Starting phenix.real_space_refine on Fri Oct 10 14:50:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sf7_25076/10_2025/7sf7_25076_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sf7_25076/10_2025/7sf7_25076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sf7_25076/10_2025/7sf7_25076_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sf7_25076/10_2025/7sf7_25076_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sf7_25076/10_2025/7sf7_25076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sf7_25076/10_2025/7sf7_25076.map" } resolution = 2.9 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= 0.001 sd= 0.018 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 47 5.16 5 C 4354 2.51 5 N 1146 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6776 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2175 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 270} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1681 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 6, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 2551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2551 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 366 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 1.40, per 1000 atoms: 0.21 Number of scatterers: 6776 At special positions: 0 Unit cell: (85.21, 112.477, 119.294, 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 47 16.00 O 1229 8.00 N 1146 7.00 C 4354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 927 " - pdb=" SG CYS A 999 " distance=2.02 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: 0.50 Conformation dependent library (CDL) restraints added in 360.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1662 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 38.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 859 through 879 removed outlier: 3.892A pdb=" N LEU A 863 " --> pdb=" O VAL A 859 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 889 removed outlier: 3.721A pdb=" N PHE A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 917 Processing helix chain 'A' and resid 923 through 957 removed outlier: 3.576A pdb=" N VAL A 929 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A 941 " --> pdb=" O PHE A 937 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 942 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 948 " --> pdb=" O TRP A 944 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 949 " --> pdb=" O MET A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 975 Processing helix chain 'A' and resid 976 through 989 removed outlier: 3.792A pdb=" N VAL A 982 " --> pdb=" O PRO A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1038 removed outlier: 3.650A pdb=" N GLY A1013 " --> pdb=" O TRP A1009 " (cutoff:3.500A) Proline residue: A1014 - end of helix removed outlier: 3.568A pdb=" N ILE A1024 " --> pdb=" O MET A1020 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A1037 " --> pdb=" O MET A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1053 through 1058 removed outlier: 4.022A pdb=" N ALA A1057 " --> pdb=" O TRP A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1065 removed outlier: 4.001A pdb=" N LEU A1063 " --> pdb=" O ALA A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1073 removed outlier: 3.727A pdb=" N ALA A1069 " --> pdb=" O LEU A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1090 removed outlier: 3.826A pdb=" N LEU A1085 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A1086 " --> pdb=" O MET A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1102 removed outlier: 4.035A pdb=" N PHE A1096 " --> pdb=" O LEU A1092 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A1101 " --> pdb=" O ILE A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 3.537A pdb=" N CYS A1115 " --> pdb=" O GLU A1111 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 11 Processing helix chain 'B' and resid 12 through 25 removed outlier: 3.559A pdb=" N ASP B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 removed outlier: 3.727A pdb=" N VAL B 30 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 31' Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.623A pdb=" N SER B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 185 removed outlier: 3.653A pdb=" N VAL B 175 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 removed outlier: 3.845A pdb=" N ASP B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS B 225 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 21 through 25 removed outlier: 3.605A pdb=" N ALA C 24 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS C 25 " --> pdb=" O ARG C 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 25' Processing helix chain 'C' and resid 29 through 35 removed outlier: 4.110A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 29 through 44 removed outlier: 4.055A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 75 removed outlier: 3.678A pdb=" N VAL B 34 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 84 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYS B 35 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N LEU B 107 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 37 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 39 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B 139 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N HIS B 198 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 141 " --> pdb=" O HIS B 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.816A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 62 removed outlier: 4.148A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 72 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 103 removed outlier: 6.990A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.693A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 190 through 192 removed outlier: 4.044A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 232 removed outlier: 6.953A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.794A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) 263 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.90 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1215 1.33 - 1.45: 1780 1.45 - 1.57: 3852 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 6912 Sorted by residual: bond pdb=" N ILE A 918 " pdb=" CA ILE A 918 " ideal model delta sigma weight residual 1.457 1.511 -0.055 1.07e-02 8.73e+03 2.62e+01 bond pdb=" N ASP A 989 " pdb=" CA ASP A 989 " ideal model delta sigma weight residual 1.459 1.507 -0.047 1.20e-02 6.94e+03 1.57e+01 bond pdb=" N VAL A1023 " pdb=" CA VAL A1023 " ideal model delta sigma weight residual 1.460 1.497 -0.036 1.19e-02 7.06e+03 9.37e+00 bond pdb=" N SER A 962 " pdb=" CA SER A 962 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.21e-02 6.83e+03 9.36e+00 bond pdb=" N ILE A1050 " pdb=" CA ILE A1050 " ideal model delta sigma weight residual 1.461 1.497 -0.035 1.17e-02 7.31e+03 9.19e+00 ... (remaining 6907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 9033 1.93 - 3.87: 281 3.87 - 5.80: 55 5.80 - 7.74: 7 7.74 - 9.67: 3 Bond angle restraints: 9379 Sorted by residual: angle pdb=" N ILE A1008 " pdb=" CA ILE A1008 " pdb=" C ILE A1008 " ideal model delta sigma weight residual 112.80 104.27 8.53 1.15e+00 7.56e-01 5.50e+01 angle pdb=" C TYR A1006 " pdb=" N PHE A1007 " pdb=" CA PHE A1007 " ideal model delta sigma weight residual 122.60 112.93 9.67 1.56e+00 4.11e-01 3.84e+01 angle pdb=" CA PHE A1086 " pdb=" CB PHE A1086 " pdb=" CG PHE A1086 " ideal model delta sigma weight residual 113.80 119.02 -5.22 1.00e+00 1.00e+00 2.73e+01 angle pdb=" N ALA A1083 " pdb=" CA ALA A1083 " pdb=" C ALA A1083 " ideal model delta sigma weight residual 113.50 107.89 5.61 1.23e+00 6.61e-01 2.08e+01 angle pdb=" N PHE A 844 " pdb=" CA PHE A 844 " pdb=" C PHE A 844 " ideal model delta sigma weight residual 114.31 108.50 5.81 1.29e+00 6.01e-01 2.03e+01 ... (remaining 9374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.75: 3602 14.75 - 29.50: 345 29.50 - 44.25: 98 44.25 - 59.00: 18 59.00 - 73.75: 3 Dihedral angle restraints: 4066 sinusoidal: 1506 harmonic: 2560 Sorted by residual: dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ASP A 857 " pdb=" C ASP A 857 " pdb=" N ALA A 858 " pdb=" CA ALA A 858 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO A1042 " pdb=" C PRO A1042 " pdb=" N GLU A1043 " pdb=" CA GLU A1043 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 4063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 820 0.049 - 0.098: 202 0.098 - 0.146: 61 0.146 - 0.195: 10 0.195 - 0.244: 4 Chirality restraints: 1097 Sorted by residual: chirality pdb=" CA GLU A 958 " pdb=" N GLU A 958 " pdb=" C GLU A 958 " pdb=" CB GLU A 958 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CB ILE A 918 " pdb=" CA ILE A 918 " pdb=" CG1 ILE A 918 " pdb=" CG2 ILE A 918 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB VAL A 998 " pdb=" CA VAL A 998 " pdb=" CG1 VAL A 998 " pdb=" CG2 VAL A 998 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1094 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 988 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C VAL A 988 " -0.057 2.00e-02 2.50e+03 