Starting phenix.real_space_refine on Tue Jun 17 12:39:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcj_38245/06_2025/8xcj_38245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcj_38245/06_2025/8xcj_38245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcj_38245/06_2025/8xcj_38245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcj_38245/06_2025/8xcj_38245.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcj_38245/06_2025/8xcj_38245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcj_38245/06_2025/8xcj_38245.cif" } resolution = 2.98 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= 0.002 sd= 0.088 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 12528 2.51 5 N 3366 2.21 5 O 3843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19809 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3360 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 412} Chain: "B" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3360 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 412} Chain: "C" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3360 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 412} Chain: "Z" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3243 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 19, 'TRANS': 400} Chain: "J" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3243 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 19, 'TRANS': 400} Chain: "F" Number of atoms: 3243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3243 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 19, 'TRANS': 400} Time building chain proxies: 11.82, per 1000 atoms: 0.60 Number of scatterers: 19809 At special positions: 0 Unit cell: (111.717, 110.643, 204.098, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3843 8.00 N 3366 7.00 C 12528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 38 " distance=2.03 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: 4.19 Conformation dependent library (CDL) restraints added in 2.4 seconds 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 31 sheets defined 5.1% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.662A pdb=" N GLY A 400 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 397 through 401 removed outlier: 4.126A pdb=" N GLY C 400 " --> pdb=" O ASP C 397 " (cutoff:3.500A) Processing helix chain 'Z' and resid 758 through 763 Processing helix chain 'Z' and resid 810 through 824 removed outlier: 3.549A pdb=" N ASP Z 816 " --> pdb=" O GLU Z 812 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE Z 817 " --> pdb=" O GLY Z 813 " (cutoff:3.500A) Processing helix chain 'Z' and resid 827 through 832 Processing helix chain 'Z' and resid 907 through 911 Processing helix chain 'J' and resid 758 through 763 removed outlier: 3.618A pdb=" N SER J 762 " --> pdb=" O GLN J 758 " (cutoff:3.500A) Processing helix chain 'J' and resid 811 through 824 Processing helix chain 'J' and resid 825 through 831 Processing helix chain 'J' and resid 907 through 911 Processing helix chain 'F' and resid 758 through 763 Processing helix chain 'F' and resid 810 through 824 Processing helix chain 'F' and resid 827 through 832 Processing helix chain 'F' and resid 907 through 911 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 14 removed outlier: 3.836A pdb=" N LEU A 46 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 62 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 58 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 52 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LYS A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA A 65 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N PHE A 81 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 131 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 139 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 150 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN A 165 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 168 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A 187 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU A 180 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLY A 185 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLY A 267 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 112 removed outlier: 6.818A pdb=" N HIS A 110 " --> pdb=" O TYR A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 14 removed outlier: 3.599A pdb=" N LEU B 46 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 62 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE B 58 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS B 52 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 57 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY B 88 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B 59 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL B 86 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP B 61 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA B 84 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN B 63 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU B 139 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 150 