Starting phenix.real_space_refine on Thu Jan 23 09:06:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcj_38245/01_2025/8xcj_38245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcj_38245/01_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_38245/01_2025/8xcj_38245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcj_38245/01_2025/8xcj_38245.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcj_38245/01_2025/8xcj_38245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcj_38245/01_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-5571/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: 12.53, per 1000 atoms: 0.63 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: 4.84 Conformation dependent library (CDL) restraints added in 2.5 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: 2.57 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: 8.58 Time building geometry restraints manager: 5.66 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: 1.920 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: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 47.800 Find NCS groups from input model: 0.910 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: 0.010 Load rotamer database and sin/cos tables:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.610 ------------------------------------------------------------------------------- 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 20301 Z= 0.263 Angle : 0.694 12.380 27564 Z= 0.431 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 *********************** 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 : 2.369 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: 0.9790 time to fit residues: 332.8742 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 : 2.699 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.130830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.090727 restraints weight = 24571.053| |-----------------------------------------------------------------------------| 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: 0.2704 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 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 20301 Z= 0.379 Angle : 0.613 9.181 27564 Z= 0.334 Chirality : 0.048 0.218 2910 Planarity : 0.006 0.143 3603 Dihedral : 10.089 145.938 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 *********************** 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 : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8426 (mt) REVERT: A 417 MET cc_start: 0.9162 (pp-130) cc_final: 0.8482 (pp-130) REVERT: B 19 GLU cc_start: 0.8276 (pm20) cc_final: 0.8070 (pm20) REVERT: B 39 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7275 (pp20) REVERT: Z 997 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7547 (pp) REVERT: J 1032 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6858 (mtp180) outliers start: 146 outliers final: 83 residues processed: 267 average time/residue: 1.0777 time to fit residues: 335.3698 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 : 2.389 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** Z 860 ASN J 909 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.129996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.089411 restraints weight = 24538.870| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.54 r_work: 0.2794 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 20301 Z= 0.419 Angle : 0.623 9.180 27564 Z= 0.340 Chirality : 0.048 0.188 2910 Planarity : 0.006 0.139 3603 Dihedral : 8.752 59.816 2848 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.14 % Favored : 95.47 % Rotamer: Outliers : 7.53 % Allowed : 24.65 % 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: -0.70 (0.16), residues: 2514 helix: -2.03 (0.49), residues: 102 sheet: 0.56 (0.14), residues: 1188 loop : -1.40 (0.16), residues: 1224 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 0.005 0.001 ARG B 335 *********************** 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 292 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 136 time to evaluate : 2.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8740 (tp) REVERT: A 37 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: A 95 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8439 (mt) REVERT: A 286 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8196 (ttt) REVERT: A 355 ASP cc_start: 0.8664 (p0) cc_final: 0.8459 (p0) REVERT: A 417 MET cc_start: 0.9148 (pp-130) cc_final: 0.8622 (pp-130) REVERT: B 39 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7279 (pp20) REVERT: B 116 ASP cc_start: 0.8717 (t0) cc_final: 0.8385 (t0) REVERT: C 22 CYS cc_start: 0.7461 (p) cc_final: 0.6960 (m) REVERT: Z 829 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7023 (mmtp) REVERT: Z 962 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8527 (mt) REVERT: J 808 SER cc_start: 0.8852 (m) cc_final: 0.8504 (p) REVERT: J 809 ASP cc_start: 0.8438 (m-30) cc_final: 0.7999 (p0) REVERT: J 1032 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6803 (mtp180) REVERT: F 844 ARG cc_start: 0.7555 (ptm160) cc_final: 0.7179 (ptm160) REVERT: F 882 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8051 (tp) REVERT: F 1063 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7789 (tpt) outliers start: 156 outliers final: 89 residues processed: 278 average time/residue: 1.0832 time to fit residues: 352.5171 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 : 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 