Starting phenix.real_space_refine on Sun Apr 7 14:50:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ruc_24702/04_2024/7ruc_24702_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ruc_24702/04_2024/7ruc_24702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ruc_24702/04_2024/7ruc_24702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ruc_24702/04_2024/7ruc_24702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ruc_24702/04_2024/7ruc_24702_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ruc_24702/04_2024/7ruc_24702_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 6835 2.51 5 N 1832 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "G TYR 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10766 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2417 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 18, 'TRANS': 287} Chain breaks: 1 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2412 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 18, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "D" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 340 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 8, 'TRANS': 34} Chain: "F" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "G" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 12, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1952 SG CYS A 283 54.155 67.467 98.552 1.00142.37 S ATOM 1975 SG CYS A 286 55.590 69.741 96.078 1.00127.85 S ATOM 4364 SG CYS B 283 53.181 71.227 98.454 1.00138.48 S ATOM 4387 SG CYS B 286 51.745 68.778 96.011 1.00126.91 S Time building chain proxies: 6.07, per 1000 atoms: 0.56 Number of scatterers: 10766 At special positions: 0 Unit cell: (108.9, 125.4, 113.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 64 16.00 P 6 15.00 Mg 2 11.99 O 2026 8.00 N 1832 7.00 C 6835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 283 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 283 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 286 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 286 " Number of angles added : 6 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 2 sheets defined 62.9% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.592A pdb=" N ALA A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 164 through 187 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 210 through 231 removed outlier: 3.686A pdb=" N LEU A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 246 through 262 Processing helix chain 'A' and resid 284 through 303 Processing helix chain 'A' and resid 322 through 333 removed outlier: 3.897A pdb=" N GLN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.517A pdb=" N ALA B 57 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 Processing helix chain 'B' and resid 117 through 132 removed outlier: 4.975A pdb=" N GLY B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ALA B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 4.347A pdb=" N ASP B 137 " --> pdb=" O PRO B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 189 Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 211 through 231 removed outlier: 3.956A pdb=" N LEU B 220 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Proline residue: B 221 - end of helix removed outlier: 3.749A pdb=" N GLU B 228 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 262 Processing helix chain 'B' and resid 284 through 303 Processing helix chain 'B' and resid 322 through 333 removed outlier: 4.003A pdb=" N GLN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 36 Processing helix chain 'C' and resid 39 through 56 Processing helix chain 'C' and resid 59 through 75 Processing helix chain 'C' and resid 79 through 95 Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 120 through 132 Processing helix chain 'C' and resid 143 through 155 Processing helix chain 'C' and resid 159 through 168 Processing helix chain 'C' and resid 172 through 185 Processing helix chain 'C' and resid 189 through 205 removed outlier: 3.936A pdb=" N VAL C 192 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASP C 193 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 195 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 Processing helix chain 'C' and resid 235 through 249 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.581A pdb=" N ARG C 268 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 284 removed outlier: 3.902A pdb=" N GLU C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1013 