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN B 165 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA B 168 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU B 187 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLU B 180 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLY B 185 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B 267 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 112 removed outlier: 6.879A pdb=" N HIS B 110 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AA8, first strand: chain 'B' and resid 376 through 378 Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 14 removed outlier: 3.755A pdb=" N LEU C 46 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR C 62 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE C 58 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LYS C 52 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA C 65 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE C 81 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU C 139 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY C 150 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN C 165 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 168 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU C 187 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLU C 180 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLY C 185 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLY C 267 " --> pdb=" O ASP C 237 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 112 removed outlier: 6.849A pdb=" N HIS C 110 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 252 through 254 Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 378 Processing sheet with id=AB4, first strand: chain 'Z' and resid 719 through 725 Processing sheet with id=AB5, first strand: chain 'Z' and resid 764 through 769 removed outlier: 5.157A pdb=" N TYR Z 765 " --> pdb=" O PHE Z 748 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE Z 748 " --> pdb=" O TYR Z 765 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Z' and resid 843 through 845 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 843 through 845 current: chain 'Z' and resid 859 through 871 removed outlier: 8.269A pdb=" N TRP Z 859 " --> pdb=" O ASP Z 886 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP Z 886 " --> pdb=" O TRP Z 859 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 891 through 898 current: chain 'Z' and resid 914 through 918 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 923 through 925 current: chain 'Z' and resid 948 through 949 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 954 through 957 current: chain 'J' and resid 859 through 871 removed outlier: 8.281A pdb=" N TRP J 859 " --> pdb=" O ASP J 886 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP J 886 " --> pdb=" O TRP J 859 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 890 through 898 current: chain 'J' and resid 914 through 918 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 923 through 925 current: chain 'J' and resid 948 through 949 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 954 through 957 current: chain 'F' and resid 859 through 871 removed outlier: 8.440A pdb=" N TRP F 859 " --> pdb=" O ASP F 886 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ASP F 886 " --> pdb=" O TRP F 859 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 890 through 898 current: chain 'F' and resid 914 through 919 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 922 through 925 current: chain 'F' and resid 948 through 949 Processing sheet with id=AB7, first strand: chain 'Z' and resid 999 through 1003 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 999 through 1003 current: chain 'Z' and resid 1078 through 1086 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'Z' and resid 1007 through 1010 Processing sheet with id=AB9, first strand: chain 'Z' and resid 1066 through 1073 removed outlier: 5.349A pdb=" N VAL Z1067 " --> pdb=" O MET Z1063 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET Z1063 " --> pdb=" O VAL Z1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Z' and resid 1044 through 1048 Processing sheet with id=AC2, first strand: chain 'Z' and resid 1129 through 1132 removed outlier: 6.314A pdb=" N MET F1063 " --> pdb=" O VAL F1067 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL F1067 " --> pdb=" O MET F1063 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 719 through 721 Processing sheet with id=AC4, first strand: chain 'J' and resid 764 through 769 removed outlier: 5.250A pdb=" N TYR J 765 " --> pdb=" O PHE J 748 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE J 748 " --> pdb=" O TYR J 765 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 999 through 1003 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 999 through 1003 current: chain 'J' and resid 1078 through 1086 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'J' and resid 1007 through 1010 Processing sheet with id=AC7, first strand: chain 'J' and resid 1066 through 1073 removed outlier: 6.448A pdb=" N VAL J1061 " --> pdb=" O ILE J1068 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP J1070 " --> pdb=" O LEU J1059 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU J1059 " --> pdb=" O ASP J1070 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA J1072 " --> pdb=" O CYS J1057 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS J1057 " --> pdb=" O ALA J1072 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 1044 through 1048 Processing sheet with id=AC9, first strand: chain 'F' and resid 719 through 721 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 719 through 721 current: chain 'F' and resid 728 through 734 Processing sheet with id=AD1, first strand: chain 'F' and resid 764 through 769 removed outlier: 5.422A pdb=" N TYR F 765 " --> pdb=" O PHE F 748 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE F 748 " --> pdb=" O TYR F 765 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 999 through 1003 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 999 through 1003 current: chain 'F' and resid 1078 through 1086 No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 1007 through 1010 Processing sheet with id=AD4, first strand: chain 'F' and resid 1044 through 1048 875 hydrogen bonds defined for protein. 2355 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: 7.82 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 3384 1.29 - 1.42: 5593 1.42 - 1.55: 11188 1.55 - 1.68: 4 1.68 - 1.82: 132 Bond restraints: 20301 Sorted by residual: bond pdb=" CA SER A 359 " pdb=" CB SER A 359 " ideal model delta sigma weight residual 1.528 1.414 0.114 1.49e-02 4.50e+03 5.88e+01 bond pdb=" CA SER C 359 " pdb=" CB SER C 359 " ideal model delta sigma weight residual 1.527 1.435 0.092 1.38e-02 5.25e+03 4.41e+01 bond pdb=" C ILE A 363 " pdb=" O ILE A 363 " ideal model delta sigma weight residual 1.238 1.165 0.072 1.09e-02 8.42e+03 4.37e+01 bond pdb=" C PRO B 361 " pdb=" O PRO B 361 " ideal model delta sigma weight residual 1.235 1.152 0.083 1.30e-02 5.92e+03 4.06e+01 bond pdb=" C PRO C 361 " pdb=" O PRO C 361 " ideal model delta sigma weight residual 1.235 1.156 0.079 1.30e-02 5.92e+03 3.66e+01 ... (remaining 20296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 27227 2.48 - 4.95: 263 4.95 - 7.43: 52 7.43 - 9.90: 13 9.90 - 12.38: 9 Bond angle restraints: 27564 Sorted by residual: angle pdb=" N PRO Z 944 " pdb=" CA PRO Z 944 " pdb=" CB PRO Z 944 " ideal model delta sigma weight residual 103.08 90.70 12.38 9.70e-01 1.06e+00 1.63e+02 angle pdb=" N PRO J 944 " pdb=" CA PRO J 944 " pdb=" CB PRO J 944 " ideal model delta sigma weight residual 103.08 91.50 11.58 9.70e-01 1.06e+00 1.43e+02 angle pdb=" N PRO F 944 " pdb=" CA PRO F 944 " pdb=" CB PRO F 944 " ideal model delta sigma weight residual 103.08 91.59 11.49 9.70e-01 1.06e+00 1.40e+02 angle pdb=" C PRO F 944 " pdb=" CA PRO F 944 " pdb=" CB PRO F 944 " ideal model delta sigma weight residual 110.92 122.08 -11.16 1.22e+00 6.72e-01 8.37e+01 angle pdb=" N ASN Z 943 " pdb=" CA ASN Z 943 " pdb=" C ASN Z 943 " ideal model delta sigma weight residual 109.83 98.76 11.07 1.27e+00 6.20e-01 7.60e+01 ... (remaining 27559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 9934 17.61 - 35.23: 1307 35.23 - 52.84: 413 52.84 - 70.45: 104 70.45 - 88.06: 38 Dihedral angle restraints: 11796 sinusoidal: 4578 harmonic: 7218 Sorted by residual: dihedral pdb=" C ARG A 360 " pdb=" N ARG A 360 " pdb=" CA ARG A 360 " pdb=" CB ARG A 360 " ideal model delta harmonic sigma weight residual -122.60 -140.21 17.61 0 2.50e+00 1.60e-01 4.96e+01 dihedral pdb=" N ARG A 360 " pdb=" C ARG A 360 " pdb=" CA ARG A 360 " pdb=" CB ARG A 360 " ideal model delta harmonic sigma weight residual 122.80 139.53 -16.73 0 2.50e+00 1.60e-01 4.48e+01 dihedral pdb=" C ARG C 360 " pdb=" N ARG C 360 " pdb=" CA ARG C 360 " pdb=" CB ARG C 360 " ideal model delta harmonic sigma weight residual -122.60 -138.41 15.81 0 2.50e+00 1.60e-01 4.00e+01 ... (remaining 11793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 2903 0.153 - 0.306: 4 0.306 - 0.458: 0 0.458 - 0.611: 0 0.611 - 0.764: 3 Chirality restraints: 2910 Sorted by residual: chirality pdb=" CA ARG A 360 " pdb=" N ARG A 360 " pdb=" C ARG A 360 " pdb=" CB ARG A 360 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CA ARG C 360 " pdb=" N ARG C 360 " pdb=" C ARG C 360 " pdb=" CB ARG C 360 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA ARG B 360 " pdb=" N ARG B 360 " pdb=" C ARG B 360 " pdb=" CB ARG B 360 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 2907 not shown) Planarity restraints: 3603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 357 " -0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ILE C 357 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE C 357 " -0.023 2.00e-02 2.50e+03 pdb=" N TRP C 358 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 943 " 0.061 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO F 944 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO F 944 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 944 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN Z 943 " -0.060 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO Z 944 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO Z 944 