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 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 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 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 C residue 360 ARG Chi-restraints excluded: chain Z residue 804 VAL Chi-restraints excluded: chain Z residue 829 LYS 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 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 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 838 THR 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 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1012 SER 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 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 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 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: 2.9990 chunk 174 optimal weight: 0.0570 chunk 157 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 215 optimal weight: 0.0370 chunk 220 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 734 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093365 restraints weight = 24694.213| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.62 r_work: 0.2853 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 20301 Z= 0.174 Angle : 0.521 8.424 27564 Z= 0.288 Chirality : 0.045 0.192 2910 Planarity : 0.005 0.134 3603 Dihedral : 7.511 59.211 2833 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.74 % Favored : 95.86 % Rotamer: Outliers : 4.92 % Allowed : 27.26 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.16), residues: 2514 helix: -1.61 (0.54), residues: 96 sheet: 0.66 (0.15), residues: 1182 loop : -1.26 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Z 863 HIS 0.003 0.001 HIS Z 734 PHE 0.014 0.001 PHE Z 848 TYR 0.014 0.001 TYR Z 765 ARG 0.004 0.000 ARG B 335 *********************** 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 252 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 150 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8739 (tp) REVERT: A 340 ASN cc_start: 0.8515 (p0) cc_final: 0.8247 (p0) REVERT: A 355 ASP cc_start: 0.8619 (p0) cc_final: 0.8364 (p0) REVERT: A 417 MET cc_start: 0.9184 (pp-130) cc_final: 0.8631 (pp-130) REVERT: B 39 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7399 (pp20) REVERT: B 116 ASP cc_start: 0.8657 (t0) cc_final: 0.8356 (t0) REVERT: B 179 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8864 (mtp) REVERT: B 340 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8230 (p0) REVERT: C 165 ASN cc_start: 0.8855 (m110) cc_final: 0.8631 (m-40) REVERT: Z 831 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6963 (tt) REVERT: Z 997 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7373 (pp) REVERT: Z 1009 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8166 (ptm-80) REVERT: J 809 ASP cc_start: 0.8261 (m-30) cc_final: 0.7971 (p0) REVERT: J 948 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8488 (m) REVERT: J 1042 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7925 (ttm170) REVERT: F 844 ARG cc_start: 0.7517 (ptm160) cc_final: 0.7201 (ptm-80) outliers start: 102 outliers final: 58 residues processed: 240 average time/residue: 1.1032 time to fit residues: 309.6235 Evaluate side-chains 202 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 135 time to evaluate : 2.104 ------------------------------------------------------------------------------- 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 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 157 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 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 340 ASN 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 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 346 THR Chi-restraints excluded: chain Z residue 734 HIS Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 831 LEU 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 883 SER 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 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 801 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 948 SER Chi-restraints excluded: chain J residue 998 VAL 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 928 VAL Chi-restraints excluded: chain F residue 939 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 1100 THR 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: 0.0870 chunk 162 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** Z 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 921 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.089319 restraints weight = 24748.893| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.55 r_work: 0.2792 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 20301 Z= 0.432 Angle : 0.622 8.496 27564 Z= 0.339 Chirality : 0.048 0.211 2910 Planarity : 0.006 0.134 3603 Dihedral : 7.407 59.496 2799 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.34 % Favored : 95.27 % Rotamer: Outliers : 6.66 % Allowed : 25.62 % Favored : 67.73 % 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: -1.93 (0.49), residues: 103 sheet: 0.60 (0.15), residues: 1190 loop : -1.34 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Z 863 HIS 0.008 0.001 HIS Z 734 PHE 0.024 0.002 PHE Z 848 TYR 0.021 0.002 TYR C 163 ARG 0.003 0.001 ARG Z1103 *********************** 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 268 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 130 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8733 (tp) REVERT: A 37 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: A 95 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8424 (mt) REVERT: A 355 ASP cc_start: 0.8637 (p0) cc_final: 0.8381 (p0) REVERT: A 417 MET cc_start: 0.9212 (pp-130) cc_final: 0.8639 (pp-130) REVERT: B 39 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: C 282 ASP cc_start: 0.8131 (m-30) cc_final: 0.7808 (m-30) REVERT: Z 962 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8352 (mt) REVERT: J 809 ASP cc_start: 0.8398 (m-30) cc_final: 0.8016 (p0) REVERT: J 1009 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8543 (ttm-80) REVERT: J 1042 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7947 (ttm-80) REVERT: F 882 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8132 (tp) outliers start: 138 outliers final: 91 residues processed: 254 average time/residue: 1.0357 time to fit residues: 308.8598 Evaluate side-chains 229 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 130 time to evaluate : 2.337 ------------------------------------------------------------------------------- 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 55 ASP 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 157 SER 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 280 MET Chi-restraints excluded: chain A residue 342 GLN 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 141 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 174 VAL 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 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 800 PHE 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 883 SER Chi-restraints excluded: chain Z residue 921 ASN 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 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 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 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 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 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 1117 VAL Chi-restraints excluded: chain F residue 1121 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: 0.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 ** Z 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.130637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.089959 restraints weight = 24623.132| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.54 r_work: 0.2806 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20301 Z= 0.352 Angle : 0.593 8.299 27564 Z= 0.324 Chirality : 0.047 0.248 2910 Planarity : 0.005 0.132 3603 Dihedral : 7.309 57.095 2798 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.06 % Favored : 95.54 % Rotamer: Outliers : 6.51 % Allowed : 26.05 % 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: -0.63 (0.16), residues: 2514 helix: -1.88 (0.49), residues: 103 sheet: 0.60 (0.15), residues: 1187 loop : -1.35 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Z 863 HIS 0.004 0.001 HIS Z 734 PHE 0.016 0.001 PHE Z 848 TYR 0.017 0.002 TYR C 163 ARG 0.003 0.000 ARG Z 932 *********************** 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 271 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 136 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8755 (tp) REVERT: A 37 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: A 340 ASN cc_start: 0.8763 (p0) cc_final: 0.8423 (p0) REVERT: A 355 ASP cc_start: 0.8572 (p0) cc_final: 0.8296 (p0) REVERT: A 371 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.7980 (tttt) REVERT: A 417 MET cc_start: 0.9216 (pp-130) cc_final: 0.8686 (pp-130) REVERT: B 39 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7301 (pp20) REVERT: B 242 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: Z 962 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8355 (mt) REVERT: Z 1009 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8122 (ptm-80) REVERT: Z 1075 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7655 (mt-10) REVERT: J 809 ASP cc_start: 0.8379 (m-30) cc_final: 0.8001 (p0) REVERT: J 1009 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8550 (ttm-80) REVERT: J 1032 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6789 (mtp180) REVERT: J 1042 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8044 (ttm170) REVERT: F 846 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5909 (tm-30) REVERT: F 882 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8185 (tp) REVERT: F 1063 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7755 (tpt) outliers start: 135 outliers final: 85 residues processed: 262 average time/residue: 1.1116 time to fit residues: 338.6398 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 : 2.261 ------------------------------------------------------------------------------- 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 157 SER Chi-restraints excluded: chain A residue 186 THR 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 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 174 VAL 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 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 734 HIS Chi-restraints excluded: chain Z residue 800 PHE 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 883 SER Chi-restraints excluded: chain Z residue 923 ILE 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 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 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 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 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 F residue 732 THR 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 1117 VAL Chi-restraints excluded: chain F residue 1121 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 177 optimal weight: 0.0030 chunk 100 optimal weight: 1.