214) covalent geometry : angle 0.69372 / 0.35 (12518) hydrogen bonds : bond 0.05432 / 3.71 ( 471) hydrogen bonds : angle 3.89664 / 2.82 ( 1332) Misc. bond : bond 0.00007 / 0.00 ( 1) link_BETA1-4 : bond 0.01188 / 0.58 ( 4) link_BETA1-4 : angle 3.24850 / 1.92 ( 12) link_NAG-ASN : bond 0.01132 / 0.59 ( 6) link_NAG-ASN : angle 5.37451 / 2.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 597 LEU cc_start: 0.8138 (tp) cc_final: 0.7808 (mt) REVERT: B 745 ASP cc_start: 0.8327 (t0) cc_final: 0.7610 (m-30) REVERT: B 754 MET cc_start: 0.9029 (mtt) cc_final: 0.8631 (mtt) REVERT: B 907 ASP cc_start: 0.8514 (t0) cc_final: 0.8285 (t0) REVERT: B 966 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8698 (t) REVERT: B 1044 MET cc_start: 0.8519 (mtm) cc_final: 0.8094 (mtm) REVERT: A 635 GLU cc_start: 0.8000 (tt0) cc_final: 0.7587 (mm-30) REVERT: A 745 ASP cc_start: 0.8181 (t0) cc_final: 0.7424 (m-30) REVERT: A 748 GLU cc_start: 0.8407 (tt0) cc_final: 0.7949 (mt-10) REVERT: A 758 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 900 TRP cc_start: 0.6824 (m-10) cc_final: 0.6261 (m-10) REVERT: A 907 ASP cc_start: 0.8540 (t0) cc_final: 0.8215 (t0) REVERT: A 966 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8685 (t) REVERT: A 1014 MET cc_start: 0.8300 (tpp) cc_final: 0.8051 (mmm) REVERT: A 1019 MET cc_start: 0.8886 (ttm) cc_final: 0.8657 (ttm) REVERT: A 1044 MET cc_start: 0.8525 (mtm) cc_final: 0.8081 (mtm) REVERT: A 1107 VAL cc_start: 0.4798 (OUTLIER) cc_final: 0.4504 (m) REVERT: A 1111 MET cc_start: 0.6112 (tpp) cc_final: 0.4988 (ppp) REVERT: A 1122 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.5881 (mtm) outliers start: 23 outliers final: 15 residues processed: 123 average time/residue: 0.0710 time to fit residues: 12.7906 Evaluate side-chains 118 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 766 CYS Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 766 CYS Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1077 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1122 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 0.0010 chunk 57 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1083 HIS ** 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 = 0.4174 r_free = 0.4174 target = 0.199991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.164936 restraints weight = 9126.306| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.85 r_work: 0.3350 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9225 Z= 0.156 Angle : 0.674 11.337 12548 Z= 0.323 Chirality : 0.044 0.355 1502 Planarity : 0.005 0.052 1504 Dihedral : 12.035 86.830 1396 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 1.73 % Allowed : 10.47 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 1112 helix: 1.07 (0.21), residues: 696 sheet: 0.16 (0.94), residues: 20 loop : -1.76 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.015 0.001 TYR B 764 PHE 0.016 0.001 PHE B 832 TRP 0.009 0.001 TRP B 911 HIS 0.005 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 9214) covalent geometry : angle 0.63673 / 0.31 (12518) hydrogen bonds : bond 0.04761 / 3.26 ( 471) hydrogen bonds : angle 3.73875 / 2.72 ( 1332) Misc. bond : bond 0.00077 / 0.04 ( 1) link_BETA1-4 : bond 0.01026 / 0.51 ( 4) link_BETA1-4 : angle 3.29663 / 1.92 ( 12) link_NAG-ASN : bond 0.01102 / 0.57 ( 6) link_NAG-ASN : angle 5.28572 / 2.