pdb=" O VAL A 988 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 989 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A1005 " -0.014 2.00e-02 2.50e+03 2.65e-02 7.05e+00 pdb=" C THR A1005 " 0.046 2.00e-02 2.50e+03 pdb=" O THR A1005 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR A1006 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 917 " -0.011 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C GLY A 917 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY A 917 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE A 918 " -0.012 2.00e-02 2.50e+03 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1143 2.77 - 3.30: 5965 3.30 - 3.83: 9934 3.83 - 4.37: 11555 4.37 - 4.90: 20562 Nonbonded interactions: 49159 Sorted by model distance: nonbonded pdb=" ND1 HIS C 142 " pdb=" OG SER C 161 " model vdw 2.234 3.120 nonbonded pdb=" OG1 THR A 885 " pdb=" OH TYR A1112 " model vdw 2.258 3.040 nonbonded pdb=" NH1 ARG C 197 " pdb=" OD1 ASP C 212 " model vdw 2.272 3.120 nonbonded pdb=" NZ LYS B 46 " pdb=" OD1 ASP B 85 " model vdw 2.293 3.120 nonbonded pdb=" ND2 ASN B 43 " pdb=" OD2 ASP B 111 " model vdw 2.323 3.120 ... (remaining 49154 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.760 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.005 0.055 6913 Z= 0.317 Angle : 0.780 9.671 9381 Z= 0.520 Chirality : 0.050 0.244 1097 Planarity : 0.004 0.036 1179 Dihedral : 12.922 73.752 2401 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.56 % Allowed : 1.41 % Favored : 98.03 % 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: -1.73 (0.29), residues: 869 helix: -0.16 (0.30), residues: 326 sheet: -0.10 (0.41), residues: 161 loop : -2.54 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 32 TYR 0.032 0.002 TYR A1006 PHE 0.026 0.002 PHE A1086 TRP 0.028 0.002 TRP A1000 HIS 0.008 0.001 HIS A 964 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 6912) covalent geometry : angle 0.77953 ( 9379) SS BOND : bond 0.01184 ( 1) SS BOND : angle 2.16164 ( 2) hydrogen bonds : bond 0.17892 ( 263) hydrogen bonds : angle 5.75463 ( 750) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 1084 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: B 139 ILE cc_start: 0.8563 (mm) cc_final: 0.8341 (mp) REVERT: C 258 ASP cc_start: 0.7315 (t0) cc_final: 0.6885 (t0) outliers start: 4 outliers final: 2 residues processed: 133 average time/residue: 0.3863 time to fit residues: 54.9379 Evaluate side-chains 117 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1084 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.0060 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 843 ASN A 919 ASN B 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.154106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.134002 restraints weight = 9909.054| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.24 r_work: 0.3715 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6913 Z= 0.136 Angle : 0.549 8.164 9381 Z= 0.300 Chirality : 0.042 0.166 1097 Planarity : 0.003 0.033 1179 Dihedral : 5.154 53.296 943 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.96 % Allowed : 9.17 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.29), residues: 869 helix: 0.15 (0.31), residues: 333 sheet: -0.15 (0.40), residues: 173 loop : -2.50 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.014 0.001 TYR A1006 PHE 0.012 0.001 PHE C 241 TRP 0.016 0.001 TRP A1000 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6912) covalent geometry : angle 0.54725 ( 9379) SS BOND : bond 0.00877 ( 1) SS BOND : angle 3.30768 ( 2) hydrogen bonds : bond 0.05719 ( 263) hydrogen bonds : angle 4.39477 ( 750) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.255 Fit side-chains REVERT: B 83 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7956 (tpp) REVERT: B 111 ASP cc_start: 0.7340 (p0) cc_final: 0.7131 (p0) REVERT: B 114 ASP cc_start: 0.7340 (m-30) cc_final: 0.7072 (p0) REVERT: B 139 ILE cc_start: 0.8826 (mm) cc_final: 0.8604 (mp) REVERT: B 152 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6760 (tptt) REVERT: C 175 GLN cc_start: 0.8649 (mt0) cc_final: 0.8430 (mt0) REVERT: C 258 ASP cc_start: 0.7899 (t0) cc_final: 0.7541 (t0) REVERT: C 262 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.6310 (mpt) REVERT: C 298 ASP cc_start: 0.7548 (p0) cc_final: 0.7102 (p0) outliers start: 21 outliers final: 10 residues processed: 129 average time/residue: 0.3800 time to fit residues: 52.6097 Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 894 SER Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 225 HIS C 