Starting phenix.real_space_refine on Thu Sep 18 20:32:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcj_38245/09_2025/8xcj_38245.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcj_38245/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xcj_38245/09_2025/8xcj_38245.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcj_38245/09_2025/8xcj_38245.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xcj_38245/09_2025/8xcj_38245.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcj_38245/09_2025/8xcj_38245.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.96, per 1000 atoms: 0.25 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: 1.80 Conformation dependent library (CDL) restraints added in 875.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.77 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: 3.77 Time building geometry restraints manager: 2.40 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 19.810 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 20304 Z= 0.238 Angle : 0.695 12.380 27570 Z= 0.432 Chirality : 0.051 0.764 2910 Planarity : 0.005 0.089 3603 Dihedral : 18.494 88.062 7197 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.18 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A 360 TYR 0.013 0.001 TYR Z 786 PHE 0.011 0.001 PHE J1041 TRP 0.037 0.001 TRP Z 863 HIS 0.003 0.001 HIS B 268 Details of bonding type rmsd covalent geometry : bond 0.00403 (20301) covalent geometry : angle 0.69438 (27564) SS BOND : bond 0.00241 ( 3) SS BOND : angle 2.57778 ( 6) hydrogen bonds : bond 0.06466 ( 875) hydrogen bonds : angle 5.85776 ( 2355) *********************** 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 : 0.791 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: 0.4667 time to fit residues: 157.8047 Evaluate side-chains 266 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 136 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 216 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 247 optimal weight: 0.1980 chunk 130 optimal weight: 0.0030 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 C 169 ASN C 340 ASN J 909 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094603 restraints weight = 24456.055| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.58 r_work: 0.2868 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 20304 Z= 0.112 Angle : 0.523 8.675 27570 Z= 0.288 Chirality : 0.045 0.162 2910 Planarity : 0.005 0.141 3603 Dihedral : 9.464 146.715 2947 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.54 % Favored : 96.06 % Rotamer: Outliers : 5.89 % Allowed : 25.76 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.16), residues: 2514 helix: -1.37 (0.55), residues: 96 sheet: 0.71 (0.15), residues: 1176 loop : -1.19 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 360 TYR 0.017 0.001 TYR Z 765 PHE 0.010 0.001 PHE Z 848 TRP 0.021 0.001 TRP Z 863 HIS 0.002 0.000 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00268 (20301) covalent geometry : angle 0.52213 (27564) SS BOND : bond 0.00449 ( 3) SS BOND : angle 1.73960 ( 6) hydrogen bonds : bond 0.02764 ( 875) hydrogen bonds : angle 5.37380 ( 2355) *********************** 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 276 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 154 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8322 (mt) REVERT: A 417 MET cc_start: 0.9168 (pp-130) cc_final: 0.8595 (pp-130) REVERT: B 39 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7177 (pp20) REVERT: B 116 ASP cc_start: 0.8610 (t0) cc_final: 0.8313 (t0) REVERT: B 179 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8668 (mtp) REVERT: B 340 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8134 (p0) REVERT: C 165 ASN cc_start: 0.8817 (m110) cc_final: 0.8596 (m-40) REVERT: Z 829 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.6958 (mmtp) REVERT: Z 831 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7191 (tt) REVERT: Z 962 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8522 (mt) REVERT: Z 997 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7645 (pp) REVERT: Z 1052 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8880 (m) REVERT: J 809 ASP cc_start: 0.8196 (m-30) cc_final: 0.7794 (p0) REVERT: F 1012 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.9008 (p) outliers start: 122 outliers final: 62 residues processed: 263 average time/residue: 0.4550 time to fit residues: 140.3109 Evaluate side-chains 207 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 135 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 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 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 804 VAL Chi-restraints excluded: chain Z residue 829 LYS Chi-restraints excluded: chain Z residue 831 LEU Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 930 LEU Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 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 892 LEU Chi-restraints excluded: chain J residue 998 VAL 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 1012 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 36 optimal weight: 3.9990 chunk 161 optimal weight: 0.2980 chunk 87 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 138 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS B 340 ASN Z 860 ASN Z 943 ASN F 921 