removed outlier: 4.370A pdb=" N ALA D1013 " --> pdb=" O PRO D1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1009 through 1013' Processing helix chain 'D' and resid 1016 through 1029 Proline residue: D1020 - end of helix removed outlier: 3.729A pdb=" N GLN D1023 " --> pdb=" O VAL D1019 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D1024 " --> pdb=" O PRO D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1045 removed outlier: 4.063A pdb=" N GLY D1045 " --> pdb=" O ALA D1041 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 39 through 56 Processing helix chain 'F' and resid 59 through 76 Processing helix chain 'F' and resid 79 through 96 Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'F' and resid 143 through 155 Processing helix chain 'F' and resid 159 through 168 Processing helix chain 'F' and resid 173 through 186 Processing helix chain 'F' and resid 189 through 205 removed outlier: 4.145A pdb=" N VAL F 192 " --> pdb=" O ARG F 189 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ASP F 193 " --> pdb=" O SER F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 222 Processing helix chain 'F' and resid 235 through 247 Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 263 through 268 removed outlier: 3.709A pdb=" N ARG F 268 " --> pdb=" O PRO F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 283 removed outlier: 4.328A pdb=" N GLU F 274 " --> pdb=" O PRO F 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 1016 through 1031 Proline residue: G1020 - end of helix removed outlier: 3.798A pdb=" N ARG G1030 " --> pdb=" O ILE G1026 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS G1031 " --> pdb=" O GLN G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1040 through 1044 Processing helix chain 'G' and resid 1063 through 1074 Processing helix chain 'G' and resid 1082 through 1088 Processing helix chain 'G' and resid 1093 through 1113 removed outlier: 4.357A pdb=" N TYR G1098 " --> pdb=" O VAL G1094 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG G1099 " --> pdb=" O GLN G1095 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN G1111 " --> pdb=" O GLN G1107 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU G1112 " --> pdb=" O LYS G1108 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP G1113 " --> pdb=" O ARG G1109 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 106 removed outlier: 4.329A pdb=" N VAL H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 133 through 139 removed outlier: 3.503A pdb=" N LEU H 138 " --> pdb=" O ILE H 135 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 308 through 311 removed outlier: 10.241A pdb=" N ASN A 268 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 238 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE A 270 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS A 240 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN A 272 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N CYS A 242 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP A 33 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 239 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 35 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A 241 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLY A 37 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ILE A 243 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 157 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL A 36 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 159 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 308 through 311 removed outlier: 4.898A pdb=" N ASN B 268 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 240 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP B 33 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE B 239 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE B 35 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 241 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY B 37 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 157 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL B 36 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 159 " --> pdb=" O VAL B 36 " (cutoff:3.500A) 576 hydrogen bonds defined for protein. 