Starting phenix.real_space_refine on Tue Sep 24 03:55:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/09_2024/7sf7_25076_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/09_2024/7sf7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/09_2024/7sf7_25076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/09_2024/7sf7_25076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/09_2024/7sf7_25076_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/09_2024/7sf7_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-5461/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: 4.50, per 1000 atoms: 0.66 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: 1.50 Conformation dependent library (CDL) restraints added in 964.0 milliseconds 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: 0.73 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: 1.83 Time building geometry restraints manager: 1.77 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: 3.170 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 0.775 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: 0.8244 time to fit residues: 117.6247 Evaluate side-chains 117 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 0.728 Fit side-chains REVERT: B 139 ILE cc_start: 0.8599 (mm) cc_final: 0.8356 (mp) REVERT: B 152 LYS cc_start: 0.6882 (OUTLIER) cc_final: 0.6626 (tptt) REVERT: C 175 GLN cc_start: 0.8263 (mt0) cc_final: 0.8061 (mt0) REVERT: C 258 ASP cc_start: 0.7286 (t0) cc_final: 0.7042 (t0) REVERT: C 298 ASP cc_start: 0.6834 (p0) cc_final: 0.6364 (p0) outliers start: 23 outliers final: 12 residues processed: 129 average time/residue: 0.7967 time to fit residues: 110.6974 Evaluate side-chains 126 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 0.0010 chunk 84 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1691 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= 0.219 Angle : 0.557 7.098 9379 Z= 0.306 Chirality : 0.043 0.164 1097 Planarity : 0.003 0.033 1179 Dihedral : 4.815 47.502 941 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.67 % Allowed : 11.71 % Favored : 84.63 % 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: -1.39 (0.29), residues: 869 helix: 0.18 (0.31), residues: 332 sheet: -0.03 (0.40), residues: 173 loop : -2.46 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1000 HIS 0.005 0.001 HIS C 183 PHE 0.025 0.002 PHE A 908 TYR 0.017 0.001 TYR A1006 ARG 0.004 0.000 ARG C 197 *********************** 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 135 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 139 ILE cc_start: 0.8605 (mm) cc_final: 0.8363 (mp) REVERT: B 152 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6623 (tptt) REVERT: C 153 ASP cc_start: 0.7467 (p0) cc_final: 0.7259 (p0) REVERT: C 155 ASN cc_start: 0.7599 (t0) cc_final: 0.7246 (m-40) REVERT: C 175 GLN cc_start: 0.8267 (mt0) cc_final: 0.8041 (mt0) REVERT: C 258 ASP cc_start: 0.7301 (t0) cc_final: 0.6996 (t0) REVERT: C 262 MET cc_start: 0.5839 (OUTLIER) cc_final: 0.5014 (mpt) REVERT: C 297 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7657 (m-90) REVERT: C 298 ASP cc_start: 0.6764 (p0) cc_final: 0.6285 (p0) outliers start: 26 outliers final: 14 residues processed: 120 average time/residue: 0.7610 time to fit residues: 98.9775 Evaluate side-chains 126 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 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 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 8 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 overall best weight: 0.3590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6912 Z= 0.177 Angle : 0.532 9.322 9379 Z= 0.289 Chirality : 0.042 0.156 1097 Planarity : 0.003 0.032 1179 Dihedral : 4.620 44.649 941 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.67 % Allowed : 13.26 % Favored : 83.07 % 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: -1.28 (0.29), residues: 869 helix: 0.29 (0.31), residues: 332 sheet: 0.07 (0.40), residues: 173 loop : -2.45 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1000 HIS 0.003 0.001 HIS C 183 PHE 0.012 0.001 PHE C 199 TYR 0.016 0.001 TYR A1006 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 140 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 1006 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: B 139 ILE cc_start: 0.8615 (mm) cc_final: 0.8373 (mp) REVERT: B 220 LEU cc_start: 0.7234 (tp) cc_final: 0.6973 (tt) REVERT: C 175 GLN cc_start: 0.8252 (mt0) cc_final: 0.8010 (mt0) REVERT: C 258 ASP cc_start: 0.7265 (t0) cc_final: 0.6967 (t0) REVERT: C 262 MET cc_start: 0.5864 (OUTLIER) cc_final: 0.5036 (mpt) REVERT: C 297 TRP cc_start: 0.8303 (OUTLIER) cc_final: 0.7653 (m-90) REVERT: C 298 ASP cc_start: 0.6744 (p0) cc_final: 0.6278 (p0) outliers start: 26 outliers final: 14 residues processed: 125 average time/residue: 0.8137 time to fit residues: 109.9759 Evaluate side-chains 126 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6912 Z= 0.325 Angle : 0.611 7.100 9379 Z= 0.338 Chirality : 0.045 0.179 1097 Planarity : 0.004 