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.089365 restraints weight = 24896.645| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.55 r_work: 0.2790 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 20304 Z= 0.301 Angle : 0.641 8.807 27570 Z= 0.350 Chirality : 0.049 0.227 2910 Planarity : 0.006 0.138 3603 Dihedral : 8.244 58.990 2827 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.06 % Favored : 95.54 % Rotamer: Outliers : 6.90 % Allowed : 24.79 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.16), residues: 2514 helix: -1.94 (0.49), residues: 103 sheet: 0.63 (0.14), residues: 1188 loop : -1.35 (0.16), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Z1103 TYR 0.022 0.002 TYR C 163 PHE 0.017 0.002 PHE J1041 TRP 0.019 0.002 TRP Z 863 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00717 (20301) covalent geometry : angle 0.63986 (27564) SS BOND : bond 0.00556 ( 3) SS BOND : angle 2.89723 ( 6) hydrogen bonds : bond 0.03694 ( 875) hydrogen bonds : angle 5.61723 ( 2355) *********************** 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 276 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 133 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 95 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 286 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8172 (ttt) REVERT: A 355 ASP cc_start: 0.8674 (p0) cc_final: 0.8461 (p0) REVERT: A 417 MET cc_start: 0.9145 (pp-130) cc_final: 0.8607 (pp-130) REVERT: B 39 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7313 (pp20) REVERT: Z 829 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.6957 (mmtp) REVERT: Z 962 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8563 (mt) REVERT: J 808 SER cc_start: 0.8885 (m) cc_final: 0.8548 (p) REVERT: J 809 ASP cc_start: 0.8422 (m-30) cc_final: 0.7984 (p0) REVERT: J 954 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8646 (tptp) REVERT: F 844 ARG cc_start: 0.7559 (ptm160) cc_final: 0.7255 (ptm160) REVERT: F 1039 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8888 (tp) REVERT: F 1063 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7765 (tpt) outliers start: 143 outliers final: 79 residues processed: 263 average time/residue: 0.4805 time to fit residues: 146.6366 Evaluate side-chains 216 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 128 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 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 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 762 SER Chi-restraints excluded: chain Z residue 800 PHE 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 987 THR 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 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 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 948 SER Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1012 SER Chi-restraints excluded: chain J residue 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 1039 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 chunk 3 optimal weight: 0.0470 overall best weight: 1.1884 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.091636 restraints weight = 24728.552| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.57 r_work: 0.2824 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 20304 Z= 0.173 Angle : 0.561 8.435 27570 Z= 0.308 Chirality : 0.046 0.236 2910 Planarity : 0.005 0.134 3603 Dihedral : 7.562 58.849 2816 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.82 % Favored : 95.78 % Rotamer: Outliers : 6.17 % Allowed : 25.47 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.16), residues: 2514 helix: -1.53 (0.54), residues: 97 sheet: 0.67 (0.15), residues: 1193 loop : -1.28 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 335 TYR 0.014 0.001 TYR C 163 PHE 0.011 0.001 PHE J1041 TRP 0.020 0.001 TRP Z 863 HIS 0.004 0.001 HIS Z 734 Details of bonding type rmsd covalent geometry : bond 0.00415 (20301) covalent geometry : angle 0.55885 (27564) SS BOND : bond 0.00585 ( 3) SS BOND : angle 3.04714 ( 6) hydrogen bonds : bond 0.03097 ( 875) hydrogen bonds : angle 5.43402 ( 2355) *********************** 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 265 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 137 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8774 (tp) REVERT: A 37 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7520 (mm-30) REVERT: A 355 ASP cc_start: 0.8615 (p0) cc_final: 0.8368 (p0) REVERT: A 417 MET cc_start: 0.9180 (pp-130) cc_final: 0.8543 (pp-130) REVERT: B 39 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7419 (pp20) REVERT: B 179 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8834 (mtp) REVERT: Z 829 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.6937 (mmtp) REVERT: Z 997 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7429 (pp) REVERT: Z 1009 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8105 (ptm-80) REVERT: J 809 ASP cc_start: 0.8323 (m-30) cc_final: 0.8007 (p0) REVERT: J 1042 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7995 (ttm170) REVERT: F 773 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8184 (pp) REVERT: F 882 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8138 (tp) outliers start: 128 outliers final: 71 residues processed: 253 average time/residue: 0.5000 time to fit residues: 146.0737 Evaluate