Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 10:30:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/04_2023/7sf7_25076_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/04_2023/7sf7_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_25076/04_2023/7sf7_25076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/04_2023/7sf7_25076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/04_2023/7sf7_25076_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf7_25076/04_2023/7sf7_25076_neut.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A GLU 963": "OE1" <-> "OE2" Residue "A TYR 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 3.88, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 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: 0.37 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: 1.69 Time building geometry restraints manager: 2.53 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: 100.38 - 107.19: 145 107.19 - 113.99: 3954 113.99 - 120.80: 3028 120.80 - 127.60: 2190 127.60 - 134.41: 62 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 2.520 nonbonded pdb=" OG1 THR A 885 " pdb=" OH TYR A1112 " model vdw 2.258 2.440 nonbonded pdb=" NH1 ARG C 197 " pdb=" OD1 ASP C 212 " model vdw 2.272 2.520 nonbonded pdb=" NZ LYS B 46 " pdb=" OD1 ASP B 85 " model vdw 2.293 2.520 nonbonded pdb=" ND2 ASN B 43 " pdb=" OD2 ASP B 111 " model vdw 2.323 2.520 ... (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 ========== 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: 0.010 Extract box with map and model: 9.640 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 20.360 Find NCS groups from input model: 0.180 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:13.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.160 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 0.771 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 133 average time/residue: 0.8673 time to fit residues: 123.8606 Evaluate side-chains 116 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.2406 time to fit residues: 1.4775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.0170 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.0040 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 overall best weight: 0.5430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 843 ASN A 860 HIS A 919 ASN B 144 ASN B 230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 6912 Z= 0.233 Angle : 0.562 8.689 9379 Z= 0.307 Chirality : 0.043 0.167 1097 Planarity : 0.003 0.033 1179 Dihedral : 4.392 22.703 937 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 3.24 % 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: -1.59 (0.29), residues: 869 helix: 0.08 (0.31), residues: 333 sheet: -0.27 (0.40), residues: 163 loop : -2.51 (0.30), residues: 373 *********************** 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 146 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 0.933 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 132 average time/residue: 0.8265 time to fit residues: 117.6665 Evaluate side-chains 128 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 7 average time/residue: 0.2404 time to fit residues: 3.5553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 951 GLN C 156 GLN C 183 HIS C 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 6912 Z= 0.358 Angle : 0.627 7.895 9379 Z= 0.346 Chirality : 0.045 0.164 1097 Planarity : 0.004 0.034 1179 Dihedral : 4.719 22.722 937 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer Outliers : 4.23 % 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: -1.69 (0.29), residues: 869 helix: -0.03 (0.30), residues: 334 sheet: -0.32 (0.41), residues: 157 loop : -2.51 (0.30), residues: 378 *********************** 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 142 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 112 time to evaluate : 0.771 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 125 average time/residue: 0.7325 time to fit residues: 99.4567 Evaluate side-chains 127 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 8 residues processed: 10 average time/residue: 0.1165 time to fit residues: 2.7653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 6912 Z= 0.211 Angle : 0.547 9.557 9379 Z= 0.301 Chirality : 0.042 0.176 1097 Planarity : 0.003 0.033 1179 Dihedral : 4.512 22.454 937 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer Outliers : 4.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.52 (0.29), residues: 869 helix: 0.19 (0.31), residues: 329 sheet: -0.15 (0.41), residues: 162 loop : -2.55 (0.29), residues: 378 *********************** 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 143 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 0.702 Fit side-chains outliers start: 31 outliers final: 14 residues processed: 125 average time/residue: 0.7892 time to fit residues: 107.1467 Evaluate side-chains 123 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 8 average time/residue: 0.4007 time to fit residues: 4.8388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0070 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 0.0170 chunk 20 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 6912 Z= 0.202 Angle : 0.534 7.285 9379 Z= 0.297 Chirality : 0.042 0.166 1097 Planarity : 0.003 0.032 1179 Dihedral : 4.345 22.348 937 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer Outliers : 4.65 % 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: 0.28 (0.31), residues: 328 sheet: -0.00 (0.40), residues: 173 loop : -2.57 (0.30), residues: 368 *********************** 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 145 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 0.801 