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO Z 944 " -0.047 5.00e-02 4.00e+02 ... (remaining 3600 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 596 2.69 - 3.24: 17416 3.24 - 3.80: 31298 3.80 - 4.35: 43618 4.35 - 4.90: 74680 Nonbonded interactions: 167608 Sorted by model distance: nonbonded pdb=" OG1 THR A 14 " pdb=" O GLU A 19 " model vdw 2.138 3.040 nonbonded pdb=" OD2 ASP B 383 " pdb=" OH TYR F1111 " model vdw 2.145 3.040 nonbonded pdb=" O ARG C 360 " pdb=" C PRO C 361 " model vdw 2.151 3.270 nonbonded pdb=" O ARG A 360 " pdb=" C PRO A 361 " model vdw 2.161 3.270 nonbonded pdb=" OD1 ASP B 162 " pdb=" OH TYR Z1058 " model vdw 2.169 3.040 ... (remaining 167603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } 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: 3.390 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: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 45.180 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 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:11.560 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.004 0.114 20304 Z= 0.238 Angle : 0.695 12.380 27570 Z= 0.432 Chirality : 0.051 0.764 2910 Planarity : 0.005 0.089 3603 Dihedral : 18.494 88.062 7197 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.26 % Favored : 96.10 % Rotamer: Outliers : 6.95 % Allowed : 27.21 % Favored : 65.85 % Cbeta Deviations : 0.26 % 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: -0.54 (0.16), residues: 2514 helix: -1.58 (0.55), residues: 96 sheet: 0.68 (0.15), residues: 1175 loop : -1.33 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP Z 863 HIS 0.003 0.001 HIS B 268 PHE 0.011 0.001 PHE J1041 TYR 0.013 0.001 TYR Z 786 ARG 0.005 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.06466 ( 875) hydrogen bonds : angle 5.85776 ( 2355) SS BOND : bond 0.00241 ( 3) SS BOND : angle 2.57778 ( 6) covalent geometry : bond 0.00403 (20301) covalent geometry : angle 0.69438 (27564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 147 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ASN cc_start: 0.8813 (p0) cc_final: 0.8519 (p0) REVERT: Z 997 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7430 (pp) outliers start: 144 outliers final: 129 residues processed: 287 average time/residue: 0.9534 time to fit residues: 324.1447 Evaluate side-chains 267 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 137 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain Z residue 729 ILE Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 868 GLU Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 930 LEU Chi-restraints excluded: chain Z residue 944 PRO Chi-restraints excluded: chain Z residue 956 THR Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1024 VAL Chi-restraints excluded: chain Z residue 1025 THR Chi-restraints excluded: chain Z residue 1049 SER Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1096 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1103 ARG Chi-restraints excluded: chain Z residue 1105 SER Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 723 THR Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 887 THR Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 944 PRO Chi-restraints excluded: chain J residue 952 ASP Chi-restraints excluded: chain J residue 956 THR Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1012 SER Chi-restraints excluded: chain J residue 1019 THR Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1023 THR Chi-restraints excluded: chain J residue 1025 THR Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 751 LYS Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 784 ASP Chi-restraints excluded: chain F residue 801 VAL Chi-restraints excluded: chain F residue 849 SER Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 889 GLU Chi-restraints excluded: chain F residue 905 ILE Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 940 SER Chi-restraints excluded: chain F residue 944 PRO Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 981 ASN Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 993 ILE Chi-restraints excluded: chain F residue 1011 SER Chi-restraints excluded: chain F residue 1025 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1121 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 ASN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.090740 restraints weight = 24571.287| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.52 r_work: 0.2802 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 20304 Z= 0.246 Angle : 0.614 9.181 27570 Z= 0.335 Chirality : 0.048 0.218 2910 Planarity : 0.006 0.143 3603 Dihedral : 10.089 145.937 2947 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.98 % Favored : 95.62 % Rotamer: Outliers : 7.04 % Allowed : 25.33 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.57 % 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 (0.16), residues: 2514 helix: -1.95 (0.50), residues: 102 sheet: 0.63 (0.15), residues: 1170 loop : -1.37 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Z 863 HIS 0.005 0.001 HIS A 113 PHE 0.014 0.002 PHE J1041 TYR 0.020 0.002 TYR C 163 ARG 0.004 0.001 ARG F1009 