side-chains 209 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 128 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 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 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 317 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 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 883 SER 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 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 804 VAL Chi-restraints excluded: chain J residue 824 GLU Chi-restraints excluded: chain J residue 827 LEU Chi-restraints excluded: chain J residue 854 ASP Chi-restraints excluded: chain J residue 867 ILE Chi-restraints excluded: chain J residue 870 THR Chi-restraints excluded: chain J residue 877 VAL Chi-restraints excluded: chain J residue 892 LEU Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL 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 773 ILE Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 882 LEU Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1040 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR Chi-restraints excluded: chain F residue 1103 ARG Chi-restraints excluded: chain F residue 1117 VAL Chi-restraints excluded: chain F residue 1121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 223 optimal weight: 10.0000 chunk 57 optimal weight: 0.0370 chunk 152 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 overall best weight: 1.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Z 734 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.131463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.090721 restraints weight = 24555.999| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.55 r_work: 0.2817 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 20304 Z= 0.193 Angle : 0.572 8.196 27570 Z= 0.314 Chirality : 0.046 0.245 2910 Planarity : 0.005 0.132 3603 Dihedral : 7.471 58.548 2813 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.90 % Favored : 95.70 % Rotamer: Outliers : 5.84 % Allowed : 26.00 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.16), residues: 2514 helix: -1.67 (0.51), residues: 103 sheet: 0.65 (0.15), residues: 1190 loop : -1.30 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 335 TYR 0.016 0.001 TYR C 163 PHE 0.012 0.001 PHE J1041 TRP 0.022 0.001 TRP Z 863 HIS 0.003 0.001 HIS Z 734 Details of bonding type rmsd covalent geometry : bond 0.00463 (20301) covalent geometry : angle 0.57092 (27564) SS BOND : bond 0.00549 ( 3) SS BOND : angle 2.79642 ( 6) hydrogen bonds : bond 0.03203 ( 875) hydrogen bonds : angle 5.44773 ( 2355) *********************** 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 254 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 133 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8770 (tp) REVERT: A 37 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: A 95 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8400 (mt) REVERT: A 286 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8665 (tpt) REVERT: A 355 ASP cc_start: 0.8581 (p0) cc_final: 0.8324 (p0) REVERT: A 417 MET cc_start: 0.9193 (pp-130) cc_final: 0.8590 (pp-130) REVERT: B 39 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7290 (pp20) REVERT: B 116 ASP cc_start: 0.8707 (t0) cc_final: 0.8398 (t0) REVERT: B 242 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8678 (tt0) REVERT: Z 962 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8523 (mt) REVERT: J 809 ASP cc_start: 0.8353 (m-30) cc_final: 0.8019 (p0) REVERT: J 954 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8600 (tptp) REVERT: J 1042 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8011 (ttm170) REVERT: F 882 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8145 (tp) outliers start: 121 outliers final: 79 residues processed: 243 average time/residue: 0.5077 time to fit residues: 143.1456 Evaluate side-chains 217 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 128 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 89 LYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 210 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 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 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 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 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 925 MET Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1052 THR Chi-restraints excluded: chain Z residue 1077 VAL Chi-restraints excluded: chain Z residue 1100 THR Chi-restraints excluded: chain Z residue 1102 THR Chi-restraints excluded: chain Z residue 1117 VAL Chi-restraints excluded: chain Z residue 1129 ILE Chi-restraints excluded: chain J residue 728 GLN Chi-restraints excluded: chain J residue 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 948 SER Chi-restraints excluded: chain J residue 954 LYS Chi-restraints excluded: chain J residue 955 LEU Chi-restraints excluded: chain J residue 998 VAL Chi-restraints excluded: chain J residue 1012 SER Chi-restraints excluded: chain J residue 1023 THR Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 732 THR Chi-restraints excluded: chain F residue 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 0.0670 chunk 121 optimal weight: 0.8980 chunk 249 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.133297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.092836 