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 597 LEU cc_start: 0.8298 (tp) cc_final: 0.7919 (mt) REVERT: B 675 GLU cc_start: 0.5391 (mp0) cc_final: 0.4269 (mt-10) REVERT: B 745 ASP cc_start: 0.8290 (t0) cc_final: 0.7638 (m-30) REVERT: B 754 MET cc_start: 0.8937 (mtt) cc_final: 0.8608 (mtt) REVERT: B 907 ASP cc_start: 0.8295 (t0) cc_final: 0.8077 (t0) REVERT: B 966 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8700 (t) REVERT: B 1019 MET cc_start: 0.8952 (ttm) cc_final: 0.8537 (ttm) REVERT: B 1044 MET cc_start: 0.8625 (mtm) cc_final: 0.8237 (mtm) REVERT: B 1063 MET cc_start: 0.3377 (ppp) cc_final: 0.2468 (ppp) REVERT: A 580 ARG cc_start: 0.6246 (ptp90) cc_final: 0.5889 (ttm-80) REVERT: A 601 LYS cc_start: 0.8301 (ttpp) cc_final: 0.8049 (ttmt) REVERT: A 635 GLU cc_start: 0.8054 (tt0) cc_final: 0.7838 (mm-30) REVERT: A 745 ASP cc_start: 0.8102 (t0) cc_final: 0.7567 (m-30) REVERT: A 748 GLU cc_start: 0.8105 (tt0) cc_final: 0.7871 (mt-10) REVERT: A 900 TRP cc_start: 0.6841 (m-10) cc_final: 0.6206 (m-10) REVERT: A 907 ASP cc_start: 0.8342 (t0) cc_final: 0.8078 (t0) REVERT: A 1014 MET cc_start: 0.8256 (tpp) cc_final: 0.8036 (mmm) REVERT: A 1044 MET cc_start: 0.8637 (mtm) cc_final: 0.8234 (mtm) outliers start: 17 outliers final: 8 residues processed: 115 average time/residue: 0.0685 time to fit residues: 11.3795 Evaluate side-chains 105 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 766 CYS Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 1077 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 49 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 983 HIS ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.196146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138765 restraints weight = 9085.560| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 4.08 r_work: 0.2883 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9225 Z= 0.200 Angle : 0.708 11.168 12548 Z= 0.343 Chirality : 0.045 0.351 1502 Planarity : 0.005 0.061 1504 Dihedral : 11.634 88.756 1395 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.08 % Rotamer: Outliers : 1.93 % Allowed : 10.37 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1112 helix: 0.97 (0.21), residues: 694 sheet: 0.81 (1.08), residues: 20 loop : -1.76 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.018 0.001 TYR B 764 PHE 0.021 0.002 PHE A 681 TRP 0.010 0.001 TRP B 911 HIS 0.007 0.001 HIS B 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.20 ( 9214) covalent geometry : angle 0.67207 / 0.34 (12518) hydrogen bonds : bond 0.05488 / 3.75 ( 471) hydrogen bonds : angle 3.78093 / 2.74 ( 1332) Misc. bond : bond 0.00173 / 0.09 ( 1) link_BETA1-4 : bond 0.00936 / 0.47 ( 4) link_BETA1-4 : angle 3.04380 / 1.79 ( 12) link_NAG-ASN : bond 0.01152 / 0.59 ( 6) link_NAG-ASN : angle 5.38080 / 2.92 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 597 LEU cc_start: 0.8171 (tp) cc_final: 0.7780 (mt) REVERT: B 745 ASP cc_start: 0.8211 (t0) cc_final: 0.7487 (m-30) REVERT: B 907 ASP cc_start: 0.8567 (t0) cc_final: 0.8311 (t0) REVERT: B 966 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8658 (t) REVERT: B 1019 MET cc_start: 0.8950 (ttm) cc_final: 0.8539 (ttm) REVERT: B 1044 MET cc_start: 0.8384 (mtm) cc_final: 0.7982 (mtm) REVERT: A 580 ARG cc_start: 0.6030 (ptp90) cc_final: 0.5502 (ttm-80) REVERT: A 635 GLU cc_start: 0.8177 (tt0) cc_final: 0.7560 (mm-30) REVERT: A 745 ASP cc_start: 0.8176 (t0) cc_final: 0.7510 (m-30) REVERT: A 748 GLU cc_start: 0.8439 (tt0) cc_final: 0.7893 (mt-10) REVERT: A 907 ASP cc_start: 0.8622 (t0) cc_final: 0.8306 (t0) REVERT: A 1014 MET cc_start: 0.8397 (tpp) cc_final: 0.8184 (mmm) REVERT: A 1044 MET cc_start: 0.8404 (mtm) cc_final: 0.8001 (mtm) outliers start: 19 outliers final: 14 residues processed: 113 average time/residue: 0.0693 time to fit residues: 11.6959 Evaluate side-chains 110 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 766 CYS Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1077 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1083 HIS ** 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 = 0.3935 r_free = 0.3935 target = 0.180443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.131547 restraints weight = 