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 875) hydrogen bonds : angle 5.62434 ( 2355) SS BOND : bond 0.00485 ( 3) SS BOND : angle 2.51506 ( 6) covalent geometry : bond 0.00585 (20301) covalent geometry : angle 0.61261 (27564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 134 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8420 (mt) REVERT: A 417 MET cc_start: 0.9164 (pp-130) cc_final: 0.8486 (pp-130) REVERT: B 19 GLU cc_start: 0.8274 (pm20) cc_final: 0.8069 (pm20) REVERT: B 39 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7273 (pp20) REVERT: Z 997 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7535 (pp) REVERT: J 1032 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.6844 (mtp180) outliers start: 146 outliers final: 83 residues processed: 267 average time/residue: 1.4505 time to fit residues: 453.0701 Evaluate side-chains 211 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 124 time to evaluate : 4.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1012 SER Chi-restraints excluded: chain J residue 1023 THR Chi-restraints excluded: chain J residue 1032 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 868 GLU Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1121 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 202 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 909 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.090213 restraints weight = 24454.286| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.57 r_work: 0.2805 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 20304 Z= 0.224 Angle : 0.592 9.082 27570 Z= 0.324 Chirality : 0.047 0.182 2910 Planarity : 0.005 0.139 3603 Dihedral : 8.562 59.003 2848 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.26 % Favored : 95.35 % Rotamer: Outliers : 7.33 % Allowed : 24.84 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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 (0.16), residues: 2514 helix: -1.95 (0.50), residues: 102 sheet: 0.60 (0.15), residues: 1188 loop : -1.35 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Z 863 HIS 0.004 0.001 HIS A 113 PHE 0.013 0.001 PHE J1041 TYR 0.018 0.002 TYR C 163 ARG 0.003 0.000 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 875) hydrogen bonds : angle 5.56372 ( 2355) SS BOND : bond 0.00605 ( 3) SS BOND : angle 3.09790 ( 6) covalent geometry : bond 0.00534 (20301) covalent geometry : angle 0.59060 (27564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 139 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8746 (tp) REVERT: A 37 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7492 (mm-30) REVERT: A 95 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 286 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.7975 (tpt) REVERT: A 355 ASP cc_start: 0.8647 (p0) cc_final: 0.8440 (p0) REVERT: A 417 MET cc_start: 0.9172 (pp-130) cc_final: 0.8615 (pp-130) REVERT: B 39 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: B 116 ASP cc_start: 0.8707 (t0) cc_final: 0.8359 (t0) REVERT: B 179 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8837 (mtp) REVERT: C 37 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: Z 962 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8513 (mt) REVERT: Z 997 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7439 (pp) REVERT: J 808 SER cc_start: 0.8894 (m) cc_final: 0.8544 (p) REVERT: J 809 ASP cc_start: 0.8391 (m-30) cc_final: 0.8037 (p0) REVERT: J 954 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8693 (tptp) REVERT: J 1032 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6845 (mtp180) REVERT: F 844 ARG cc_start: 0.7564 (ptm160) cc_final: 0.7174 (ptm160) REVERT: F 1063 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7754 (tpt) outliers start: 152 outliers final: 84 residues processed: 275 average time/residue: 1.0583 time to fit residues: 341.0180 Evaluate side-chains 223 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 127 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 37 GLU Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1127 LEU Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 893 SER Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1012 SER Chi-restraints excluded: chain J residue 1025 THR Chi-restraints excluded: chain J residue 1032 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1063 MET Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 160 optimal weight: 0.9990 chunk 174 optimal weight: 0.0070 chunk 157 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 overall best weight: 1.