restraints weight = 24443.793| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.50 r_work: 0.2860 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 20304 Z= 0.122 Angle : 0.527 7.784 27570 Z= 0.291 Chirality : 0.045 0.227 2910 Planarity : 0.005 0.129 3603 Dihedral : 7.073 59.954 2809 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.54 % Favored : 96.06 % Rotamer: Outliers : 4.87 % Allowed : 26.87 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.16), residues: 2514 helix: -1.39 (0.54), residues: 97 sheet: 0.71 (0.15), residues: 1185 loop : -1.22 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 844 TYR 0.015 0.001 TYR Z 765 PHE 0.010 0.001 PHE Z 848 TRP 0.024 0.001 TRP Z 863 HIS 0.012 0.001 HIS Z 734 Details of bonding type rmsd covalent geometry : bond 0.00295 (20301) covalent geometry : angle 0.52648 (27564) SS BOND : bond 0.00316 ( 3) SS BOND : angle 2.06056 ( 6) hydrogen bonds : bond 0.02794 ( 875) hydrogen bonds : angle 5.30967 ( 2355) *********************** 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 253 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 152 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 95 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 355 ASP cc_start: 0.8531 (p0) cc_final: 0.8292 (p0) REVERT: A 417 MET cc_start: 0.9178 (pp-130) cc_final: 0.8772 (pp-130) REVERT: B 39 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7407 (pp20) REVERT: B 116 ASP cc_start: 0.8623 (t0) cc_final: 0.8292 (t0) REVERT: B 179 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8820 (mtp) REVERT: B 242 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8668 (tt0) REVERT: Z 997 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7441 (pp) REVERT: Z 1009 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8136 (ptm-80) REVERT: J 809 ASP cc_start: 0.8261 (m-30) cc_final: 0.7984 (p0) REVERT: J 1042 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7938 (ttm170) REVERT: F 751 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7895 (tttp) outliers start: 101 outliers final: 64 residues processed: 243 average time/residue: 0.5063 time to fit residues: 142.6644 Evaluate side-chains 211 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 138 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 57 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 157 SER 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 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 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 845 LEU 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 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG 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 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 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 955 LEU Chi-restraints excluded: chain J residue 998 VAL 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 751 LYS Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 880 ILE Chi-restraints excluded: chain F residue 928 VAL Chi-restraints excluded: chain F residue 939 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1035 VAL Chi-restraints excluded: chain F residue 1099 LEU Chi-restraints excluded: chain F residue 1100 THR 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 38 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 179 optimal weight: 0.0030 chunk 198 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 209 optimal weight: 0.0000 chunk 86 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 113 HIS C 341 ASN Z 734 HIS Z 826 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.134506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.094504 restraints weight = 24466.188| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.47 r_work: 0.2883 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 20304 Z= 0.109 Angle : 0.544 24.666 27570 Z= 0.290 Chirality : 0.045 0.207 2910 Planarity : 0.005 0.193 3603 Dihedral : 6.671 58.695 2793 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.46 % Favored : 96.14 % Rotamer: Outliers : 4.63 % Allowed : 27.45 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2514 helix: -1.31 (0.52), residues: 109 sheet: 0.77 (0.15), residues: 1188 loop : -1.18 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 844 TYR 0.013 0.001 TYR Z 876 PHE 0.031 0.001 PHE Z 848 TRP 0.027 0.001 TRP Z 863 HIS 0.004 0.000 HIS Z 734 Details of bonding type rmsd covalent geometry : bond 0.00262 (20301) covalent geometry : angle 0.54294 (27564) SS BOND : bond 0.00286 ( 3) SS BOND : angle 1.95014 ( 6) hydrogen bonds : bond 0.02616 ( 875) hydrogen bonds : angle 5.20467 ( 2355) *********************** 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 242 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 146 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8795 (tp) REVERT: A 95 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8314 (mt) REVERT: A 355 ASP cc_start: 0.8510 (p0) cc_final: 0.8273 (p0) REVERT: A 417 MET cc_start: 0.9201 (pp-130) cc_final: 0.8639 (pp-130) REVERT: B 39 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.7398 (pp20) REVERT: B 116 ASP cc_start: 0.8614 (t0) cc_final: 0.8293 (t0) REVERT: B 179 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8800 (mtp) REVERT: B 242 