Starting phenix.real_space_refine on Tue Feb 11 23:23:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sf7_25076/02_2025/7sf7_25076_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sf7_25076/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sf7_25076/02_2025/7sf7_25076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sf7_25076/02_2025/7sf7_25076.map" model { file = "/net/cci-nas-00/data/ceres_data/7sf7_25076/02_2025/7sf7_25076_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sf7_25076/02_2025/7sf7_25076_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} 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, 'GLU:plan': 2, 'ARG: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, 'GLU:plan': 1, 'ARG: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: 5.10, per 1000 atoms: 0.75 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: 1.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.68 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: 1.81 Time building geometry restraints manager: 1.72 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.050 ------------------------------------------------------------------------------- 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 6912 Z= 0.291 Angle : 0.780 9.671 9379 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 : 6.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.028 0.002 TRP A1000 HIS 0.008 0.001 HIS A 964 PHE 0.026 0.002 PHE A1086 TYR 0.032 0.002 TYR A1006 ARG 0.007 0.000 ARG B 32 *********************** 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 : 0.713 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: 0.8903 time to fit residues: 127.0314 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 : 0.738 ------------------------------------------------------------------------------- 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 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 67 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.153299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.133201 restraints weight = 9748.598| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.21 r_work: 0.3704 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6912 Z= 0.213 Angle : 0.561 8.207 9379 Z= 0.307 Chirality : 0.043 0.170 1097 Planarity : 0.003 0.033 1179 Dihedral : 5.213 52.150 943 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.24 % Allowed : 9.03 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.29), residues: 869 helix: 0.11 (0.31), residues: 333 sheet: -0.17 (0.40), residues: 173 loop : -2.50 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1000 HIS 0.004 0.001 HIS C 183 PHE 0.013 0.002 PHE C 199 TYR 0.014 0.001 TYR A1006 ARG 0.005 0.000 ARG C 197 *********************** 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 143 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.784 Fit side-chains REVERT: B 111 ASP cc_start: 0.7343 (p0) cc_final: 0.7124 (p0) REVERT: B 114 ASP cc_start: 0.7344 (m-30) cc_final: 0.7103 (p0) REVERT: B 139 ILE cc_start: 0.8824 (mm) cc_final: 0.8605 (mp) REVERT: B 152 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6776 (tptt) REVERT: C 175 GLN cc_start: 0.8652 (mt0) cc_final: 0.8438 (mt0) REVERT: C 258 ASP cc_start: 0.7895 (t0) cc_final: 0.7541 (t0) REVERT: C 262 MET cc_start: 0.6531 (OUTLIER) cc_final: 0.6318 (mpt) REVERT: C 293 ASN cc_start: 0.7394 (m110) cc_final: 0.7175 (m110) REVERT: C 298 ASP cc_start: 0.7559 (p0) cc_final: 0.7093 (p0) outliers start: 23 outliers final: 12 residues processed: 129 average time/residue: 0.8564 time to fit residues: 118.7502 Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 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 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 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.0060 chunk 84 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 183 HIS C 225 HIS C 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.151952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131597 restraints weight = 9916.120| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.23 r_work: 0.3679 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6912 Z= 0.235 Angle : 0.559 7.081 9379 Z= 0.307 Chirality : 0.043 0.162 1097 Planarity : 0.003 0.034 1179 Dihedral : 4.871 46.615 941 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.09 % Allowed : 11.71 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.29), residues: 869 helix: 0.16 (0.31), residues: 333 sheet: -0.04 (0.39), residues: 174 loop : -2.48 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1000 HIS 0.006 0.001 HIS C 183 PHE 0.026 0.002 PHE A 908 TYR 0.018 0.002 TYR A1006 ARG 0.004 0.000 ARG C 134 *********************** 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 139 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: A 1055 ILE cc_start: 0.8018 (mp) cc_final: 0.7673 (tp) REVERT: B 111 ASP cc_start: 0.7338 (p0) cc_final: 0.7066 (p0) REVERT: B 114 ASP cc_start: 0.7363 (m-30) cc_final: 0.7092 (p0) REVERT: B 139 ILE cc_start: 0.8833 (mm) cc_final: 0.8618 (mp) REVERT: B 152 LYS cc_start: 0.6982 (OUTLIER) cc_final: 0.6753 (tptt) REVERT: C 153 ASP cc_start: 0.7999 (p0) cc_final: 0.7780 (p0) REVERT: C 175 GLN cc_start: 0.8653 (mt0) cc_final: 0.8418 (mt0) REVERT: C 258 ASP