Fit side-chains outliers start: 33 outliers final: 15 residues processed: 131 average time/residue: 0.7616 time to fit residues: 108.4370 Evaluate side-chains 124 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 7 average time/residue: 0.2606 time to fit residues: 3.3180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 6912 Z= 0.251 Angle : 0.576 9.358 9379 Z= 0.315 Chirality : 0.043 0.154 1097 Planarity : 0.003 0.033 1179 Dihedral : 4.446 22.668 937 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 4.09 % 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: -1.45 (0.29), residues: 869 helix: 0.27 (0.31), residues: 329 sheet: -0.05 (0.41), residues: 161 loop : -2.56 (0.29), residues: 379 *********************** 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: 29 poor density : 108 time to evaluate : 0.769 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 121 average time/residue: 0.7988 time to fit residues: 104.5035 Evaluate side-chains 121 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.794 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 7 average time/residue: 0.1274 time to fit residues: 2.3981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 0.0870 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 6912 Z= 0.255 Angle : 0.568 8.462 9379 Z= 0.316 Chirality : 0.043 0.150 1097 Planarity : 0.003 0.033 1179 Dihedral : 4.467 22.825 937 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 3.24 % 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: 0.30 (0.31), residues: 327 sheet: 0.07 (0.40), residues: 172 loop : -2.59 (0.30), residues: 370 *********************** 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 136 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.749 Fit side-chains outliers start: 23 outliers final: 17 residues processed: 123 average time/residue: 0.7798 time to fit residues: 103.8022 Evaluate side-chains 129 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.762 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 8 average time/residue: 0.6010 time to fit residues: 6.3035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7152 moved from start: 0.2312 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= 0.265 Angle : 0.580 8.252 9379 Z= 0.322 Chirality : 0.043 0.153 1097 Planarity : 0.004 0.032 1179 Dihedral : 4.513 22.704 937 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer Outliers : 3.67 % 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: -1.43 (0.29), residues: 869 helix: 0.25 (0.31), residues: 331 sheet: 0.06 (0.42), residues: 156 loop : -2.55 (0.29), residues: 382 *********************** 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 138 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.754 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 124 average time/residue: 0.7554 time to fit residues: 101.5755 Evaluate side-chains 126 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 6 average time/residue: 0.3332 time to fit residues: 3.5382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 60 optimal weight: 0.0770 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2349 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= 0.258 Angle : 0.582 8.069 9379 Z= 0.324 Chirality : 0.043 0.149 1097 Planarity : 0.003 0.034 1179 Dihedral : 4.489 22.942 937 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 2.40 % 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: -1.44 (0.29), residues: 869 helix: 0.31 (0.31), residues: 329 sheet: -0.06 (0.41), residues: 161 loop : -2.59 (0.29), residues: 379 *********************** 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 127 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.683 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 120 average time/residue: 0.7495 time to fit residues: 97.5919 Evaluate side-chains 119 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 0.4898 time to fit residues: 2.7140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 78 optimal weight: 0.0060 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.004 0.047 6912 Z= 0.256 Angle : 0.588 8.455 9379 Z= 0.327 Chirality : 0.043 0.151 1097 Planarity : 0.003 0.031 1179 Dihedral : 4.478 22.825 937 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 1.97 % 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: 0.34 (0.31), residues: 329 sheet: 0.06 (0.40), residues: 172 loop : -2.60 (0.30), residues: 368 ********************** 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 125 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.756 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 120 average time/residue: 0.7821 time to fit residues: 102.2871 Evaluate side-chains 123 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.773 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 0.1535 time to fit residues: 1.7314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.150221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.130426 restraints weight = 9749.515| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.16 r_work: 0.3668 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2431 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= 0.270 Angle : 0.593 8.785 9379 Z= 0.330 Chirality : 0.044 0.152 1097 Planarity : 0.004 0.066 1179 Dihedral : 4.509 22.689 937 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 2.68 % 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: 0.37 (0.31), residues: 329 sheet: -0.03 (0.41), residues: 161 loop : -2.58 (0.29), residues: 379 =============================================================================== Job complete usr+sys time: 2588.48 seconds wall clock time: 46 minutes 31.28 seconds (2791.28 seconds total)