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: Z 751 LYS cc_start: 0.8655 (tppt) cc_final: 0.8009 (tmmm) REVERT: Z 997 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7433 (pp) REVERT: Z 1052 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8896 (m) REVERT: J 809 ASP cc_start: 0.8158 (m-30) cc_final: 0.7926 (p0) REVERT: J 846 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6609 (pp20) REVERT: J 948 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8453 (m) REVERT: J 1042 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7984 (ttm170) REVERT: J 1103 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7578 (ptm160) REVERT: F 846 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5960 (tm-30) outliers start: 96 outliers final: 59 residues processed: 234 average time/residue: 0.5256 time to fit residues: 142.3886 Evaluate side-chains 205 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 134 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 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 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 285 ASP 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 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 835 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 930 LEU Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE 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 728 GLN 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 1023 THR Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain J residue 1121 VAL Chi-restraints excluded: chain F residue 804 VAL Chi-restraints excluded: chain F residue 846 GLU 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 939 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1100 THR 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 172 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 167 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** A 256 ASN C 341 ASN Z 734 HIS Z 826 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.134065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.094121 restraints weight = 24408.202| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.58 r_work: 0.2867 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 20304 Z= 0.123 Angle : 0.541 16.633 27570 Z= 0.292 Chirality : 0.045 0.209 2910 Planarity : 0.005 0.166 3603 Dihedral : 6.558 59.930 2785 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.42 % Favored : 96.18 % Rotamer: Outliers : 4.25 % Allowed : 27.88 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2514 helix: -1.29 (0.51), residues: 109 sheet: 0.77 (0.15), residues: 1177 loop : -1.17 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 844 TYR 0.016 0.001 TYR Z 765 PHE 0.032 0.001 PHE Z 848 TRP 0.028 0.001 TRP Z 863 HIS 0.005 0.000 HIS Z 734 Details of bonding type rmsd covalent geometry : bond 0.00293 (20301) covalent geometry : angle 0.54033 (27564) SS BOND : bond 0.00225 ( 3) SS BOND : angle 1.90395 ( 6) hydrogen bonds : bond 0.02679 ( 875) hydrogen bonds : angle 5.20337 ( 2355) *********************** 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 225 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 137 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 95 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8322 (mt) REVERT: A 286 MET cc_start: 0.8894 (tpt) cc_final: 0.8112 (tmm) REVERT: A 355 ASP cc_start: 0.8536 (p0) cc_final: 0.8296 (p0) REVERT: A 417 MET cc_start: 0.9209 (pp-130) cc_final: 0.8611 (pp-130) REVERT: B 39 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: B 116 ASP cc_start: 0.8647 (t0) cc_final: 0.8315 (t0) REVERT: B 179 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8839 (mtp) REVERT: B 242 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8660 (tt0) REVERT: Z 751 LYS cc_start: 0.8658 (tppt) cc_final: 0.7990 (tmmm) REVERT: Z 962 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8304 (mt) REVERT: Z 997 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7499 (pp) REVERT: Z 1009 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8248 (ptm-80) REVERT: Z 1052 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8889 (m) REVERT: J 809 ASP cc_start: 0.8224 (m-30) cc_final: 0.7950 (p0) REVERT: J 846 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6614 (pp20) REVERT: J 948 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8456 (m) REVERT: J 1042 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8004 (ttm170) REVERT: J 1075 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6939 (mt-10) REVERT: J 1103 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.7792 (ptm160) REVERT: F 751 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7882 (tttp) outliers start: 88 outliers final: 60 residues processed: 213 average time/residue: 0.5236 time to fit residues: 129.0167 Evaluate side-chains 209 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 134 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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 256 ASN 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 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 1 VAL 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 307 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 800 PHE 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 877 VAL Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG 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 728 GLN 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 1021 THR Chi-restraints excluded: chain J residue 1023 THR Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1075 GLU 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 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 939 THR Chi-restraints excluded: chain F residue 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1100 THR 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 89 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 170 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 218 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** A 256 ASN B 340 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 = 0.3534 r_free = 0.3534 target = 0.131977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.091401 restraints weight = 24500.529| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.59 r_work: 0.2830 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 20304 Z= 0.202 Angle : 0.591 13.075 27570 Z= 0.320 Chirality : 0.047 0.239 2910 Planarity : 0.005 0.152 3603 Dihedral : 6.787 58.387 2784 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.74 % Favored : 95.86 % Rotamer: Outliers : 4.73 % Allowed : 27.50 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2514 helix: -1.38 (0.53), residues: 97 sheet: 0.73 (0.15), residues: 1194 loop : -1.21 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 844 TYR 0.014 0.001 TYR C 163 PHE 0.029 0.001 PHE Z 848 TRP 0.033 0.001 TRP Z 863 HIS 0.005 0.001 HIS Z 734 Details of bonding type rmsd covalent geometry : bond 0.00482 (20301) covalent geometry : angle 0.58899 (27564) SS BOND : bond 0.00565 ( 3) SS BOND : angle 3.26802 ( 6) hydrogen bonds : bond 0.03132 ( 875) hydrogen bonds : angle 5.34892 ( 2355) *********************** 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 239 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 141 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8778 (tp) REVERT: A 95 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 355 ASP cc_start: 0.8596 (p0) cc_final: 0.8361 (p0) REVERT: A 417 MET cc_start: 0.9208 (pp-130) cc_final: 0.8660 (pp-130) REVERT: B 39 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7286 (pp20) REVERT: B 179 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8866 (mtp) REVERT: B 242 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: B 371 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8269 (tttp) REVERT: Z 751 LYS cc_start: 0.8670 (tppt) cc_final: 0.8018 (tmmm) REVERT: Z 962 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8295 (mt) REVERT: Z 997 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7530 (pp) REVERT: Z 1009 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8143 (ptm-80) REVERT: J 809 ASP cc_start: 0.8313 (m-30) cc_final: 0.8022 (p0) REVERT: J 846 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6604 (pp20) REVERT: J 1009 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8502 (ttm-80) REVERT: J 1042 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8008 (ttm170) REVERT: J 1075 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: F 751 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7840 (tttp) REVERT: F 846 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5914 (tm-30) REVERT: F 882 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8178 (tp) outliers start: 98 outliers final: 66 residues processed: 228 average time/residue: 0.5391 time to fit residues: 141.3632 Evaluate side-chains 219 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 137 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 256 ASN 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 157 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 231 VAL 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 B residue 371 LYS Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain Z residue 800 PHE Chi-restraints excluded: chain Z residue 835 VAL Chi-restraints excluded: chain Z residue 845 LEU Chi-restraints excluded: chain Z residue 852 TRP Chi-restraints excluded: chain Z residue 862 MET Chi-restraints excluded: chain Z residue 868 GLU Chi-restraints excluded: chain Z residue 877 VAL Chi-restraints excluded: chain Z residue 962 ILE Chi-restraints excluded: chain Z residue 987 THR Chi-restraints excluded: chain Z residue 997 ILE Chi-restraints excluded: chain Z residue 1009 ARG 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 728 GLN 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 1009 ARG Chi-restraints excluded: chain J residue 1012 SER Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1023 THR Chi-restraints excluded: chain J residue 1042 ARG Chi-restraints excluded: chain J residue 1075 GLU 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 751 LYS 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 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1100 THR 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 162 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 231 optimal weight: 0.0070 chunk 171 optimal weight: 10.0000 chunk 218 optimal weight: 0.1980 chunk 102 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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** C 341 ASN Z 734 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094500 