cc_start: 0.7927 (t0) cc_final: 0.7506 (t0) REVERT: C 262 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6372 (mpt) REVERT: C 293 ASN cc_start: 0.7546 (m110) cc_final: 0.7199 (m110) REVERT: C 297 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.7969 (m-90) REVERT: C 298 ASP cc_start: 0.7490 (p0) cc_final: 0.7027 (p0) outliers start: 29 outliers final: 15 residues processed: 123 average time/residue: 0.7766 time to fit residues: 103.7862 Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 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 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 2 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 20 optimal weight: 0.0270 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.152833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132641 restraints weight = 9908.537| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.22 r_work: 0.3686 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6912 Z= 0.192 Angle : 0.534 9.528 9379 Z= 0.290 Chirality : 0.042 0.155 1097 Planarity : 0.003 0.035 1179 Dihedral : 4.714 44.444 941 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.67 % Allowed : 14.53 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.29), residues: 869 helix: 0.25 (0.31), residues: 332 sheet: 0.06 (0.40), residues: 173 loop : -2.48 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1000 HIS 0.003 0.001 HIS B 198 PHE 0.024 0.001 PHE A 908 TYR 0.018 0.001 TYR A1031 ARG 0.005 0.000 ARG C 197 *********************** 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 139 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.723 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 1055 ILE cc_start: 0.8013 (mp) cc_final: 0.7673 (tp) REVERT: B 111 ASP cc_start: 0.7294 (p0) cc_final: 0.7024 (p0) REVERT: B 114 ASP cc_start: 0.7375 (m-30) cc_final: 0.7091 (p0) REVERT: B 139 ILE cc_start: 0.8842 (mm) cc_final: 0.8620 (mp) REVERT: B 220 LEU cc_start: 0.7596 (tp) cc_final: 0.7333 (tt) REVERT: C 175 GLN cc_start: 0.8654 (mt0) cc_final: 0.8407 (mt0) REVERT: C 258 ASP cc_start: 0.7911 (t0) cc_final: 0.7485 (t0) REVERT: C 262 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6415 (mpt) REVERT: C 293 ASN cc_start: 0.7551 (m110) cc_final: 0.7276 (m110) REVERT: C 297 TRP cc_start: 0.8572 (OUTLIER) cc_final: 0.7967 (m-90) REVERT: C 298 ASP cc_start: 0.7487 (p0) cc_final: 0.7069 (p0) outliers start: 26 outliers final: 13 residues processed: 123 average time/residue: 0.8468 time to fit residues: 111.9376 Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 83 MET 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 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 0.0060 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.151634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131569 restraints weight = 9845.175| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.21 r_work: 0.3677 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6912 Z= 0.237 Angle : 0.551 6.800 9379 Z= 0.306 Chirality : 0.043 0.164 1097 Planarity : 0.003 0.034 1179 Dihedral : 4.887 47.804 941 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.37 % Allowed : 15.94 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.29), residues: 869 helix: 0.19 (0.31), residues: 334 sheet: 0.09 (0.40), residues: 174 loop : -2.52 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1000 HIS 0.004 0.001 HIS A 850 PHE 0.026 0.002 PHE A 908 TYR 0.018 0.001 TYR A1006 ARG 0.006 0.000 ARG C 197 *********************** 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 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.781 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: A 1055 ILE cc_start: 0.8035 (mp) cc_final: 0.7722 (tp) REVERT: B 111 ASP cc_start: 0.7319 (p0) cc_final: 0.7017 (p0) REVERT: B 114 ASP cc_start: 0.7387 (m-30) cc_final: 0.7081 (p0) REVERT: B 139 ILE cc_start: 0.8834 (mm) cc_final: 0.8617 (mp) REVERT: C 175 GLN cc_start: 0.8658 (mt0) cc_final: 0.8401 (mt0) REVERT: C 258 ASP cc_start: 0.7888 (t0) cc_final: 0.7474 (t0) REVERT: C 262 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6457 (mpt) REVERT: C 293 ASN cc_start: 0.7571 (m110) cc_final: 0.7218 (m110) REVERT: C 297 TRP cc_start: 0.8552 (OUTLIER) cc_final: 0.7976 (m-90) REVERT: C 298 ASP cc_start: 0.7504 (p0) cc_final: 0.7084 (p0) outliers start: 31 outliers final: 19 residues processed: 121 average time/residue: 0.7881 time to fit residues: 103.2349 Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 862 LEU 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 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 83 MET 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 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 58 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 63 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.153151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133039 restraints weight = 9925.047| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.22 r_work: 0.3693 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6912 Z= 0.187 Angle : 0.537 8.275 9379 Z= 0.295 Chirality : 0.042 0.158 1097 Planarity : 0.003 0.034 1179 Dihedral : 4.756 46.902 941 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.09 % Allowed : 17.63 