9185.808| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.73 r_work: 0.2917 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9225 Z= 0.187 Angle : 0.698 10.922 12548 Z= 0.335 Chirality : 0.045 0.355 1502 Planarity : 0.005 0.066 1504 Dihedral : 10.960 85.380 1395 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.08 % Rotamer: Outliers : 2.03 % Allowed : 12.09 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1112 helix: 1.01 (0.21), residues: 696 sheet: 0.72 (1.01), residues: 20 loop : -1.71 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 721 TYR 0.017 0.001 TYR B 764 PHE 0.022 0.002 PHE A 681 TRP 0.010 0.001 TRP A 900 HIS 0.007 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.19 ( 9214) covalent geometry : angle 0.66136 / 0.33 (12518) hydrogen bonds : bond 0.05218 / 3.56 ( 471) hydrogen bonds : angle 3.72097 / 2.70 ( 1332) Misc. bond : bond 0.00098 / 0.05 ( 1) link_BETA1-4 : bond 0.00867 / 0.43 ( 4) link_BETA1-4 : angle 2.96547 / 1.72 ( 12) link_NAG-ASN : bond 0.01057 / 0.55 ( 6) link_NAG-ASN : angle 5.40325 / 2.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: B 597 LEU cc_start: 0.8291 (tp) cc_final: 0.7913 (mt) REVERT: B 601 LYS cc_start: 0.8292 (ttpp) cc_final: 0.8031 (ttmt) REVERT: B 675 GLU cc_start: 0.5973 (mp0) cc_final: 0.4686 (mt-10) REVERT: B 716 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7560 (t) REVERT: B 745 ASP cc_start: 0.8322 (t0) cc_final: 0.7692 (m-30) REVERT: B 907 ASP cc_start: 0.8382 (t0) cc_final: 0.8091 (t0) REVERT: B 966 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8772 (t) REVERT: B 1019 MET cc_start: 0.8981 (ttm) cc_final: 0.8602 (ttm) REVERT: B 1044 MET cc_start: 0.8584 (mtm) cc_final: 0.8180 (mtm) REVERT: B 1063 MET cc_start: 0.2236 (ppp) cc_final: 0.1564 (ppp) REVERT: A 580 ARG cc_start: 0.6252 (ptp90) cc_final: 0.5774 (ttm-80) REVERT: A 635 GLU cc_start: 0.8269 (tt0) cc_final: 0.7813 (mm-30) REVERT: A 745 ASP cc_start: 0.8325 (t0) cc_final: 0.7727 (m-30) REVERT: A 748 GLU cc_start: 0.8429 (tt0) cc_final: 0.8058 (mt-10) REVERT: A 907 ASP cc_start: 0.8375 (t0) cc_final: 0.8047 (t0) REVERT: A 1044 MET cc_start: 0.8605 (mtm) cc_final: 0.8206 (mtm) outliers start: 20 outliers final: 14 residues processed: 115 average time/residue: 0.0718 time to fit residues: 12.0565 Evaluate side-chains 112 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 586 ILE Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 766 CYS Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain A residue 591 ARG Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1060 LEU Chi-restraints excluded: chain A residue 1077 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 42 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 79 optimal weight: 0.3980 chunk 85 optimal weight: 0.2980 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.199789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.145585 restraints weight = 9097.352| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 4.15 r_work: 0.2945 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9225 Z= 0.126 Angle : 0.638 10.873 12548 Z= 0.304 Chirality : 0.042 0.356 1502 Planarity : 0.005 0.066 1504 Dihedral : 10.085 77.202 1395 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 1.52 % Allowed : 14.33 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.27), residues: 1112 helix: 1.27 (0.21), residues: 696 sheet: 0.40 (0.81), residues: 20 loop : -1.65 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 795 TYR 0.010 0.001 TYR B 764 PHE 0.022 0.001 PHE A 681 TRP 0.008 0.001 TRP B 911 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 9214) covalent geometry : angle 0.60241 / 0.30 (12518) hydrogen bonds : bond 0.04051 / 2.77 ( 471) hydrogen bonds : angle 3.55836 / 2.59 ( 1332) Misc. bond : bond 0.00051 / 0.03 ( 1) link_BETA1-4 : bond 0.00917 / 0.46 ( 4) link_BETA1-4 : angle 3.03190 / 1.76 ( 12) link_NAG-ASN : bond 0.01014 / 0.52 ( 6) link_NAG-ASN : angle 5.05697 / 2.