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.151307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.130982 restraints weight = 9796.754| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.20 r_work: 0.3672 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6913 Z= 0.185 Angle : 0.579 7.162 9381 Z= 0.318 Chirality : 0.043 0.161 1097 Planarity : 0.003 0.034 1179 Dihedral : 4.932 46.558 941 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.67 % Allowed : 11.85 % Favored : 84.49 % 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: -1.44 (0.29), residues: 869 helix: 0.12 (0.31), residues: 334 sheet: -0.09 (0.39), residues: 174 loop : -2.47 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 27 TYR 0.020 0.002 TYR A1006 PHE 0.025 0.002 PHE A 908 TRP 0.015 0.002 TRP A1000 HIS 0.006 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6912) covalent geometry : angle 0.57729 ( 9379) SS BOND : bond 0.00035 ( 1) SS BOND : angle 2.83694 ( 2) hydrogen bonds : bond 0.06748 ( 263) hydrogen bonds : angle 4.43659 ( 750) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1055 ILE cc_start: 0.8021 (mp) cc_final: 0.7664 (tp) REVERT: B 111 ASP cc_start: 0.7332 (p0) cc_final: 0.7030 (p0) REVERT: B 114 ASP cc_start: 0.7360 (m-30) cc_final: 0.7091 (p0) REVERT: B 139 ILE cc_start: 0.8828 (mm) cc_final: 0.8610 (mp) REVERT: B 152 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6740 (tptt) REVERT: C 153 ASP cc_start: 0.8003 (p0) cc_final: 0.7771 (p0) REVERT: C 175 GLN cc_start: 0.8651 (mt0) cc_final: 0.8405 (mt0) REVERT: C 258 ASP cc_start: 0.7939 (t0) cc_final: 0.7524 (t0) REVERT: C 262 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6413 (mpt) REVERT: C 297 TRP cc_start: 0.8527 (OUTLIER) cc_final: 0.7959 (m-90) REVERT: C 298 ASP cc_start: 0.7490 (p0) cc_final: 0.7022 (p0) outliers start: 26 outliers final: 15 residues processed: 122 average time/residue: 0.3752 time to fit residues: 49.2726 Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 894 SER Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 918 ILE Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 46 optimal weight: 0.9990 chunk 85 optimal weight: 0.0020 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 65 optimal weight: 0.0370 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 overall best weight: 0.3066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.154079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.133887 restraints weight = 9967.221| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.23 r_work: 0.3706 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6913 Z= 0.116 Angle : 0.516 9.321 9381 Z= 0.282 Chirality : 0.041 0.155 1097 Planarity : 0.003 0.033 1179 Dihedral : 4.605 43.896 941 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.95 % Allowed : 13.68 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.30 (0.29), residues: 869 helix: 0.28 (0.31), residues: 332 sheet: 0.04 (0.40), residues: 173 loop : -2.45 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 197 TYR 0.016 0.001 TYR A1031 PHE 0.024 0.001 PHE A 908 TRP 0.012 0.001 TRP A1000 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6912) covalent geometry : angle 0.51545 ( 9379) SS BOND : bond 0.00122 ( 1) SS BOND : angle 1.92722 ( 2) hydrogen bonds : bond 0.05134 ( 263) hydrogen bonds : angle 4.11410 ( 750) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 1006 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: A 1055 ILE cc_start: 0.8002 (mp) cc_final: 0.7649 (tp) REVERT: B 111 ASP cc_start: 0.7273 (p0) cc_final: 0.7009 (p0) REVERT: B 114 ASP cc_start: 0.7339 (m-30) cc_final: 0.7059 (p0) REVERT: B 139 ILE cc_start: 0.8843 (mm) cc_final: 0.8619 (mp) REVERT: C 175 GLN cc_start: 0.8633 (mt0) cc_final: 0.8369 (mt0) REVERT: C 258 ASP cc_start: 0.7886 (t0) cc_final: 0.7456 (t0) REVERT: C 262 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6411 (mpt) REVERT: C 297 TRP cc_start: 0.8520 (OUTLIER) cc_final: 0.7931 (m-90) REVERT: C 298 ASP cc_start: 0.7476 (p0) cc_final: 0.7049 (p0) outliers start: 28 outliers final: 12 residues processed: 125 average time/residue: 0.3832 time to fit residues: 51.7076 Evaluate side-chains 121 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 894 SER Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain C residue 325 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 16 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 75 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.153776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.133732 restraints weight = 9979.303| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.23 