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN C 165 ASN Z 860 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.091797 restraints weight = 24724.075| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.58 r_work: 0.2827 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 20304 Z= 0.153 Angle : 0.551 8.507 27570 Z= 0.303 Chirality : 0.046 0.228 2910 Planarity : 0.005 0.134 3603 Dihedral : 7.641 59.338 2826 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.98 % Favored : 95.62 % Rotamer: Outliers : 5.74 % Allowed : 26.72 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.53 (0.16), residues: 2514 helix: -1.68 (0.53), residues: 96 sheet: 0.65 (0.15), residues: 1190 loop : -1.27 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Z 863 HIS 0.004 0.001 HIS Z 734 PHE 0.019 0.001 PHE Z 848 TYR 0.014 0.001 TYR C 163 ARG 0.004 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03013 ( 875) hydrogen bonds : angle 5.43150 ( 2355) SS BOND : bond 0.00423 ( 3) SS BOND : angle 2.52450 ( 6) covalent geometry : bond 0.00368 (20301) covalent geometry : angle 0.54987 (27564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 140 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8733 (tp) REVERT: A 37 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: A 95 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8382 (mt) REVERT: A 340 ASN cc_start: 0.8649 (p0) cc_final: 0.8308 (p0) REVERT: A 355 ASP cc_start: 0.8621 (p0) cc_final: 0.8368 (p0) REVERT: A 417 MET cc_start: 0.9186 (pp-130) cc_final: 0.8552 (pp-130) REVERT: B 39 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7275 (pp20) REVERT: B 116 ASP cc_start: 0.8704 (t0) cc_final: 0.8373 (t0) REVERT: B 179 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8817 (mtp) REVERT: Z 962 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8488 (mt) REVERT: Z 997 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7421 (pp) REVERT: Z 1009 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8158 (ptm-80) REVERT: J 809 ASP cc_start: 0.8323 (m-30) cc_final: 0.7999 (p0) REVERT: J 954 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8627 (tptp) REVERT: J 1042 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7957 (ttm170) REVERT: F 882 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8069 (tp) outliers start: 119 outliers final: 71 residues processed: 247 average time/residue: 1.1567 time to fit residues: 333.1417 Evaluate side-chains 211 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 129 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 893 SER Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1025 THR Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 202 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 340 ASN F 921 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.089447 restraints weight = 24708.213| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.55 r_work: 0.2791 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 20304 Z= 0.271 Angle : 0.623 8.533 27570 Z= 0.339 Chirality : 0.048 0.263 2910 Planarity : 0.006 0.134 3603 Dihedral : 7.755 59.129 2814 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.30 % Favored : 95.31 % Rotamer: Outliers : 7.09 % Allowed : 25.47 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.66 (0.16), residues: 2514 helix: -1.96 (0.49), residues: 103 sheet: 0.60 (0.15), residues: 1186 loop : -1.37 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Z 863 HIS 0.005 0.001 HIS A 113 PHE 0.019 0.002 PHE Z 848 TYR 0.020 0.002 TYR C 163 ARG 0.003 0.001 ARG Z 844 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 875) hydrogen bonds : angle 5.59161 ( 2355) SS BOND : bond 0.00622 ( 3) SS BOND : angle 3.06132 ( 6) covalent geometry : bond 0.00647 (20301) covalent geometry : angle 0.62151 (27564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 129 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8726 (tp) REVERT: A 37 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: A 95 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8430 (mt) REVERT: A 286 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8755 (tpt) REVERT: A 355 ASP cc_start: 0.8630 (p0) cc_final: 0.8370 (p0) REVERT: A 371 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.7972 (tttt) REVERT: A 417 MET cc_start: 0.9183 (pp-130) cc_final: 0.8677 (pp-130) REVERT: B 39 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: B 179 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8871 (mtp) REVERT: Z 829 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7595 (pmmt) REVERT: Z 962 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8498 (mt) REVERT: Z 1009 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8140 (ptm-80) REVERT: J 808 SER cc_start: 0.8838 (m) cc_final: 0.8489 (p) REVERT: J 809 ASP cc_start: 0.8430 (m-30) cc_final: 0.8024 (p0) REVERT: J 954 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8673 (tptp) REVERT: J 1032 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6821 (mtp180) REVERT: J 1042 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8015 (ttm170) REVERT: F 846 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.5855 (tm-30) REVERT: F 882 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8141 (tp) REVERT: F 1063 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.7736 (tpt) outliers start: 147 outliers final: 92 residues processed: 264 average time/residue: 1.0633 time to fit residues: 325.9183 Evaluate side-chains 237 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 129 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 829 LYS Chi-restraints excluded: chain Z residue 835 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 868 GLU Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 925 MET Chi-restraints