0.034 1179 Dihedral : 5.075 48.049 941 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.80 % Allowed : 15.66 % Favored : 79.55 % 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: -1.38 (0.29), residues: 869 helix: 0.20 (0.31), residues: 329 sheet: 0.03 (0.40), residues: 174 loop : -2.50 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1000 HIS 0.005 0.001 HIS A 850 PHE 0.028 0.002 PHE A 908 TYR 0.022 0.002 TYR A1006 ARG 0.006 0.001 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 142 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 108 time to evaluate : 0.733 Fit side-chains REVERT: B 139 ILE cc_start: 0.8622 (mm) cc_final: 0.8386 (mp) REVERT: C 175 GLN cc_start: 0.8282 (mt0) cc_final: 0.8049 (mt0) REVERT: C 258 ASP cc_start: 0.7297 (t0) cc_final: 0.6992 (t0) REVERT: C 262 MET cc_start: 0.5923 (OUTLIER) cc_final: 0.5096 (mpt) REVERT: C 289 TYR cc_start: 0.7600 (m-80) cc_final: 0.7391 (m-80) REVERT: C 297 TRP cc_start: 0.8310 (OUTLIER) cc_final: 0.7687 (m-90) REVERT: C 298 ASP cc_start: 0.6803 (p0) cc_final: 0.6360 (p0) outliers start: 34 outliers final: 21 residues processed: 124 average time/residue: 0.7242 time to fit residues: 97.5789 Evaluate side-chains 127 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 912 LEU Chi-restraints excluded: chain A residue 929 VAL Chi-restraints excluded: chain A residue 995 THR 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 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 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 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 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.0020 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6912 Z= 0.210 Angle : 0.560 7.954 9379 Z= 0.309 Chirality : 0.043 0.155 1097 Planarity : 0.003 0.035 1179 Dihedral : 4.696 49.626 939 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.37 % Allowed : 17.07 % 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 (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: -1.29 (0.29), residues: 869 helix: 0.30 (0.31), residues: 329 sheet: 0.13 (0.40), residues: 174 loop : -2.49 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1000 HIS 0.003 0.001 HIS B 198 PHE 0.026 0.001 PHE A 908 TYR 0.018 0.001 TYR A1031 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 fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 0.643 Fit side-chains REVERT: B 139 ILE cc_start: 0.8628 (mm) cc_final: 0.8384 (mp) REVERT: C 175 GLN cc_start: 0.8259 (mt0) cc_final: 0.8021 (mt0) REVERT: C 258 ASP cc_start: 0.7266 (t0) cc_final: 0.6952 (t0) REVERT: C 297 TRP cc_start: 0.8295 (OUTLIER) cc_final: 0.7683 (m-90) REVERT: C 298 ASP cc_start: 0.6753 (p0) cc_final: 0.6301 (p0) outliers start: 31 outliers final: 22 residues processed: 119 average time/residue: 0.7089 time to fit residues: 91.6649 Evaluate side-chains 128 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 929 VAL Chi-restraints excluded: chain A residue 1000 TRP 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 30 VAL 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 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 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.0470 chunk 46 optimal weight: 0.0980 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5280 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6912 Z= 0.236 Angle : 0.583 8.796 9379 Z= 0.319 Chirality : 0.043 0.151 1097 Planarity : 0.003 0.035 1179 Dihedral : 4.757 49.507 939 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.81 % Allowed : 19.18 % 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: -1.33 (0.29), residues: 869 helix: 0.26 (0.31), residues: 331 sheet: 0.11 (0.40), residues: 174 loop : -2.54 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1000 HIS 0.004 0.001 HIS A 850 PHE 0.027 0.002 PHE A 908 TYR 0.012 0.001 TYR A1006 ARG 0.003 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 134 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.759 Fit side-chains REVERT: A 1055 ILE cc_start: 0.7491 (mp) cc_final: 0.7255 (tp) REVERT: B 139 ILE cc_start: 0.8628 (mm) cc_final: 0.8385 (mp) REVERT: C 175 GLN cc_start: 0.8268 (mt0) cc_final: 0.8045 (mt0) REVERT: C 258 ASP cc_start: 0.7267 (t0) cc_final: 0.6953 (t0) outliers start: 27 outliers final: 20 residues processed: 119 average time/residue: 0.7443 time to fit residues: 96.0922 Evaluate side-chains 127 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 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 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 158 VAL Chi-restraints excluded: chain C residue 263 THR 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 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 0.0020 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 overall best weight: 0.4588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2309 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= 0.213 Angle : 0.582 9.994 9379 Z= 0.316 Chirality : 0.043 0.156 1097 Planarity : 0.003 0.034 1179 Dihedral : 4.716 49.701 939 