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 597 LEU cc_start: 0.8134 (tp) cc_final: 0.7761 (mt) REVERT: B 601 LYS cc_start: 0.8070 (ttpp) cc_final: 0.7736 (ttmt) REVERT: B 675 GLU cc_start: 0.5687 (mp0) cc_final: 0.4442 (mt-10) REVERT: B 716 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.7399 (t) REVERT: B 745 ASP cc_start: 0.8135 (t0) cc_final: 0.7457 (m-30) REVERT: B 907 ASP cc_start: 0.8572 (t0) cc_final: 0.8283 (t0) REVERT: B 1019 MET cc_start: 0.8923 (ttm) cc_final: 0.8556 (ttm) REVERT: B 1044 MET cc_start: 0.8261 (mtm) cc_final: 0.7902 (mtm) REVERT: B 1063 MET cc_start: 0.2222 (ppp) cc_final: 0.1811 (ppp) REVERT: A 580 ARG cc_start: 0.5973 (ptp90) cc_final: 0.5414 (ttm-80) REVERT: A 601 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7849 (ttmt) REVERT: A 635 GLU cc_start: 0.8190 (tt0) cc_final: 0.7563 (mm-30) REVERT: A 745 ASP cc_start: 0.8133 (t0) cc_final: 0.7489 (m-30) REVERT: A 748 GLU cc_start: 0.8412 (tt0) cc_final: 0.7953 (mt-10) REVERT: A 907 ASP cc_start: 0.8530 (t0) cc_final: 0.8165 (t0) REVERT: A 1044 MET cc_start: 0.8284 (mtm) cc_final: 0.7935 (mtm) outliers start: 15 outliers final: 7 residues processed: 112 average time/residue: 0.0706 time to fit residues: 11.5018 Evaluate side-chains 107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1060 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 0.0000 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1083 HIS ** 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 = 0.4159 r_free = 0.4159 target = 0.199012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143934 restraints weight = 9054.629| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.92 r_work: 0.2938 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9225 Z= 0.138 Angle : 0.645 10.781 12548 Z= 0.306 Chirality : 0.043 0.353 1502 Planarity : 0.005 0.067 1504 Dihedral : 9.493 71.481 1394 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.92 % Favored : 92.99 % Rotamer: Outliers : 0.91 % Allowed : 14.94 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.27), residues: 1112 helix: 1.37 (0.21), residues: 688 sheet: 0.42 (0.79), residues: 20 loop : -1.58 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 795 TYR 0.014 0.001 TYR A 764 PHE 0.023 0.001 PHE A 681 TRP 0.008 0.001 TRP B 911 HIS 0.005 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9214) covalent geometry : angle 0.60951 / 0.30 (12518) hydrogen bonds : bond 0.04310 / 2.95 ( 471) hydrogen bonds : angle 3.53558 / 2.58 ( 1332) Misc. bond : bond 0.00052 / 0.03 ( 1) link_BETA1-4 : bond 0.00957 / 0.47 ( 4) link_BETA1-4 : angle 2.83989 / 1.55 ( 12) link_NAG-ASN : bond 0.00996 / 0.51 ( 6) link_NAG-ASN : angle 5.11662 / 3.06 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 597 LEU cc_start: 0.8160 (tp) cc_final: 0.7768 (mt) REVERT: B 601 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7765 (ttmt) REVERT: B 675 GLU cc_start: 0.5648 (mp0) cc_final: 0.4330 (mt-10) REVERT: B 716 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7410 (t) REVERT: B 745 ASP cc_start: 0.8212 (t0) cc_final: 0.7521 (m-30) REVERT: B 907 ASP cc_start: 0.8565 (t0) cc_final: 0.8260 (t0) REVERT: B 1019 MET cc_start: 0.8960 (ttm) cc_final: 0.8572 (ttm) REVERT: B 1044 MET cc_start: 0.8276 (mtm) cc_final: 0.7880 (mtm) REVERT: B 1063 MET cc_start: 0.2385 (ppp) cc_final: 0.1816 (ppp) REVERT: A 580 ARG cc_start: 0.6005 (ptp90) cc_final: 0.5501 (ttm-80) REVERT: A 601 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7820 (ttmt) REVERT: A 635 GLU cc_start: 0.8199 (tt0) cc_final: 0.7586 (mm-30) REVERT: A 745 ASP cc_start: 0.8143 (t0) cc_final: 0.7495 (m-30) REVERT: A 748 GLU cc_start: 0.8375 (tt0) cc_final: 