1551 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: 2.93 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3527 1.34 - 1.46: 1966 1.46 - 1.58: 5393 1.58 - 1.69: 6 1.69 - 1.81: 106 Bond restraints: 10998 Sorted by residual: bond pdb=" C LEU A 314 " pdb=" N LEU A 315 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.47e-02 4.63e+03 3.26e+00 bond pdb=" CA PRO B 163 " pdb=" C PRO B 163 " ideal model delta sigma weight residual 1.525 1.514 0.012 9.70e-03 1.06e+04 1.49e+00 bond pdb=" O3B ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 1.592 1.562 0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" C1' ATP B 402 " pdb=" C2' ATP B 402 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.73e-01 bond pdb=" C1' ATP A 401 " pdb=" C2' ATP A 401 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.51e-01 ... (remaining 10993 not shown) Histogram of bond angle deviations from ideal: 99.63 - 107.63: 512 107.63 - 115.63: 6655 115.63 - 123.63: 7456 123.63 - 131.63: 240 131.63 - 139.63: 19 Bond angle restraints: 14882 Sorted by residual: angle pdb=" N ASP B 116 " pdb=" CA ASP B 116 " pdb=" C ASP B 116 " ideal model delta sigma weight residual 112.97 110.05 2.92 1.06e+00 8.90e-01 7.61e+00 angle pdb=" N SER G1097 " pdb=" CA SER G1097 " pdb=" C SER G1097 " ideal model delta sigma weight residual 111.75 108.44 3.31 1.28e+00 6.10e-01 6.68e+00 angle pdb=" C2' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" O3' ATP A 401 " ideal model delta sigma weight residual 111.83 105.10 6.73 2.67e+00 1.40e-01 6.35e+00 angle pdb=" C1' ATP A 401 " pdb=" C2' ATP A 401 " pdb=" O2' ATP A 401 " ideal model delta sigma weight residual 110.58 103.60 6.98 2.79e+00 1.28e-01 6.25e+00 angle pdb=" C2' ATP B 402 " pdb=" C3' ATP B 402 " pdb=" O3' ATP B 402 " ideal model delta sigma weight residual 111.83 105.29 6.54 2.67e+00 1.40e-01 6.01e+00 ... (remaining 14877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 6045 17.61 - 35.21: 567 35.21 - 52.82: 114 52.82 - 70.43: 28 70.43 - 88.04: 12 Dihedral angle restraints: 6766 sinusoidal: 2838 harmonic: 3928 Sorted by residual: dihedral pdb=" CA LEU A 303 " pdb=" C LEU A 303 " pdb=" N TYR A 304 " pdb=" CA TYR A 304 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU F 181 " pdb=" CG GLU F 181 " pdb=" CD GLU F 181 " pdb=" OE1 GLU F 181 " ideal model delta sinusoidal sigma weight residual 0.00 88.04 -88.04 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CG ARG B 263 " pdb=" CD ARG B 263 " pdb=" NE ARG B 263 " pdb=" CZ ARG B 263 " ideal model delta sinusoidal sigma weight residual 180.00 135.99 44.01 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 6763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1462 0.060 - 0.120: 157 0.120 - 0.180: 12 0.180 - 0.240: 2 0.240 - 0.300: 4 Chirality restraints: 1637 Sorted by residual: chirality pdb=" C2' ATP A 401 " pdb=" C1' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" O2' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C2' ATP B 402 " pdb=" C1' ATP B 402 " pdb=" C3' ATP B 402 " pdb=" O2' ATP B 402 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP A 401 " pdb=" C2' ATP A 401 " pdb=" C4' ATP A 401 " pdb=" O3' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1634 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 230 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO F 231 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 231 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 231 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 122 " -0.132 9.50e-02 1.11e+02 5.95e-02 2.76e+00 pdb=" NE ARG C 122 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 122 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 122 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 122 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 197 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C ALA C 197 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA C 197 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN C 198 " 0.009 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 49 2.40 - 3.02: 7528 3.02 - 3.65: 17133 3.65 - 4.27: 25078 4.27 - 4.90: 41589 Nonbonded interactions: 91377 Sorted by model distance: nonbonded pdb=" O2B ATP A 401 " pdb="MG MG A 402 " model vdw 1.772 2.170 nonbonded pdb=" O2G ATP A 401 " pdb="MG MG A 402 " model vdw 1.780 2.170 nonbonded pdb=" O2G ATP B 402 " pdb="MG MG B 403 " model vdw 1.856 2.170 nonbonded pdb=" O2B ATP B 402 " pdb="MG MG B 403 " model vdw 1.858 2.170 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 403 " model vdw 1.962 2.170 ... (remaining 91372 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 190 or resid 210 through 339)) selection = (chain 'B' and resid 16 through 339) } ncs_group { reference = chain 