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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** ** Z 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.090950 restraints weight = 24546.554| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.57 r_work: 0.2819 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20301 Z= 0.265 Angle : 0.584 24.783 27564 Z= 0.313 Chirality : 0.046 0.246 2910 Planarity : 0.006 0.193 3603 Dihedral : 7.180 58.124 2798 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.90 % Favored : 95.70 % Rotamer: Outliers : 5.89 % Allowed : 26.63 % Favored : 67.49 % 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: -0.58 (0.16), residues: 2514 helix: -1.81 (0.50), residues: 103 sheet: 0.64 (0.15), residues: 1187 loop : -1.32 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Z 863 HIS 0.007 0.001 HIS Z 734 PHE 0.025 0.001 PHE Z 848 TYR 0.015 0.001 TYR C 163 ARG 0.004 0.000 ARG Z 844 *********************** 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 258 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 136 time to evaluate : 2.309 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8754 (tp) REVERT: A 340 ASN cc_start: 0.8702 (p0) cc_final: 0.8364 (p0) REVERT: A 355 ASP cc_start: 0.8550 (p0) cc_final: 0.8256 (p0) REVERT: A 371 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.7986 (tttt) REVERT: A 417 MET cc_start: 0.9217 (pp-130) cc_final: 0.8643 (pp-130) REVERT: B 39 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7388 (pp20) REVERT: B 242 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: Z 962 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8338 (mt) REVERT: Z 1009 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8197 (ptm-80) REVERT: J 809 ASP cc_start: 0.8332 (m-30) cc_final: 0.8017 (p0) REVERT: J 846 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6425 (pp20) REVERT: J 1009 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8522 (ttm-80) REVERT: J 1032 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6796 (mtp180) REVERT: J 1042 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8034 (ttm170) REVERT: F 844 ARG cc_start: 0.7536 (ptm160) cc_final: 0.6853 (ptt180) REVERT: F 846 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5912 (tm-30) REVERT: F 882 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8136 (tp) REVERT: F 1063 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7743 (tpt) outliers start: 122 outliers final: 82 residues processed: 247 average time/residue: 1.1448 time to fit residues: 328.9048 Evaluate side-chains 224 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 129 time to evaluate : 2.299 ------------------------------------------------------------------------------- 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 55 ASP 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 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 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 174 VAL 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 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 804 VAL Chi-restraints excluded: chain Z residue 835 VAL 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 883 SER Chi-restraints excluded: chain Z residue 921 ASN Chi-restraints excluded: chain Z residue 930 LEU 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 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 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 846 GLU 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 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 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 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 1117 VAL Chi-restraints excluded: chain F residue 1121 VAL Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 69 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** Z 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.089837 restraints weight = 24820.787| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.48 r_work: 0.2802 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 20301 Z= 0.386 Angle : 0.622 16.911 27564 Z= 0.336 Chirality : 0.048 0.270 2910 Planarity : 0.006 0.167 3603 Dihedral : 7.292 58.825 2795 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.18 % Favored : 95.43 % Rotamer: Outliers : 6.37 % Allowed : 26.39 % Favored : 67.25 % 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: -0.66 (0.16), residues: 2514 helix: -1.82 (0.51), residues: 97 sheet: 0.60 (0.15), residues: 1182 loop : -1.39 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Z 863 HIS 0.003 0.001 HIS A 113 PHE 0.016 0.002 PHE Z 848 TYR 0.019 0.002 TYR C 163 ARG 0.003 0.000 ARG Z 844 *********************** REFINEMENT MACRO_CYCLE 8 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 261 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 129 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8740 (tp) REVERT: A 37 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: A 95 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8433 (mt) REVERT: A 355 ASP cc_start: 0.8552 (p0) cc_final: 0.8261 (p0) REVERT: A 371 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.7992 (tttt) REVERT: A 375 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8763 (mmtm) REVERT: A 417 MET cc_start: 0.9200 (pp-130) cc_final: 0.8716 (pp-130) REVERT: B 39 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: B 116 ASP cc_start: 0.8722 (t0) cc_final: 0.8414 (t0) REVERT: B 242 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8657 (tt0) REVERT: Z 962 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8360 (mt) REVERT: Z 970 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.7757 (m) REVERT: Z 1009 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8123 (ptm-80) REVERT: J 809 ASP cc_start: 0.8452 (m-30) cc_final: 0.8091 (p0) REVERT: J 846 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6418 (pp20) REVERT: J 1009 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8551 (ttm-80) REVERT: J 1032 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6839 (mtp180) REVERT: J 1042 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8053 (ttm170) REVERT: F 844 ARG cc_start: 0.7546 (ptm160) cc_final: 0.6852 (ptt180) REVERT: F 846 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5930 (tm-30) REVERT: F 882 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8199 (tp) REVERT: F 1063 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7751 (tpt) REVERT: F 1103 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8595 (ptm160) outliers start: 132 outliers final: 91 residues processed: 251 average time/residue: 1.1824 time to fit residues: 341.5779 Evaluate side-chains 236 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 127 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 55 ASP 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 157 SER 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 346 THR Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 375 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 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 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 753 ILE 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 921 ASN Chi-restraints excluded: chain Z residue 923 ILE Chi-restraints excluded: chain Z residue 930 LEU Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 970 SER 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 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 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 846 GLU 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 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 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 889 GLU 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 Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 46 optimal weight: 1.9990 chunk 238 optimal weight: 0.4980 chunk 159 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.091433 restraints weight = 24571.294| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.58 r_work: 0.2829 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20301 Z= 0.244 Angle : 0.567 12.924 27564 Z= 0.309 Chirality : 0.046 0.256 2910 Planarity : 0.005 0.152 3603 Dihedral : 7.029 58.468 2795 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.82 % Favored : 95.78 % Rotamer: Outliers : 5.16 % Allowed : 27.59 % Favored : 67.25 % 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: -0.56 (0.16), residues: 2514 helix: -1.50 (0.53), residues: 97 sheet: 0.66 (0.15), residues: 1178 loop : -1.33 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Z 863 HIS 0.003 0.001 HIS B 268 PHE 0.020 0.001 PHE Z 848 TYR 0.014 0.001 TYR C 163 ARG 0.008 0.000 ARG Z 844 *********************** REFINEMENT MACRO_CYCLE 9 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 243 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 136 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8763 (tp) REVERT: A 340 ASN cc_start: 0.8618 (p0) cc_final: 0.8278 (p0) REVERT: A 355 ASP cc_start: 0.8542 (p0) cc_final: 0.8242 (p0) REVERT: A 371 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.7983 (tttt) REVERT: A 417 MET cc_start: 0.9221 (pp-130) cc_final: 0.8824 (pp-130) REVERT: B 39 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: B 116 ASP cc_start: 0.8698 (t0) cc_final: 0.8371 (t0) REVERT: B 242 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: Z 962 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8330 (mt) REVERT: Z 970 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7708 (m) REVERT: Z 1009 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8268 (ptm-80) REVERT: J 809 ASP cc_start: 0.8321 (m-30) cc_final: 0.8009 (p0) REVERT: J 846 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6466 (pp20) REVERT: J 1009 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8519 (ttm-80) REVERT: J 1032 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6769 (mtp180) REVERT: J 1042 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8019 (ttm170) REVERT: F 844 ARG cc_start: 0.7504 (ptm160) cc_final: 0.6822 (ptt180) REVERT: F 1103 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8600 (ptm160) outliers start: 107 outliers final: 80 residues processed: 234 average time/residue: 1.1819 time to fit residues: 322.1494 Evaluate side-chains 222 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 130 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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 55 ASP 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 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 371 LYS 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 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 99 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 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 921 ASN Chi-restraints excluded: chain Z residue 930 LEU Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 