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.29), residues: 869 helix: 0.35 (0.31), residues: 328 sheet: 0.20 (0.40), residues: 174 loop : -2.47 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1000 HIS 0.003 0.001 HIS B 198 PHE 0.027 0.001 PHE A 908 TYR 0.016 0.001 TYR A1006 ARG 0.005 0.000 ARG C 134 *********************** 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 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.856 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: A 1055 ILE cc_start: 0.8007 (mp) cc_final: 0.7706 (tp) REVERT: B 111 ASP cc_start: 0.7305 (p0) cc_final: 0.6984 (p0) REVERT: B 114 ASP cc_start: 0.7372 (m-30) cc_final: 0.7076 (p0) REVERT: B 139 ILE cc_start: 0.8836 (mm) cc_final: 0.8613 (mp) REVERT: C 175 GLN cc_start: 0.8656 (mt0) cc_final: 0.8412 (mt0) REVERT: C 258 ASP cc_start: 0.7857 (t0) cc_final: 0.7429 (t0) REVERT: C 262 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6425 (mpt) REVERT: C 293 ASN cc_start: 0.7555 (m110) cc_final: 0.7253 (m110) REVERT: C 298 ASP cc_start: 0.7483 (p0) cc_final: 0.7063 (p0) outliers start: 29 outliers final: 19 residues processed: 119 average time/residue: 0.7709 time to fit residues: 99.5381 Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 862 LEU 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 36 ILE Chi-restraints excluded: chain B residue 83 MET 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 138 GLU 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 325 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 0.0170 chunk 34 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.151349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131134 restraints weight = 9864.731| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.20 r_work: 0.3675 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6912 Z= 0.253 Angle : 0.574 8.688 9379 Z= 0.313 Chirality : 0.043 0.137 1097 Planarity : 0.003 0.034 1179 Dihedral : 4.915 47.020 941 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 4.23 % Allowed : 18.48 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.29), residues: 869 helix: 0.26 (0.31), residues: 330 sheet: 0.16 (0.40), residues: 174 loop : -2.51 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1000 HIS 0.004 0.001 HIS A 850 PHE 0.028 0.002 PHE A 908 TYR 0.019 0.001 TYR A1006 ARG 0.004 0.000 ARG C 134 *********************** 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 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.726 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7933 (m-80) REVERT: A 1055 ILE cc_start: 0.8010 (mp) cc_final: 0.7726 (tp) REVERT: B 111 ASP cc_start: 0.7328 (p0) cc_final: 0.7007 (p0) REVERT: B 114 ASP cc_start: 0.7381 (m-30) cc_final: 0.7051 (p0) REVERT: B 139 ILE cc_start: 0.8833 (mm) cc_final: 0.8611 (mp) REVERT: C 175 GLN cc_start: 0.8654 (mt0) cc_final: 0.8425 (mt0) REVERT: C 258 ASP cc_start: 0.7893 (t0) cc_final: 0.7457 (t0) REVERT: C 262 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6443 (mpt) REVERT: C 293 ASN cc_start: 0.7592 (m110) cc_final: 0.7219 (m110) REVERT: C 297 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.7964 (m-90) REVERT: C 298 ASP cc_start: 0.7475 (p0) cc_final: 0.7047 (p0) outliers start: 30 outliers final: 17 residues processed: 122 average time/residue: 0.7463 time to fit residues: 98.9865 Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 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 138 GLU 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 70 optimal weight: 0.0570 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 0.0170 chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 75 optimal weight: 0.0040 chunk 83 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 0.0370 chunk 18 optimal weight: 0.9990 overall best weight: 0.1426 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.155843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.135820 restraints weight = 9991.342| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.24 r_work: 0.3738 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6912 Z= 0.135 Angle : 0.516 8.306 9379 Z= 0.282 Chirality : 0.041 0.149 1097 Planarity : 0.003 0.034 1179 Dihedral : 4.523 45.056 941 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.10 % Allowed : 19.89 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 869 helix: 0.45 (0.31), residues: 329 sheet: 0.34 (0.41), residues: 173 loop : -2.38 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1000 HIS 0.002 0.000 HIS B 198 PHE 0.028 0.001 PHE A 908 TYR 0.018 0.001 TYR A1031 ARG 0.004 0.000 ARG C 134 *********************** 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 137 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.730 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: A 1055 ILE cc_start: 0.7973 (mp) cc_final: 0.7687 (tp) REVERT: B 111 ASP cc_start: 0.7268 (p0) cc_final: 0.6993 (p0) REVERT: B 114 ASP cc_start: 0.7356 (m-30) cc_final: 0.7028 (p0) REVERT: B 139 ILE cc_start: 0.8843 (mm) cc_final: 0.8610 (mp) REVERT: C 175 GLN cc_start: 0.8623 (mt0) cc_final: 0.8387 (mt0) REVERT: C 258 ASP cc_start: 0.7891 (t0) cc_final: 0.7403 (t0) REVERT: C 262 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6409 (mpt) REVERT: C 293 ASN cc_start: 0.7498 (m110) cc_final: 0.7273 (m-40) REVERT: C 297 TRP cc_start: 0.8450 (OUTLIER) cc_final: 0.7960 (m-90) REVERT: C 298 ASP cc_start: 0.7448 (p0) cc_final: 0.7038 (p0) outliers start: 22 outliers final: 13 residues processed: 122 average time/residue: 0.8439 time to fit residues: 111.9785 Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 29 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.3984 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.153647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.133540 restraints weight = 9929.172| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.22 r_work: 0.3703 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6912 Z= 0.193 Angle : 0.550 8.207 9379 Z= 0.300 Chirality : 0.042 0.140 1097 Planarity : 0.003 0.035 1179 Dihedral : 4.586 44.365 941 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.82 % Allowed : 20.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.29), residues: 869 helix: 0.71 (0.31), residues: 322 sheet: 0.36 (0.40), residues: 174 loop : -2.41 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1000 HIS 0.003 0.001 HIS B 198 PHE 0.014 0.001 PHE C 335 TYR 0.016 0.001 TYR A1006 ARG 0.003 0.000 ARG C 134 *********************** 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 133 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.775 Fit side-chains REVERT: A 1006 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: A 1055 ILE cc_start: 0.7987 (mp) cc_final: 0.7695 (tp) REVERT: B 111 ASP cc_start: 0.7293 (p0) cc_final: 0.6997 (p0) REVERT: B 114 ASP cc_start: 0.7350 (m-30) cc_final: 0.7031 (p0) REVERT: B 139 ILE cc_start: 0.8834 (mm) cc_final: 0.8609 (mp) REVERT: C 175 GLN cc_start: 0.8644 (mt0) cc_final: 0.8397 (mt0) REVERT: C 258 ASP cc_start: 0.7863 (t0) cc_final: 0.7385 (t0) REVERT: C 262 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6426 (mpt) REVERT: C 293 ASN cc_start: 0.7483 (m110) cc_final: 0.7180 (m-40) REVERT: C 297 TRP cc_start: 0.8439 (OUTLIER) cc_final: 0.7939 (m-90) REVERT: C 298 ASP cc_start: 0.7461 (p0) cc_final: 0.7034 (p0) outliers start: 20 outliers final: 14 residues processed: 123 average time/residue: 0.8861 time to fit residues: 116.9581 Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 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 262 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 297 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 46 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.0000 chunk 18 optimal weight: 0.2980 chunk 32 optimal weight: 0.3980 overall best weight: 0.2582 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.155172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.135098 restraints weight = 10061.858| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.23 r_work: 0.3725 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6912 Z= 0.160 Angle : 0.542 9.759 9379 Z= 0.292 Chirality : 0.042 0.143 1097 Planarity : 0.003 0.035 1179 Dihedral : 4.475 44.841 941 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.54 % Allowed : 21.72 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.29), residues: 869 helix: 0.77 (0.31), residues: 323 sheet: 0.38 (0.40), residues: 174 loop : -2.36 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1000 HIS 0.003 0.000 HIS B 198 PHE 0.027 0.001 PHE A 908 TYR 0.012 0.001 TYR A1006 ARG 0.012 0.000 ARG B 184 ********************** 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 135 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.757 Fit side-chains REVERT: A 1055 ILE cc_start: 0.7973 (mp) cc_final: 0.7676 (tp) REVERT: B 139 ILE cc_start: 0.8852 (mm) cc_final: 0.8617 (mp) REVERT: B 152 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6588 (tmtp) REVERT: C 175 GLN cc_start: 0.8633 (mt0) cc_final: 0.8392 (mt0) REVERT: C 258 ASP cc_start: 0.7887 (t0) cc_final: 0.7393 (t0) REVERT: C 262 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6374 (mpt) REVERT: C 298 ASP cc_start: 0.7439 (p0) cc_final: 0.6990 (p0) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 0.9247 time to fit residues: 122.6705 Evaluate side-chains 128 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 1058 ILE Chi-restraints excluded: chain A residue 1079 THR 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 B residue 214 ASP Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 56 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 10 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.152821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.132775 restraints weight = 9896.171| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.20 r_work: 0.3695 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6912 Z= 0.222 Angle : 0.580 9.941 9379 Z= 0.314 Chirality : 0.043 0.137 1097 Planarity : 0.004 0.062 1179 Dihedral : 4.466 44.393 939 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.82 % Allowed : 21.58 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.29), residues: 869 helix: 0.75 (0.31), residues: 324 sheet: 0.37 (0.40), residues: 175 loop : -2.41 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1000 HIS 0.004 0.001 HIS A 850 PHE 0.013 0.001 PHE B 125 TYR 0.010 0.001 TYR A1006 ARG 0.015 0.001 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5514.62 seconds wall clock time: 97 minutes 56.22 seconds (5876.22 seconds total)