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.53 % Allowed : 19.61 % 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 (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: -1.27 (0.29), residues: 869 helix: 0.33 (0.31), residues: 328 sheet: 0.19 (0.40), residues: 174 loop : -2.52 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1000 HIS 0.003 0.001 HIS A 850 PHE 0.029 0.001 PHE A 908 TYR 0.011 0.001 TYR A1006 ARG 0.003 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 fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 0.634 Fit side-chains REVERT: B 139 ILE cc_start: 0.8631 (mm) cc_final: 0.8388 (mp) REVERT: C 175 GLN cc_start: 0.8260 (mt0) cc_final: 0.8034 (mt0) REVERT: C 258 ASP cc_start: 0.7255 (t0) cc_final: 0.6934 (t0) REVERT: C 262 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5289 (mpt) REVERT: C 297 TRP cc_start: 0.8264 (OUTLIER) cc_final: 0.7705 (m-90) outliers start: 25 outliers final: 21 residues processed: 122 average time/residue: 0.7299 time to fit residues: 96.6996 Evaluate side-chains 132 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 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 293 ASN 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 79 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6912 Z= 0.310 Angle : 0.636 9.684 9379 Z= 0.347 Chirality : 0.045 0.161 1097 Planarity : 0.004 0.035 1179 Dihedral : 4.945 50.491 939 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.39 % Allowed : 19.89 % Favored : 76.73 % 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: -1.35 (0.29), residues: 869 helix: 0.21 (0.31), residues: 330 sheet: 0.18 (0.40), residues: 172 loop : -2.53 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1000 HIS 0.005 0.001 HIS A 850 PHE 0.030 0.002 PHE A 908 TYR 0.017 0.002 TYR A1006 ARG 0.004 0.000 ARG B 32 *********************** 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 132 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.766 Fit side-chains REVERT: B 139 ILE cc_start: 0.8631 (mm) cc_final: 0.8391 (mp) REVERT: C 175 GLN cc_start: 0.8282 (mt0) cc_final: 0.8046 (mt0) REVERT: C 258 ASP cc_start: 0.7219 (t0) cc_final: 0.6915 (t0) REVERT: C 262 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5322 (mpt) outliers start: 24 outliers final: 19 residues processed: 117 average time/residue: 0.7787 time to fit residues: 98.4614 Evaluate side-chains 128 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1049 ASN C 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6912 Z= 0.303 Angle : 0.630 10.661 9379 Z= 0.345 Chirality : 0.045 0.178 1097 Planarity : 0.004 0.035 1179 Dihedral : 4.963 51.040 939 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 3.24 % Allowed : 20.45 % 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 (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: -1.35 (0.29), residues: 869 helix: 0.21 (0.30), residues: 331 sheet: 0.15 (0.40), residues: 172 loop : -2.53 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1000 HIS 0.005 0.001 HIS A 850 PHE 0.030 0.002 PHE A 908 TYR 0.016 0.002 TYR A1006 ARG 0.004 0.000 ARG B 32 ********************** 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 132 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.780 Fit side-chains REVERT: B 139 ILE cc_start: 0.8631 (mm) cc_final: 0.8392 (mp) REVERT: C 175 GLN cc_start: 0.8281 (mt0) cc_final: 0.8044 (mt0) REVERT: C 258 ASP cc_start: 0.7210 (t0) cc_final: 0.6903 (t0) REVERT: C 297 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7639 (m-90) outliers start: 23 outliers final: 19 residues processed: 118 average time/residue: 0.7010 time to fit residues: 90.2061 Evaluate side-chains 126 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 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 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 62 optimal weight: 0.0040 chunk 10 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.0070 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 chunk 49 optimal weight: 4.9990 overall best weight: 0.1788 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.154648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.134875 restraints weight = 9825.224| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.19 r_work: 0.3726 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6912 Z= 0.157 Angle : 0.559 10.436 9379 Z= 0.304 Chirality : 0.042 0.166 1097 Planarity : 0.003 0.034 1179 Dihedral : 4.482 48.294 939 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.68 % Allowed : 21.02 % 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 (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: -1.00 (0.29), residues: 869 helix: 0.74 (0.31), residues: 316 sheet: 0.24 (0.40), residues: 174 loop : -2.42 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1000 HIS 0.002 0.000 HIS B 198 PHE 0.029 0.001 PHE A 908 TYR 0.008 0.001 TYR C 289 ARG 0.003 0.000 ARG C 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2654.86 seconds wall clock time: 50 minutes 13.34 seconds (3013.34 seconds total)