restraints weight = 24488.863| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.55 r_work: 0.2889 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 20304 Z= 0.110 Angle : 0.533 7.660 27570 Z= 0.292 Chirality : 0.045 0.212 2910 Planarity : 0.004 0.123 3603 Dihedral : 6.493 58.479 2784 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.42 % Favored : 96.18 % Rotamer: Outliers : 3.47 % Allowed : 28.90 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.16), residues: 2514 helix: -0.87 (0.57), residues: 91 sheet: 0.78 (0.15), residues: 1179 loop : -1.19 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 844 TYR 0.016 0.001 TYR Z 765 PHE 0.011 0.001 PHE Z 848 TRP 0.034 0.001 TRP Z 863 HIS 0.005 0.000 HIS Z 734 Details of bonding type rmsd covalent geometry : bond 0.00262 (20301) covalent geometry : angle 0.53006 (27564) SS BOND : bond 0.00315 ( 3) SS BOND : angle 3.66626 ( 6) hydrogen bonds : bond 0.02612 ( 875) hydrogen bonds : angle 5.21476 ( 2355) ********************** 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 212 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 140 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8804 (tp) REVERT: A 95 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8324 (mt) REVERT: A 355 ASP cc_start: 0.8484 (p0) cc_final: 0.8228 (p0) REVERT: A 417 MET cc_start: 0.9220 (pp-130) cc_final: 0.8630 (pp-130) REVERT: B 39 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7402 (pp20) REVERT: B 179 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8789 (mtp) REVERT: B 242 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: B 360 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7782 (tpp-160) REVERT: Z 751 LYS cc_start: 0.8659 (tppt) cc_final: 0.7987 (tmmm) REVERT: Z 852 TRP cc_start: 0.7148 (OUTLIER) cc_final: 0.6705 (p-90) REVERT: Z 997 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7528 (pp) REVERT: Z 1009 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8240 (ptm-80) REVERT: Z 1075 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7434 (mt-10) REVERT: J 846 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6614 (pp20) REVERT: J 948 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8438 (m) REVERT: J 1075 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6928 (mt-10) REVERT: J 1103 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7854 (ptm160) REVERT: F 751 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7758 (tttp) REVERT: F 943 ASN cc_start: 0.7887 (m-40) cc_final: 0.7587 (m-40) outliers start: 72 outliers final: 48 residues processed: 205 average time/residue: 0.5135 time to fit residues: 121.5043 Evaluate side-chains 196 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 134 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 57 SER Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 157 SER 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 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 216 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain C residue 1 VAL 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 800 PHE 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 877 VAL 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 1100 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 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 877 VAL Chi-restraints excluded: chain J residue 948 SER Chi-restraints excluded: chain J residue 1021 THR Chi-restraints excluded: chain J residue 1075 GLU Chi-restraints excluded: chain J residue 1103 ARG Chi-restraints excluded: chain J residue 1117 VAL Chi-restraints excluded: chain F residue 751 LYS 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 955 LEU Chi-restraints excluded: chain F residue 987 THR Chi-restraints excluded: chain F residue 1052 THR Chi-restraints excluded: chain F residue 1100 THR 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 65 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 104 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 57 optimal weight: 0.0050 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Z 734 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.132086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.091245 restraints weight = 24626.525| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.54 r_work: 0.2831 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 20304 Z= 0.200 Angle : 0.589 9.352 27570 Z= 0.321 Chirality : 0.046 0.239 2910 Planarity : 0.005 0.125 3603 Dihedral : 6.683 58.388 2782 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.70 % Favored : 95.90 % Rotamer: Outliers : 3.91 % Allowed : 28.61 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2514 helix: -1.21 (0.54), residues: 97 sheet: 0.74 (0.15), residues: 1191 loop : -1.24 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 844 TYR 0.016 0.001 TYR C 343 PHE 0.030 0.001 PHE Z 848 TRP 0.033 0.001 TRP Z 863 HIS 0.005 0.001 HIS Z 734 Details of bonding type rmsd covalent geometry : bond 0.00476 (20301) covalent geometry : angle 0.58563 (27564) SS BOND : bond 0.00393 ( 3) SS BOND : angle 4.38891 ( 6) hydrogen bonds : bond 0.03126 ( 875) hydrogen bonds : angle 5.34152 ( 2355) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6562.76 seconds wall clock time: 112 minutes 41.22 seconds (6761.22 seconds total)