'C' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 10.030 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 33.240 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10998 Z= 0.235 Angle : 0.533 6.983 14882 Z= 0.283 Chirality : 0.040 0.300 1637 Planarity : 0.004 0.060 1922 Dihedral : 14.647 88.037 4212 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.89 (0.24), residues: 1324 helix: 1.87 (0.18), residues: 861 sheet: 0.70 (0.63), residues: 67 loop : 0.08 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 96 HIS 0.005 0.001 HIS B 71 PHE 0.018 0.001 PHE B 173 TYR 0.024 0.001 TYR G1098 ARG 0.014 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8479 (tppt) REVERT: A 91 TYR cc_start: 0.8539 (m-80) cc_final: 0.7911 (m-80) REVERT: A 118 MET cc_start: 0.1844 (tpp) cc_final: 0.0711 (tmm) REVERT: A 130 MET cc_start: 0.6357 (mmp) cc_final: 0.5529 (mtp) REVERT: A 140 MET cc_start: 0.6098 (mtm) cc_final: 0.5893 (mtm) REVERT: A 258 GLU cc_start: 0.7352 (tp30) cc_final: 0.7030 (tp30) REVERT: A 323 ASP cc_start: 0.7994 (p0) cc_final: 0.7427 (t0) REVERT: B 140 MET cc_start: 0.6634 (mmp) cc_final: 0.6322 (mmm) REVERT: B 146 MET cc_start: 0.8080 (mtp) cc_final: 0.7871 (mtm) REVERT: C 91 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 102 ASP cc_start: 0.7543 (t70) cc_final: 0.7095 (t0) REVERT: C 156 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7596 (mt-10) REVERT: C 158 ASN cc_start: 0.7803 (t0) cc_final: 0.6970 (t0) REVERT: C 208 ASN cc_start: 0.8714 (t0) cc_final: 0.8273 (t0) REVERT: C 209 LYS cc_start: 0.8882 (ptpt) cc_final: 0.8203 (ttpp) REVERT: C 226 ILE cc_start: 0.7488 (mm) cc_final: 0.7169 (mt) REVERT: C 228 ASP cc_start: 0.7013 (t0) cc_final: 0.6802 (t0) REVERT: D 1043 LEU cc_start: 0.8196 (mm) cc_final: 0.7879 (mm) REVERT: F 208 ASN cc_start: 0.8184 (t0) cc_final: 0.7886 (t0) REVERT: G 1026 ILE cc_start: 0.7820 (mt) cc_final: 0.7008 (mt) REVERT: G 1030 ARG cc_start: 0.7784 (mpp80) cc_final: 0.7498 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2435 time to fit residues: 67.1605 Evaluate side-chains 141 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 326 ASN ** G1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10998 Z= 0.251 Angle : 0.569 6.791 14882 Z= 0.295 Chirality : 0.041 0.146 1637 Planarity : 0.005 0.051 1922 Dihedral : 8.327 87.863 1513 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.43 % Allowed : 5.82 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.24), residues: 1324 helix: 1.91 (0.18), residues: 861 sheet: 0.65 (0.63), residues: 67 loop : 0.28 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 132 HIS 0.004 0.001 HIS C 165 PHE 0.015 0.002 PHE C 255 TYR 0.014 0.002 TYR G1042 ARG 0.010 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1862 (tpp) cc_final: 0.0784 (tmm) REVERT: A 152 MET cc_start: 0.7614 (tmm) cc_final: 0.7327 (tmm) REVERT: A 323 ASP cc_start: 0.8046 (p0) cc_final: 0.7413 (t0) REVERT: B 19 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7609 (mp0) REVERT: C 91 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7968 (mm-30) REVERT: C 121 GLU cc_start: 0.8189 (tp30) cc_final: 0.7877 (tp30) REVERT: C 156 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7550 (mt-10) REVERT: C 158 ASN cc_start: 0.7790 (t0) cc_final: 0.7157 (t0) REVERT: C 208 ASN cc_start: 0.8952 (t0) cc_final: 0.8508 (t0) REVERT: C 209 LYS cc_start: 0.8906 (ptpt) cc_final: 0.8260 (ttpp) REVERT: C 226 ILE cc_start: 0.7631 (mm) cc_final: 0.7254 (mt) REVERT: D 1027 GLN cc_start: 0.8273 (mm110) cc_final: 0.7657 (tm-30) REVERT: D 1038 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6704 (mt) REVERT: D 1043 LEU cc_start: 0.8117 (mm) cc_final: 0.7504 (tt) REVERT: F 208 ASN cc_start: 0.8380 (t0) cc_final: 0.8082 (t0) REVERT: F 269 ASP cc_start: 0.7506 (t0) cc_final: 0.6946 (t0) REVERT: G 1030 ARG cc_start: 0.7952 (mpp80) cc_final: 0.7729 (ptm160) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.1959 time to fit residues: 47.3122 Evaluate side-chains 149 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 248 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.0060 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 172 ASN A 326 ASN B 54 GLN ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1029 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10998 Z= 0.259 Angle : 0.547 8.419 14882 Z= 0.282 Chirality : 0.041 0.340 1637 Planarity : 0.005 0.054 1922 Dihedral : 8.293 88.819 1513 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.45 % Allowed : 7.09 % Favored : 90.46 % 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: 1.93 (0.24), residues: 1324 helix: 1.85 (0.18), residues: 863 sheet: 0.61 (0.63), residues: 67 loop : 0.26 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 33 HIS 0.004 0.001 HIS C 165 PHE 0.012 0.002 PHE F 166 TYR 0.018 0.002 TYR C 275 ARG 0.006 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1773 (tpp) cc_final: 0.0688 (tmm) REVERT: A 152 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7233 (tmm) REVERT: A 172 ASN cc_start: 0.6563 (m110) cc_final: 0.5586 (t0) REVERT: A 323 ASP cc_start: 0.8061 (p0) cc_final: 0.7386 (t0) REVERT: B 19 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7643 (mp0) REVERT: B 268 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8142 (p0) REVERT: C 91 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7943 (mm-30) REVERT: C 121 GLU cc_start: 0.8308 (tp30) cc_final: 0.7919 (tp30) REVERT: C 156 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7589 (mt-10) REVERT: C 158 ASN cc_start: 0.7855 (t0) cc_final: 0.7177 (t0) REVERT: C 208 ASN cc_start: 0.8991 (t0) cc_final: 0.8617 (t0) REVERT: C 209 LYS cc_start: 0.8914 (ptpt) cc_final: 0.8240 (ttpp) REVERT: C 226 ILE cc_start: 0.7643 (mm) cc_final: 0.7261 (mt) REVERT: C 255 PHE cc_start: 0.8858 (t80) cc_final: 0.8417 (t80) REVERT: D 1038 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6670 (mt) REVERT: D 1043 LEU cc_start: 0.8139 (mm) cc_final: 0.7700 (tt) REVERT: F 208 ASN cc_start: 0.8349 (t0) cc_final: 0.8021 (t0) REVERT: F 269 ASP cc_start: 0.7708 (t0) cc_final: 0.7341 (t0) REVERT: G 1042 TYR cc_start: 0.7181 (t80) cc_final: 0.6811 (t80) outliers start: 29 outliers final: 20 residues processed: 170 average time/residue: 0.2086 time to fit residues: 54.2598 Evaluate side-chains 165 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain H residue 134 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 0.0770 chunk 114 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 326 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10998 Z= 0.190 Angle : 0.514 8.259 14882 Z= 0.266 Chirality : 0.039 0.148 1637 Planarity : 0.005 0.048 1922 Dihedral : 8.044 88.561 1513 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.86 % Allowed : 9.87 % Favored : 88.27 % 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: 1.90 (0.24), residues: 1324 helix: 1.88 (0.18), residues: 859 sheet: 0.54 (0.62), residues: 67 loop : 0.13 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 241 HIS 0.004 0.001 HIS H 106 PHE 0.014 0.001 PHE C 188 TYR 0.013 0.001 TYR A 250 ARG 0.004 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1763 (tpp) cc_final: 0.0650 (tmm) REVERT: A 126 MET cc_start: 0.6716 (ppp) cc_final: 0.6510 (ppp) REVERT: A 152 MET cc_start: 0.7670 (tmm) cc_final: 0.7182 (tmm) REVERT: A 268 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8146 (p0) REVERT: A 323 ASP cc_start: 0.8058 (p0) cc_final: 0.7338 (t0) REVERT: B 19 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7634 (mp0) REVERT: B 268 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8047 (p0) REVERT: C 91 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 156 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7554 (mt-10) REVERT: C 158 ASN cc_start: 0.7926 (t0) cc_final: 0.7232 (t0) REVERT: C 208 ASN cc_start: 0.8984 (t0) cc_final: 0.8630 (t0) REVERT: C 209 LYS cc_start: 0.8932 (ptpt) cc_final: 0.8220 (ttpp) REVERT: C 226 ILE cc_start: 0.7656 (mm) cc_final: 0.7252 (mt) REVERT: C 255 PHE cc_start: 0.8860 (t80) cc_final: 0.8421 (t80) REVERT: D 1043 LEU cc_start: 0.8074 (mm) cc_final: 0.7722 (tt) REVERT: F 208 ASN cc_start: 0.8301 (t0) cc_final: 0.7955 (t0) REVERT: F 269 ASP cc_start: 0.7617 (t0) cc_final: 0.6931 (t0) REVERT: F 271 MET cc_start: 0.8293 (mpp) cc_final: 0.7888 (mpp) outliers start: 22 outliers final: 17 residues processed: 163 average time/residue: 0.1903 time to fit residues: 46.9202 Evaluate side-chains 162 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain H residue 134 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 326 ASN B 68 ASN B 308 HIS ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10998 Z= 0.341 Angle : 0.576 7.581 14882 Z= 0.299 Chirality : 0.041 0.150 1637 Planarity : 0.005 0.052 1922 Dihedral : 8.239 89.766 1513 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.54 % Allowed : 9.37 % Favored : 87.09 % 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: 1.60 (0.23), residues: 1324 helix: 1.63 (0.18), residues: 865 sheet: 0.32 (0.61), residues: 