0.7933 (mt-10) REVERT: A 907 ASP cc_start: 0.8529 (t0) cc_final: 0.8154 (t0) REVERT: A 1044 MET cc_start: 0.8296 (mtm) cc_final: 0.7929 (mtm) outliers start: 9 outliers final: 8 residues processed: 104 average time/residue: 0.0589 time to fit residues: 9.3308 Evaluate side-chains 105 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain A residue 706 VAL Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1060 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 0.0970 chunk 87 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 86 optimal weight: 0.0060 chunk 83 optimal weight: 0.9980 chunk 8 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.2632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1008 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.198800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.148280 restraints weight = 9001.164| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 3.29 r_work: 0.3211 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9225 Z= 0.115 Angle : 0.623 10.803 12548 Z= 0.293 Chirality : 0.042 0.350 1502 Planarity : 0.005 0.067 1504 Dihedral : 8.548 63.306 1394 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.56 % Favored : 93.35 % Rotamer: Outliers : 0.51 % Allowed : 15.45 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.27), residues: 1112 helix: 1.62 (0.21), residues: 676 sheet: 0.43 (0.76), residues: 20 loop : -1.61 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 795 TYR 0.009 0.001 TYR B 764 PHE 0.023 0.001 PHE A 681 TRP 0.007 0.001 TRP B 911 HIS 0.003 0.001 HIS A1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 9214) covalent geometry : angle 0.58838 / 0.29 (12518) hydrogen bonds : bond 0.03634 / 2.49 ( 471) hydrogen bonds : angle 3.45312 / 2.52 ( 1332) Misc. bond : bond 0.00053 / 0.03 ( 1) link_BETA1-4 : bond 0.00855 / 0.42 ( 4) link_BETA1-4 : angle 3.09005 / 1.80 ( 12) link_NAG-ASN : bond 0.00981 / 0.51 ( 6) link_NAG-ASN : angle 4.81166 / 2.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 597 LEU cc_start: 0.8242 (tp) cc_final: 0.7850 (mt) REVERT: B 601 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7918 (ttmt) REVERT: B 675 GLU cc_start: 0.5927 (mp0) cc_final: 0.4662 (mt-10) REVERT: B 716 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7581 (t) REVERT: B 745 ASP cc_start: 0.8243 (t0) cc_final: 0.7626 (m-30) REVERT: B 900 TRP cc_start: 0.7298 (OUTLIER) cc_final: 0.6989 (m-10) REVERT: B 907 ASP cc_start: 0.8420 (t0) cc_final: 0.8127 (t0) REVERT: B 1019 MET cc_start: 0.8969 (ttm) cc_final: 0.8563 (ttm) REVERT: B 1044 MET cc_start: 0.8483 (mtm) cc_final: 0.8141 (mtm) REVERT: B 1063 MET cc_start: 0.2206 (ppp) cc_final: 0.1925 (ppp) REVERT: A 601 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7987 (ttmt) REVERT: A 635 GLU cc_start: 0.8298 (tt0) cc_final: 0.7863 (mm-30) REVERT: A 745 ASP cc_start: 0.8184 (t0) cc_final: 0.7602 (m-30) REVERT: A 748 GLU cc_start: 0.8301 (tt0) cc_final: 0.8013 (mt-10) REVERT: A 907 ASP cc_start: 0.8357 (t0) cc_final: 0.8010 (t0) REVERT: A 1044 MET cc_start: 0.8495 (mtm) cc_final: 0.8148 (mtm) REVERT: A 1063 MET cc_start: 0.3787 (pmm) cc_final: 0.1654 (tpt) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.0706 time to fit residues: 10.6090 Evaluate side-chains 102 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 1060 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 0.0270 chunk 107 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1083 HIS ** 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 = 0.4148 r_free = 0.4148 target = 0.197732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.150791 restraints weight = 9122.028| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.74 r_work: 0.2969 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9225 Z= 0.161 Angle : 0.654 10.748 