excluded: chain Z residue 930 LEU Chi-restraints excluded: chain Z residue 956 THR Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 893 SER Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 956 THR Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1025 THR Chi-restraints excluded: chain J residue 1032 ARG Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 846 GLU Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 940 SER Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 977 THR Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1063 MET Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 0.6980 chunk 126 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Z 734 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.131034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.090395 restraints weight = 24599.206| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.56 r_work: 0.2811 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 20304 Z= 0.205 Angle : 0.581 8.251 27570 Z= 0.318 Chirality : 0.047 0.258 2910 Planarity : 0.005 0.132 3603 Dihedral : 7.486 57.696 2811 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.86 % Favored : 95.74 % Rotamer: Outliers : 6.51 % Allowed : 26.72 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.63 (0.16), residues: 2514 helix: -1.86 (0.49), residues: 103 sheet: 0.62 (0.15), residues: 1181 loop : -1.37 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Z 863 HIS 0.004 0.001 HIS Z 734 PHE 0.012 0.001 PHE J1041 TYR 0.017 0.001 TYR C 163 ARG 0.003 0.000 ARG A 360 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 875) hydrogen bonds : angle 5.50813 ( 2355) SS BOND : bond 0.00467 ( 3) SS BOND : angle 2.95100 ( 6) covalent geometry : bond 0.00490 (20301) covalent geometry : angle 0.57943 (27564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 138 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8749 (tp) REVERT: A 37 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: A 340 ASN cc_start: 0.8723 (p0) cc_final: 0.8368 (p0) REVERT: A 355 ASP cc_start: 0.8590 (p0) cc_final: 0.8317 (p0) REVERT: A 417 MET cc_start: 0.9207 (pp-130) cc_final: 0.8635 (pp-130) REVERT: B 39 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.7284 (pp20) REVERT: B 179 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8858 (mtp) REVERT: B 242 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: Z 962 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8529 (mt) REVERT: Z 1009 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.8192 (ptm-80) REVERT: J 809 ASP cc_start: 0.8370 (m-30) cc_final: 0.7990 (p0) REVERT: J 954 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8696 (tptp) REVERT: J 1009 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8517 (ttm-80) REVERT: J 1032 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6762 (mtp180) REVERT: J 1042 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8012 (ttm170) REVERT: F 844 ARG cc_start: 0.7544 (ptm160) cc_final: 0.6832 (ptt180) REVERT: F 882 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8178 (tp) outliers start: 135 outliers final: 87 residues processed: 263 average time/residue: 1.0474 time to fit residues: 320.4823 Evaluate side-chains 227 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 128 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 835 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 868 GLU Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 893 SER Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1009 ARG Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1025 THR Chi-restraints excluded: chain J residue 1032 ARG Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 940 SER Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 98 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** 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 = 0.3528 r_free = 0.3528 target = 0.131503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.090858 restraints weight = 24523.846| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.56 r_work: 0.2819 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20304 Z= 0.179 Angle : 0.591 24.908 27570 Z= 0.316 Chirality : 0.046 0.248 2910 Planarity : 0.006 0.194 3603 Dihedral : 7.377 58.592 2811 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.94 % Favored : 95.66 % Rotamer: Outliers : 6.03 % Allowed : 27.16 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % 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: -0.61 (0.16), residues: 2514 helix: -1.83 (0.50), residues: 103 sheet: 0.63 (0.15), residues: 1183 loop : -1.35 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Z 863 HIS 0.009 0.001 HIS Z 734 PHE 0.011 0.001 PHE Z1097 TYR 0.015 0.001 TYR C 163 ARG 0.006 0.000 ARG Z 844 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 875) hydrogen bonds : angle 5.45774 ( 2355) SS BOND : bond 0.00582 ( 3) SS BOND : angle 3.33868 ( 6) covalent geometry : bond 0.00426 (20301) covalent geometry : angle 0.58878 (27564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5028 Ramachandran restraints generated. 