65 loop : 0.06 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 241 HIS 0.007 0.002 HIS B 71 PHE 0.015 0.002 PHE C 188 TYR 0.015 0.002 TYR A 250 ARG 0.005 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 144 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1647 (tpp) cc_final: 0.0591 (tmm) REVERT: A 152 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7227 (tmm) REVERT: A 268 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8345 (p0) REVERT: A 323 ASP cc_start: 0.8058 (p0) cc_final: 0.7304 (t0) REVERT: B 19 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7659 (mp0) REVERT: B 71 HIS cc_start: 0.6924 (m-70) cc_final: 0.6412 (m-70) REVERT: B 234 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7914 (mt-10) REVERT: B 268 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8221 (p0) REVERT: C 91 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7932 (mm-30) REVERT: C 106 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7965 (tm-30) REVERT: C 158 ASN cc_start: 0.7933 (t0) cc_final: 0.7273 (t0) REVERT: C 208 ASN cc_start: 0.9022 (t0) cc_final: 0.8813 (t0) REVERT: C 226 ILE cc_start: 0.7637 (mm) cc_final: 0.7239 (mt) REVERT: D 1038 LEU cc_start: 0.6915 (mt) cc_final: 0.6662 (mt) REVERT: D 1043 LEU cc_start: 0.8144 (mm) cc_final: 0.7779 (tt) REVERT: F 208 ASN cc_start: 0.8332 (t0) cc_final: 0.7952 (t0) outliers start: 42 outliers final: 27 residues processed: 174 average time/residue: 0.1899 time to fit residues: 50.3067 Evaluate side-chains 168 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain G residue 1014 VAL Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Chi-restraints excluded: chain H residue 134 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 127 optimal weight: 0.0670 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10998 Z= 0.186 Angle : 0.522 6.993 14882 Z= 0.269 Chirality : 0.040 0.144 1637 Planarity : 0.005 0.054 1922 Dihedral : 7.912 84.074 1513 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.53 % Allowed : 10.89 % Favored : 86.58 % 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: 1.72 (0.24), residues: 1324 helix: 1.78 (0.18), residues: 857 sheet: 0.12 (0.61), residues: 67 loop : 0.04 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP F 241 HIS 0.003 0.001 HIS B 71 PHE 0.014 0.001 PHE C 188 TYR 0.013 0.001 TYR A 250 ARG 0.003 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1586 (tpp) cc_final: 0.0500 (tmm) REVERT: A 152 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7070 (tmm) REVERT: A 268 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8209 (p0) REVERT: A 323 ASP cc_start: 0.8041 (p0) cc_final: 0.7263 (t0) REVERT: B 19 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7612 (mp0) REVERT: B 71 HIS cc_start: 0.6959 (m-70) cc_final: 0.6443 (m-70) REVERT: B 268 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.8024 (p0) REVERT: C 91 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7928 (mm-30) REVERT: C 106 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7948 (tm-30) REVERT: C 158 ASN cc_start: 0.7975 (t0) cc_final: 0.7310 (t0) REVERT: C 226 ILE cc_start: 0.7625 (mm) cc_final: 0.7228 (mt) REVERT: D 1038 LEU cc_start: 0.6921 (mt) cc_final: 0.6671 (mt) REVERT: D 1043 LEU cc_start: 0.8069 (mm) cc_final: 0.7633 (tt) REVERT: F 164 TYR cc_start: 0.8574 (t80) cc_final: 0.8181 (t80) REVERT: F 208 ASN cc_start: 0.8311 (t0) cc_final: 0.7982 (t0) REVERT: F 241 TRP cc_start: 0.8274 (t60) cc_final: 0.8063 (t60) outliers start: 30 outliers final: 23 residues processed: 171 average time/residue: 0.1886 time to fit residues: 49.2416 Evaluate side-chains 166 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain H residue 134 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.0040 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN F 238 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10998 Z= 0.196 Angle : 0.515 7.505 14882 Z= 0.267 Chirality : 0.039 0.142 1637 Planarity : 0.005 0.060 1922 Dihedral : 7.741 79.765 1513 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.87 % Allowed : 11.48 % Favored : 85.65 % 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: 1.74 (0.24), residues: 1324 helix: 1.79 (0.18), residues: 859 sheet: 0.18 (0.62), residues: 67 loop : 0.04 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 241 HIS 0.003 0.001 HIS B 71 PHE 0.020 0.001 PHE C 283 TYR 0.012 0.001 TYR B 250 ARG 0.003 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1645 (tpp) cc_final: 0.0535 (tmm) REVERT: A 152 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7061 (tmm) REVERT: A 268 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.8194 (p0) REVERT: A 323 ASP cc_start: 0.8046 (p0) cc_final: 0.7265 (t0) REVERT: B 19 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7618 (mp0) REVERT: B 71 HIS cc_start: 0.7007 (m-70) cc_final: 0.6489 (m-70) REVERT: B 268 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.8036 (p0) REVERT: C 91 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7897 (mm-30) REVERT: C 106 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7936 (tm-30) REVERT: C 158 ASN cc_start: 0.7957 (t0) cc_final: 0.7277 (t0) REVERT: C 226 ILE cc_start: 0.7629 (mm) cc_final: 0.7226 (mt) REVERT: D 1038 LEU cc_start: 0.6951 (mt) cc_final: 0.6693 (mt) REVERT: D 1043 LEU cc_start: 0.8069 (mm) cc_final: 0.7665 (tt) REVERT: F 164 TYR cc_start: 0.8597 (t80) cc_final: 0.8211 (t80) REVERT: F 208 ASN cc_start: 0.8274 (t0) cc_final: 0.7940 (t0) outliers start: 34 outliers final: 27 residues processed: 171 average time/residue: 0.1880 time to fit residues: 48.9248 Evaluate side-chains 169 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 1014 VAL Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 0.0370 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN C 208 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10998 Z= 0.225 Angle : 0.543 12.711 14882 Z= 0.280 Chirality : 0.040 0.141 1637 Planarity : 0.005 0.056 1922 Dihedral : 7.754 79.227 1513 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.04 % Allowed : 11.90 % Favored : 85.06 % 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: 1.68 (0.24), residues: 1324 helix: 1.73 (0.18), residues: 858 sheet: 0.16 (0.62), residues: 67 loop : 0.05 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP F 241 HIS 0.003 0.001 HIS F 165 PHE 0.021 0.001 PHE F 232 TYR 0.013 0.001 TYR A 250 ARG 0.004 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1620 (tpp) cc_final: 0.0525 (tmm) REVERT: A 127 GLN cc_start: 0.6048 (pt0) cc_final: 0.5411 (mm-40) REVERT: A 152 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7024 (tmm) REVERT: A 268 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8217 (p0) REVERT: A 323 ASP cc_start: 0.8042 (p0) cc_final: 0.7263 (t0) REVERT: B 19 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7618 (mp0) REVERT: B 71 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6541 (m-70) REVERT: B 268 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.8057 (p0) REVERT: C 91 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7879 (mm-30) REVERT: C 106 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7936 (tm-30) REVERT: C 121 GLU cc_start: 0.8264 (tp30) cc_final: 0.8001 (tp30) REVERT: C 158 ASN cc_start: 0.7965 (t0) cc_final: 0.7282 (t0) REVERT: C 208 ASN cc_start: 0.9075 (t0) cc_final: 0.8869 (t0) REVERT: C 226 ILE cc_start: 0.7642 (mm) cc_final: 0.7255 (mt) REVERT: D 1038 LEU cc_start: 0.6967 (mt) cc_final: 0.6717 (mt) REVERT: D 1043 LEU cc_start: 0.8058 (mm) cc_final: 0.7646 (tt) REVERT: F 208 ASN cc_start: 0.8270 (t0) cc_final: 0.7936 (t0) REVERT: F 241 TRP cc_start: 0.8359 (t60) cc_final: 0.8121 (t-100) outliers start: 36 outliers final: 29 residues processed: 168 average time/residue: 0.1868 time to fit residues: 48.2485 Evaluate side-chains 174 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 1014 VAL Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Chi-restraints excluded: chain H residue 134 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0980 chunk 121 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10998 Z= 0.199 Angle : 0.524 7.376 14882 Z= 0.272 Chirality : 0.039 0.141 1637 Planarity : 0.005 0.063 1922 Dihedral : 7.642 76.706 1513 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.87 % Allowed : 11.81 % Favored : 85.32 % 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 (0.24), residues: 1324 helix: 1.76 (0.18), residues: 861 sheet: 0.19 (0.62), residues: 67 loop : 0.07 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP F 241 HIS 0.003 0.001 HIS F 165 PHE 0.014 0.001 PHE F 232 TYR 0.013 0.001 TYR B 250 ARG 0.003 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1540 (tpp) cc_final: 0.0496 (tmm) REVERT: A 127 GLN cc_start: 0.6097 (pt0) cc_final: 0.5435 (mm-40) REVERT: A 152 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7032 (tmm) REVERT: A 268 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8183 (p0) REVERT: A 323 ASP cc_start: 0.8041 (p0) cc_final: 0.7251 (t0) REVERT: B 19 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7615 (mp0) REVERT: B 71 HIS cc_start: 0.7007 (m-70) cc_final: 0.6515 (m-70) REVERT: B 268 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.8068 (p0) REVERT: C 91 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7852 (mm-30) REVERT: C 106 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7932 (tm-30) REVERT: C 121 GLU cc_start: 0.8287 (tp30) cc_final: 0.8019 (tp30) REVERT: C 158 ASN cc_start: 0.7984 (t0) cc_final: 0.7308 (t0) REVERT: C 226 ILE cc_start: 0.7654 (mm) cc_final: 0.7315 (mt) REVERT: D 1043 LEU cc_start: 0.8054 (mm) cc_final: 0.7651 (tt) REVERT: F 208 ASN cc_start: 0.8274 (t0) cc_final: 0.7957 (t0) REVERT: F 241 TRP cc_start: 0.8347 (t60) cc_final: 0.8124 (t-100) REVERT: F 272 TYR cc_start: 0.8371 (m-10) cc_final: 0.8093 (m-10) REVERT: F 273 ASN cc_start: 0.8759 (m-40) cc_final: 0.7939 (t0) REVERT: G 1042 TYR cc_start: 0.7401 (t80) cc_final: 0.6659 (t80) outliers start: 34 outliers final: 30 residues processed: 172 average time/residue: 0.1955 time to fit residues: 51.1371 Evaluate side-chains 173 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 1014 VAL Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN B 331 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10998 Z= 0.196 Angle : 0.543 11.039 14882 Z= 0.279 Chirality : 0.040 0.143 1637 Planarity : 0.005 0.084 1922 Dihedral : 7.578 74.396 1513 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.95 % Allowed : 12.41 % Favored : 84.64 % 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 (0.24), residues: 1324 helix: 1.71 (0.18), residues: 861 sheet: 0.27 (0.63), residues: 67 loop : 0.09 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP F 241 HIS 0.003 0.001 HIS B 71 PHE 0.014 0.001 PHE C 255 TYR 0.013 0.001 TYR F 272 ARG 0.003 0.000 ARG C 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1607 (tpp) cc_final: 0.0559 (tmm) REVERT: A 127 GLN cc_start: 0.6146 (pt0) cc_final: 0.5468 (mm-40) REVERT: A 152 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7109 (tmm) REVERT: A 268 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8211 (p0) REVERT: A 323 ASP cc_start: 0.8040 (p0) cc_final: 0.7236 (t0) REVERT: B 19 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7613 (mp0) REVERT: B 71 HIS cc_start: 0.7020 (m-70) cc_final: 0.6526 (m-70) REVERT: C 91 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7852 (mm-30) REVERT: C 106 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7930 (tm-30) REVERT: C 121 GLU cc_start: 0.8291 (tp30) cc_final: 0.8018 (tp30) REVERT: C 158 ASN cc_start: 0.7993 (t0) cc_final: 0.7326 (t0) REVERT: C 226 ILE cc_start: 0.7699 (mm) cc_final: 0.7319 (mt) REVERT: D 1043 LEU cc_start: 0.8063 (mm) cc_final: 0.7656 (tt) REVERT: F 208 ASN cc_start: 0.8261 (t0) cc_final: 0.7947 (t0) REVERT: F 272 TYR cc_start: 0.8409 (m-10) cc_final: 0.8087 (m-10) REVERT: F 273 ASN cc_start: 0.8744 (m-40) cc_final: 0.7933 (t0) REVERT: G 1042 TYR cc_start: 0.7369 (t80) cc_final: 0.6824 (t80) outliers start: 35 outliers final: 30 residues processed: 167 average time/residue: 0.1892 time to fit residues: 48.2615 Evaluate side-chains 172 residues out of total 1186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain D residue 1044 SER Chi-restraints excluded: chain F residue 184 THR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain G residue 1014 VAL Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 0.0030 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.139140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104284 restraints weight = 20279.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102304 restraints weight = 13482.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102896 restraints weight = 11588.871| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10998 Z= 0.209 Angle : 0.551 12.191 14882 Z= 0.282 Chirality : 0.040 0.267 1637 Planarity : 0.005 0.078 1922 Dihedral : 7.591 73.837 1513 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.95 % Allowed : 12.41 % Favored : 84.64 % 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: 1.65 (0.24), residues: 1324 helix: 1.70 (0.18), residues: 859 sheet: 0.29 (0.63), residues: 67 loop : 0.03 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP F 241 HIS 0.003 0.001 HIS F 165 PHE 0.020 0.001 PHE F 232 TYR 0.013 0.001 TYR B 250 ARG 0.003 0.000 ARG C 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2220.19 seconds wall clock time: 41 minutes 32.03 seconds (2492.03 seconds total)