r_work: 0.3702 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6913 Z= 0.129 Angle : 0.536 7.540 9381 Z= 0.294 Chirality : 0.042 0.167 1097 Planarity : 0.003 0.033 1179 Dihedral : 4.683 47.605 941 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.09 % Allowed : 15.66 % Favored : 80.25 % 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: -1.26 (0.29), residues: 869 helix: 0.31 (0.31), residues: 332 sheet: 0.12 (0.40), residues: 173 loop : -2.46 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.016 0.001 TYR A1006 PHE 0.012 0.001 PHE C 199 TRP 0.011 0.001 TRP A1000 HIS 0.003 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6912) covalent geometry : angle 0.52984 ( 9379) SS BOND : bond 0.00394 ( 1) SS BOND : angle 5.40707 ( 2) hydrogen bonds : bond 0.05461 ( 263) hydrogen bonds : angle 4.16135 ( 750) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 1006 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: A 1055 ILE cc_start: 0.8012 (mp) cc_final: 0.7687 (tp) REVERT: B 111 ASP cc_start: 0.7294 (p0) cc_final: 0.7027 (p0) REVERT: B 114 ASP cc_start: 0.7359 (m-30) cc_final: 0.7063 (p0) REVERT: B 139 ILE cc_start: 0.8826 (mm) cc_final: 0.8605 (mp) REVERT: C 175 GLN cc_start: 0.8644 (mt0) cc_final: 0.8402 (mt0) REVERT: C 258 ASP cc_start: 0.7868 (t0) cc_final: 0.7443 (t0) REVERT: C 262 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6416 (mpt) REVERT: C 289 TYR cc_start: 0.7898 (m-80) cc_final: 0.7690 (m-80) REVERT: C 297 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.7946 (m-90) REVERT: C 298 ASP cc_start: 0.7477 (p0) cc_final: 0.7053 (p0) outliers start: 29 outliers final: 17 residues processed: 120 average time/residue: 0.3708 time to fit residues: 48.2302 Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain C residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.0970 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.150852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.130630 restraints weight = 9867.264| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.21 r_work: 0.3663 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6913 Z= 0.194 Angle : 0.589 8.155 9381 Z= 0.324 Chirality : 0.044 0.148 1097 Planarity : 0.004 0.035 1179 Dihedral : 4.964 47.328 941 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.95 % Allowed : 17.49 % Favored : 78.56 % 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: -1.35 (0.29), residues: 869 helix: 0.21 (0.31), residues: 334 sheet: 0.08 (0.40), residues: 174 loop : -2.51 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 197 TYR 0.020 0.002 TYR A1006 PHE 0.028 0.002 PHE A 908 TRP 0.013 0.002 TRP C 297 HIS 0.004 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6912) covalent geometry : angle 0.58517 ( 9379) SS BOND : bond 0.00184 ( 1) SS BOND : angle 4.78404 ( 2) hydrogen bonds : bond 0.06809 ( 263) hydrogen bonds : angle 4.38037 ( 750) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.281 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: A 1055 ILE cc_start: 0.8039 (mp) cc_final: 0.7756 (tp) REVERT: B 111 ASP cc_start: 0.7352 (p0) cc_final: 0.7024 (p0) REVERT: B 114 ASP cc_start: 0.7410 (m-30) cc_final: 0.7113 (p0) REVERT: B 139 ILE cc_start: 0.8823 (mm) cc_final: 0.8607 (mp) REVERT: C 175 GLN cc_start: 0.8668 (mt0) cc_final: 0.8434 (mt0) REVERT: C 258 ASP cc_start: 0.7893 (t0) cc_final: 0.7478 (t0) REVERT: C 262 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6430 (mpt) REVERT: C 297 TRP cc_start: 0.8572 (OUTLIER) cc_final: 0.8013 (m-90) REVERT: C 298 ASP cc_start: 0.7529 (p0) cc_final: 0.7091 (p0) outliers start: 28 outliers final: 20 residues processed: 121 average time/residue: 0.3874 time to fit residues: 50.5923 Evaluate side-chains 130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 MET Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 894 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain C residue 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.150209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.130015 restraints weight = 9828.257| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.20 r_work: 0.3660 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6913 Z= 0.206 Angle : 0.607 8.415 9381 Z= 0.333 Chirality : 0.044 0.143 1097 Planarity : 0.004 0.036 1179 Dihedral : 5.095 49.239 941 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.81 % Allowed : 18.19 % Favored : 78.00 % 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: -1.37 (0.29), residues: 869 helix: 0.24 (0.31), residues: 331 sheet: 0.01 (0.40), residues: 174 loop : -2.52 