12548 Z= 0.311 Chirality : 0.043 0.348 1502 Planarity : 0.005 0.067 1504 Dihedral : 8.014 58.582 1394 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.56 % Favored : 93.35 % Rotamer: Outliers : 0.81 % Allowed : 15.24 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.27), residues: 1112 helix: 1.40 (0.21), residues: 688 sheet: 0.48 (0.82), residues: 20 loop : -1.50 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 721 TYR 0.016 0.001 TYR A 764 PHE 0.028 0.001 PHE A 681 TRP 0.009 0.001 TRP B 911 HIS 0.005 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 ( 9214) covalent geometry : angle 0.62294 / 0.30 (12518) hydrogen bonds : bond 0.04660 / 3.19 ( 471) hydrogen bonds : angle 3.54420 / 2.58 ( 1332) Misc. bond : bond 0.00037 / 0.02 ( 1) link_BETA1-4 : bond 0.00901 / 0.45 ( 4) link_BETA1-4 : angle 3.12080 / 1.79 ( 12) link_NAG-ASN : bond 0.00980 / 0.51 ( 6) link_NAG-ASN : angle 4.69314 / 2.56 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: B 580 ARG cc_start: 0.6267 (ptp90) cc_final: 0.5599 (ttm-80) REVERT: B 597 LEU cc_start: 0.8298 (tp) cc_final: 0.7895 (mt) REVERT: B 601 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7998 (ttmt) REVERT: B 675 GLU cc_start: 0.6035 (mp0) cc_final: 0.4791 (mt-10) REVERT: B 716 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7593 (t) REVERT: B 745 ASP cc_start: 0.8282 (t0) cc_final: 0.7658 (m-30) REVERT: B 907 ASP cc_start: 0.8277 (t0) cc_final: 0.7969 (t0) REVERT: B 1019 MET cc_start: 0.9008 (ttm) cc_final: 0.8646 (ttm) REVERT: B 1044 MET cc_start: 0.8493 (mtm) cc_final: 0.8097 (mtm) REVERT: B 1063 MET cc_start: 0.2187 (ppp) cc_final: 0.1905 (ppp) REVERT: A 601 LYS cc_start: 0.8265 (ttpp) cc_final: 0.8001 (ttmt) REVERT: A 635 GLU cc_start: 0.8187 (tt0) cc_final: 0.7776 (mm-30) REVERT: A 745 ASP cc_start: 0.8229 (t0) cc_final: 0.7649 (m-30) REVERT: A 748 GLU cc_start: 0.8333 (tt0) cc_final: 0.8009 (mt-10) REVERT: A 907 ASP cc_start: 0.8352 (t0) cc_final: 0.7974 (t0) REVERT: A 1044 MET cc_start: 0.8501 (mtm) cc_final: 0.8099 (mtm) REVERT: A 1063 MET cc_start: 0.3695 (pmm) cc_final: 0.1518 (tpt) outliers start: 8 outliers final: 5 residues processed: 104 average time/residue: 0.0618 time to fit residues: 9.5866 Evaluate side-chains 102 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 900 TRP Chi-restraints excluded: chain A residue 755 HIS Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 1060 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 983 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.181781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.131938 restraints weight = 8744.644| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.77 r_work: 0.2925 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9225 Z= 0.173 Angle : 0.670 10.825 12548 Z= 0.319 Chirality : 0.043 0.349 1502 Planarity : 0.005 0.067 1504 Dihedral : 7.423 52.210 1394 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.17 % Rotamer: Outliers : 0.81 % Allowed : 15.55 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1112 helix: 1.31 (0.21), residues: 688 sheet: 0.49 (0.84), residues: 20 loop : -1.52 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 795 TYR 0.018 0.001 TYR B 764 PHE 0.028 0.002 PHE A 681 TRP 0.009 0.001 TRP A 911 HIS 0.006 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.17 ( 9214) covalent geometry : angle 0.63848 / 0.31 (12518) hydrogen bonds : bond 0.04968 / 3.39 ( 471) hydrogen bonds : angle 3.58889 / 2.61 ( 1332) Misc. bond : bond 0.00044 / 0.02 ( 1) link_BETA1-4 : bond 0.01061 / 0.52 ( 4) link_BETA1-4 : angle 3.23409 / 1.95 ( 12) link_NAG-ASN : bond 0.00972 / 0.50 ( 6) link_NAG-ASN : angle 4.69858 / 2.62 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1760.54 seconds wall clock time: 30 minutes 53.99 seconds (1853.99 seconds total)