2514 Oldfield, 0 Emsley, 2514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 137 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8747 (tp) REVERT: A 37 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: A 340 ASN cc_start: 0.8701 (p0) cc_final: 0.8354 (p0) REVERT: A 355 ASP cc_start: 0.8545 (p0) cc_final: 0.8252 (p0) REVERT: A 417 MET cc_start: 0.9216 (pp-130) cc_final: 0.8586 (pp-130) REVERT: B 39 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7391 (pp20) REVERT: B 179 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8821 (mtp) REVERT: B 242 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: Z 829 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7517 (pmmt) REVERT: Z 831 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7329 (tt) REVERT: Z 962 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8508 (mt) REVERT: Z 1009 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8167 (ptm-80) REVERT: J 809 ASP cc_start: 0.8334 (m-30) cc_final: 0.8018 (p0) REVERT: J 1009 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8500 (ttm-80) REVERT: J 1042 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8006 (ttm170) REVERT: F 844 ARG cc_start: 0.7537 (ptm160) cc_final: 0.6840 (ptt180) REVERT: F 882 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8151 (tp) REVERT: F 1063 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7734 (tpt) outliers start: 125 outliers final: 85 residues processed: 251 average time/residue: 1.3253 time to fit residues: 393.0247 Evaluate side-chains 227 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 129 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 829 LYS Chi-restraints excluded: chain Z residue 831 LEU Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 868 GLU Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 930 LEU Chi-restraints excluded: chain Z residue 956 THR Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 982 CYS Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG Chi-restraints excluded: chain Z residue 1021 THR Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 722 LEU Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 893 SER Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 956 THR Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1009 ARG Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1025 THR Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 776 SER Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 940 SER Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 977 THR Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1063 MET Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1121 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5833 > 50: distance: 45 - 179: 10.156 distance: 48 - 176: 3.040 distance: 62 - 151: 8.355 distance: 65 - 148: 8.985 distance: 79 - 135: 8.553 distance: 82 - 132: 15.326 distance: 100 - 104: 6.628 distance: 104 - 105: 7.083 distance: 105 - 106: 16.540 distance: 105 - 108: 14.197 distance: 106 - 107: 21.140 distance: 106 - 112: 12.514 distance: 108 - 109: 13.263 distance: 109 - 110: 13.010 distance: 109 - 111: 14.666 distance: 112 - 113: 15.649 distance: 113 - 114: 14.944 distance: 113 - 116: 10.190 distance: 114 - 115: 21.324 distance: 114 - 120: 19.308 distance: 116 - 117: 12.817 distance: 117 - 118: 22.367 distance: 117 - 119: 21.201 distance: 120 - 121: 18.361 distance: 121 - 122: 23.915 distance: 121 - 124: 13.754 distance: 122 - 123: 14.940 distance: 122 - 128: 28.071 distance: 124 - 125: 12.737 distance: 125 - 126: 20.947 distance: 125 - 127: 15.407 distance: 128 - 129: 15.497 distance: 129 - 130: 6.869 distance: 130 - 131: 10.435 distance: 130 - 132: 6.540 distance: 132 - 133: 5.338 distance: 133 - 134: 3.050 distance: 133 - 136: 5.826 distance: 134 - 135: 4.953 distance: 134 - 139: 4.639 distance: 136 - 137: 8.494 distance: 136 - 138: 6.192 distance: 139 - 140: 5.563 distance: 139 - 231: 10.570 distance: 140 - 141: 4.917 distance: 140 - 143: 5.196 distance: 141 - 142: 4.245 distance: 141 - 148: 5.401 distance: 142 - 228: 5.369 distance: 143 - 144: 6.987 distance: 144 - 145: 4.791 distance: 145 - 146: 8.970 distance: 146 - 147: 11.767 distance: 148 - 149: 4.073 distance: 149 - 152: 3.952 distance: 150 - 151: 6.083 distance: 152 - 153: 5.492 distance: 153 - 154: 8.191 distance: 153 - 155: 4.688 distance: 154 - 156: 5.714 distance: 155 - 157: 7.159 distance: 155 - 158: 6.175 distance: 156 - 157: 6.247 distance: 159 - 161: 3.818 distance: 160 - 161: 5.747 distance: 162 - 218: 3.914 distance: 163 - 164: 3.425 distance: 164 - 165: 8.977 distance: 165 - 215: 9.116 distance: 167 - 168: 3.852 distance: 167 - 169: 3.156 distance: 168 - 170: 3.693 distance: 169 - 171: 5.969 distance: 169 - 172: 4.456 distance: 170 - 171: 7.876 distance: 171 - 173: 7.367 distance: 172 - 174: 3.370 distance: 176 - 177: 3.794 distance: 177 - 178: 6.097 distance: 177 - 180: 8.816 distance: 178 - 179: 5.796 distance: 178 - 183: 8.201 distance: 180 - 181: 21.632 distance: 180 - 182: 38.481 distance: 183 - 184: 3.774 distance: 183 - 204: 5.148 distance: 184 - 185: 7.147 distance: 184 - 187: 9.396 distance: 185 - 186: 5.505 distance: 185 - 190: 9.046 distance: 186 - 201: 6.490 distance: 187 - 189: 6.366