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 134 TYR 0.020 0.002 TYR A1031 PHE 0.028 0.002 PHE A 908 TRP 0.014 0.002 TRP A1000 HIS 0.005 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 6912) covalent geometry : angle 0.60412 ( 9379) SS BOND : bond 0.00272 ( 1) SS BOND : angle 4.27483 ( 2) hydrogen bonds : bond 0.06899 ( 263) hydrogen bonds : angle 4.43515 ( 750) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.265 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: A 1055 ILE cc_start: 0.8032 (mp) cc_final: 0.7754 (tp) REVERT: B 111 ASP cc_start: 0.7350 (p0) cc_final: 0.6976 (p0) REVERT: B 114 ASP cc_start: 0.7384 (m-30) cc_final: 0.7053 (p0) REVERT: B 139 ILE cc_start: 0.8833 (mm) cc_final: 0.8615 (mp) REVERT: C 175 GLN cc_start: 0.8666 (mt0) cc_final: 0.8422 (mt0) REVERT: C 258 ASP cc_start: 0.7887 (t0) cc_final: 0.7456 (t0) REVERT: C 262 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6442 (mpt) REVERT: C 289 TYR cc_start: 0.7877 (m-80) cc_final: 0.7572 (m-80) REVERT: C 297 TRP cc_start: 0.8544 (OUTLIER) cc_final: 0.7938 (m-90) REVERT: C 298 ASP cc_start: 0.7478 (p0) cc_final: 0.7050 (p0) outliers start: 27 outliers final: 18 residues processed: 123 average time/residue: 0.3553 time to fit residues: 47.1648 Evaluate side-chains 132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 894 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain C residue 325 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 51 optimal weight: 0.0060 chunk 53 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 156 GLN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.151512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131296 restraints weight = 9949.854| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.23 r_work: 0.3675 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6913 Z= 0.158 Angle : 0.582 8.672 9381 Z= 0.319 Chirality : 0.043 0.138 1097 Planarity : 0.003 0.035 1179 Dihedral : 4.989 48.791 941 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.67 % Allowed : 19.18 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.29), residues: 869 helix: 0.35 (0.31), residues: 328 sheet: 0.08 (0.40), residues: 174 loop : -2.50 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 134 TYR 0.016 0.001 TYR A1006 PHE 0.029 0.002 PHE A 908 TRP 0.012 0.001 TRP A1000 HIS 0.004 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6912) covalent geometry : angle 0.57875 ( 9379) SS BOND : bond 0.00325 ( 1) SS BOND : angle 3.98531 ( 2) hydrogen bonds : bond 0.06217 ( 263) hydrogen bonds : angle 4.34232 ( 750) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.254 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8287 (OUTLIER) cc_final: 0.7931 (m-80) REVERT: A 1055 ILE cc_start: 0.8031 (mp) cc_final: 0.7757 (tp) REVERT: B 111 ASP cc_start: 0.7329 (p0) cc_final: 0.6974 (p0) REVERT: B 114 ASP cc_start: 0.7401 (m-30) cc_final: 0.7090 (p0) REVERT: B 139 ILE cc_start: 0.8828 (mm) cc_final: 0.8611 (mp) REVERT: C 175 GLN cc_start: 0.8667 (mt0) cc_final: 0.8433 (mt0) REVERT: C 258 ASP cc_start: 0.7863 (t0) cc_final: 0.7444 (t0) REVERT: C 262 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.6469 (mpt) REVERT: C 289 TYR cc_start: 0.7892 (m-80) cc_final: 0.7615 (m-80) REVERT: C 297 TRP cc_start: 0.8565 (OUTLIER) cc_final: 0.7986 (m-90) REVERT: C 298 ASP cc_start: 0.7513 (p0) cc_final: 0.7117 (p0) outliers start: 26 outliers final: 17 residues processed: 120 average time/residue: 0.3502 time to fit residues: 45.6260 Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 894 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain C residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.0170 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.151092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.130814 restraints weight = 9948.388| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.22 r_work: 0.3669 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6913 Z= 0.171 Angle : 0.595 9.418 9381 Z= 0.326 Chirality : 0.044 0.137 1097 Planarity : 0.003 0.036 1179 Dihedral : 5.014 48.807 941 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.24 % Allowed : 19.89 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.29), residues: 869 helix: 0.37 (0.31), residues: 331 sheet: 0.09 (0.40), residues: 174 loop : -2.52 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 134 TYR 0.018 0.001 TYR A1006 PHE 0.029 0.002 PHE A 908 TRP 0.013 0.001 TRP A1000 HIS 0.004 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6912) covalent geometry : angle 0.59250 ( 9379) SS BOND : bond 0.00265 ( 1) SS BOND : angle 4.00895 ( 2) hydrogen bonds : bond 0.06384 ( 263) hydrogen bonds : angle 4.36392 ( 750) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.271 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: A 1055 ILE cc_start: 0.8018 (mp) cc_final: 0.7760 (tp) REVERT: B 111 ASP cc_start: 0.7325 (p0) cc_final: 0.7006 (p0) REVERT: B 114 ASP cc_start: 0.7383 (m-30) cc_final: 0.7009 (p0) REVERT: B 139 ILE cc_start: 0.8823 (mm) cc_final: 0.8606 (mp) REVERT: C 175 GLN cc_start: 0.8670 (mt0) cc_final: 0.8432 (mt0) REVERT: C 258 ASP cc_start: 0.7856 (t0) cc_final: 0.7434 (t0) REVERT: C 262 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6461 (mpt) REVERT: C 289 TYR cc_start: 0.7912 (m-80) cc_final: 0.7690 (m-80) REVERT: C 297 TRP cc_start: 0.8576 (OUTLIER) cc_final: 0.8035 (m-90) REVERT: C 298 ASP cc_start: 0.7502 (p0) cc_final: 0.7106 (p0) outliers start: 23 outliers final: 17 residues processed: 116 average time/residue: 0.3799 time to fit residues: 47.6610 Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 894 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain C residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.0270 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 0.0060 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.152861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.132673 restraints weight = 9973.679| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.22 r_work: 0.3697 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6913 Z= 0.130 Angle : 0.567 10.276 9381 Z= 0.310 Chirality : 0.042 0.153 1097 Planarity : 0.003 0.035 1179 Dihedral : 4.778 47.220 941 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.10 % Allowed : 20.59 % Favored : 76.30 % 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: -1.09 (0.29), residues: 869 helix: 0.62 (0.31), residues: 324 sheet: 0.15 (0.40), residues: 174 loop : -2.46 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 134 TYR 0.015 0.001 TYR A1006 PHE 0.029 0.001 PHE A 908 TRP 0.011 0.001 TRP A1000 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6912) covalent geometry : angle 0.56521 ( 9379) SS BOND : bond 0.00249 ( 1) SS BOND : angle 3.16374 ( 2) hydrogen bonds : bond 0.05378 ( 263) hydrogen bonds : angle 4.21163 ( 750) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.216 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: A 1055 ILE cc_start: 0.7985 (mp) cc_final: 0.7700 (tp) REVERT: B 111 ASP cc_start: 0.7296 (p0) cc_final: 0.6968 (p0) REVERT: B 114 ASP cc_start: 0.7372 (m-30) cc_final: 0.7039 (p0) REVERT: B 139 ILE cc_start: 0.8837 (mm) cc_final: 0.8613 (mp) REVERT: C 175 GLN cc_start: 0.8642 (mt0) cc_final: 0.8410 (mt0) REVERT: C 258 ASP cc_start: 0.7829 (t0) cc_final: 0.7389 (t0) REVERT: C 262 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6403 (mpt) REVERT: C 297 TRP cc_start: 0.8521 (OUTLIER) cc_final: 0.8001 (m-90) REVERT: C 298 ASP cc_start: 0.7475 (p0) cc_final: 0.7066 (p0) outliers start: 22 outliers final: 18 residues processed: 121 average time/residue: 0.3862 time to fit residues: 50.3979 Evaluate side-chains 130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 894 SER Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 1000 TRP Chi-restraints excluded: chain A residue 1006 TYR Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Chi-restraints excluded: chain C residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 67 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.152255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.132134 restraints weight = 9969.866| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.21 r_work: 0.3688 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6913 Z= 0.149 Angle : 0.583 11.343 9381 Z= 0.318 Chirality : 0.043 0.157 1097 Planarity : 0.003 0.035 1179 Dihedral : 4.810 46.333 941 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.39 % Allowed : 20.17 % Favored : 76.45 % 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: -1.07 (0.29), residues: 869 helix: 0.67 (0.31), residues: 324 sheet: 0.13 (0.39), residues: 174 loop : -2.47 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 134 TYR 0.017 0.001 TYR A1006 PHE 0.029 0.001 PHE A 908 TRP 0.011 0.001 TRP A1000 HIS 0.003 0.001 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6912) covalent geometry : angle 0.58121 ( 9379) SS BOND : bond 0.00206 ( 1) SS BOND : angle 3.48747 ( 2) hydrogen bonds : bond 0.05807 ( 263) hydrogen bonds : angle 4.25329 ( 750) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.40 seconds wall clock time: 49 minutes 33.14 seconds (2973.14 seconds total)