970 SER 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 722 LEU 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 846 GLU 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 948 SER 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 206 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 210 optimal weight: 0.0060 chunk 213 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 overall best weight: 1.3800 ------------------------------------------------------------------------------- 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** ** Z 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.131231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.091065 restraints weight = 24564.408| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.75 r_work: 0.2792 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20301 Z= 0.294 Angle : 0.589 11.382 27564 Z= 0.320 Chirality : 0.047 0.258 2910 Planarity : 0.005 0.145 3603 Dihedral : 7.025 58.508 2791 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.10 % Favored : 95.58 % Rotamer: Outliers : 4.97 % Allowed : 27.98 % Favored : 67.05 % 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: -0.57 (0.16), residues: 2514 helix: -1.57 (0.52), residues: 97 sheet: 0.65 (0.15), residues: 1182 loop : -1.33 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP Z 863 HIS 0.002 0.001 HIS B 268 PHE 0.017 0.001 PHE Z 848 TYR 0.016 0.001 TYR C 163 ARG 0.004 0.000 ARG Z 844 ********************** REFINEMENT MACRO_CYCLE 10 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 235 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 132 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8774 (tp) REVERT: A 95 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8431 (mt) REVERT: A 340 ASN cc_start: 0.8754 (p0) cc_final: 0.8391 (p0) REVERT: A 355 ASP cc_start: 0.8605 (p0) cc_final: 0.8286 (p0) REVERT: A 371 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8016 (tttt) REVERT: A 375 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8730 (mmtm) REVERT: A 417 MET cc_start: 0.9241 (pp-130) cc_final: 0.8680 (pp-130) REVERT: B 39 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7485 (pp20) REVERT: B 116 ASP cc_start: 0.8775 (t0) cc_final: 0.8458 (t0) REVERT: B 242 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8682 (tt0) REVERT: Z 962 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8374 (mt) REVERT: Z 970 SER cc_start: 0.8382 (OUTLIER) cc_final: 0.7785 (m) REVERT: Z 1009 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8206 (ptm-80) REVERT: J 809 ASP cc_start: 0.8361 (m-30) cc_final: 0.8044 (p0) REVERT: J 846 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6481 (pp20) REVERT: J 1009 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8551 (ttm-80) REVERT: J 1032 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6888 (mtp180) REVERT: J 1042 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8096 (ttm170) REVERT: F 844 ARG cc_start: 0.7532 (ptm160) cc_final: 0.6855 (ptt180) REVERT: F 1103 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8604 (ptm160) outliers start: 103 outliers final: 85 residues processed: 230 average time/residue: 1.1278 time to fit residues: 300.8197 Evaluate side-chains 228 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 129 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 55 ASP 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 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 371 LYS Chi-restraints excluded: chain A residue 375 LYS 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 141 LEU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 174 VAL 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 1 VAL 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 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 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 970 SER 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 1100 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 801 VAL Chi-restraints excluded: chain J residue 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 846 GLU 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 948 SER 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 889 GLU 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 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 Chi-restraints excluded: chain F residue 1129 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 194 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** ** Z 826 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.132599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.092293 restraints weight = 24582.210| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.57 r_work: 0.2841 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 20301 Z= 0.214 Angle : 0.554 7.459 27564 Z= 0.304 Chirality : 0.045 0.235 2910 Planarity : 0.005 0.126 3603 Dihedral : 6.860 59.342 2790 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.94 % Favored : 95.78 % Rotamer: Outliers : 4.49 % Allowed : 28.41 % Favored : 67.10 % 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: -0.50 (0.16), residues: 2514 helix: -1.40 (0.53), residues: 97 sheet: 0.71 (0.15), residues: 1175 loop : -1.31 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP Z 863 HIS 0.002 0.001 HIS B 268 PHE 0.026 0.001 PHE Z 848 TYR 0.012 0.001 TYR C 163 ARG 0.006 0.000 ARG Z 844 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13433.78 seconds wall clock time: 238 minutes 37.02 seconds (14317.02 seconds total)