Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 07:48:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d81_27242/04_2023/8d81_27242_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d81_27242/04_2023/8d81_27242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d81_27242/04_2023/8d81_27242.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d81_27242/04_2023/8d81_27242.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d81_27242/04_2023/8d81_27242_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d81_27242/04_2023/8d81_27242_updated.pdb" } resolution = 3.9 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= 0.042 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 56 5.16 5 C 5883 2.51 5 N 1563 2.21 5 O 1745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 47": "OE1" <-> "OE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A ASP 855": "OD1" <-> "OD2" Residue "A PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9248 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 817, 6290 Classifications: {'peptide': 817} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 790} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2958 Unusual residues: {' ZN': 1, 'Y70': 1} Classifications: {'peptide': 381, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 20, 'TRANS': 360, None: 2} Not linked: pdbres="THR B 425 " pdbres=" ZN B 501 " Not linked: pdbres=" ZN B 501 " pdbres="Y70 B 502 " Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8449 SG CYS B 323 14.794 80.857 40.508 1.00 0.00 S ATOM 8465 SG CYS B 326 11.359 81.448 42.109 1.00 0.00 S ATOM 8965 SG CYS B 391 12.206 83.079 38.765 1.00 0.00 S ATOM 8984 SG CYS B 394 13.753 84.339 41.887 1.00 0.00 S Time building chain proxies: 5.37, per 1000 atoms: 0.58 Number of scatterers: 9248 At special positions: 0 Unit cell: (98.28, 114.66, 99.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 56 16.00 O 1745 8.00 N 1563 7.00 C 5883 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=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 394 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 391 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 326 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 323 " Number of angles added : 6 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 19 sheets defined 13.0% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 986 through 989 No H-bonds generated for 'chain 'A' and resid 986 through 989' Processing helix chain 'A' and resid 1045 through 1060 removed outlier: 3.736A pdb=" N ASN A1049 " --> pdb=" O GLU A1045 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A1059 " --> pdb=" O GLN A1055 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS A1060 " --> pdb=" O ASN A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1067 No H-bonds generated for 'chain 'A' and resid 1065 through 1067' Processing helix chain 'A' and resid 1070 through 1074 Processing helix chain 'A' and resid 1091 through 1099 removed outlier: 3.792A pdb=" N PHE A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP A1099 " --> pdb=" O GLU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1108 removed outlier: 3.743A pdb=" N GLN A1106 " --> pdb=" O ARG A1102 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU A1107 " --> pdb=" O PRO A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 4.281A pdb=" N ILE A1139 " --> pdb=" O GLU A1135 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 104 through 114 Processing helix chain 'B' and resid 221 through 231 removed outlier: 3.701A pdb=" N GLN B 225 " --> pdb=" O TYR B 221 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 removed outlier: 4.219A pdb=" N ASN B 236 " --> pdb=" O HIS B 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.687A pdb=" N TYR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 292 through 300 Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing sheet with id= A, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 7.005A pdb=" N ASN A 4 " --> pdb=" O ILE A1089 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE A1037 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A1038 " --> pdb=" O PHE A1030 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A1006 " --> pdb=" O GLY A1031 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 18 through 21 removed outlier: 3.633A pdb=" N GLY A 21 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 30 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A 42 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 53 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 43 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 61 through 67 removed outlier: 6.692A pdb=" N LEU A 80 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A 64 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE A 78 " --> pdb=" O MET A 64 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A 66 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU A 76 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR A 81 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 86 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 104 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU A 90 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N THR A 102 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS A 92 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ILE A 100 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.870A pdb=" N ILE A 121 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 187 through 193 removed outlier: 3.516A pdb=" N HIS A 189 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 168 " --> pdb=" O CYS A 179 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP A 166 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN A 183 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 164 " --> pdb=" O GLN A 183 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.524A pdb=" N MET A 218 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.589A pdb=" N ILE A 248 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 258 through 263 removed outlier: 6.875A pdb=" N GLY A 274 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N HIS A 261 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU A 272 " --> pdb=" O HIS A 261 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG A 263 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ARG A 270 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP A 275 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY A 306 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET A 282 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU A 304 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU A 284 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL A 302 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 362 through 365 removed outlier: 3.641A pdb=" N ILE A 390 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 388 " --> pdb=" O THR A 377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.578A pdb=" N CYS A 732 " --> pdb=" O GLN A 727 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS A 803 " --> pdb=" O ILE A 793 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP A 795 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 801 " --> pdb=" O ASP A 795 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 811 through 819 removed outlier: 6.647A pdb=" N GLY A 832 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU A 816 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 830 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N SER A 818 " --> pdb=" O TYR A 828 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR A 828 " --> pdb=" O SER A 818 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 873 through 876 removed outlier: 4.012A pdb=" N CYS A 903 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU A 892 " --> pdb=" O THR A 901 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR A 901 " --> pdb=" O GLU A 892 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 914 through 917 removed outlier: 3.575A pdb=" N LYS A 915 " --> pdb=" O LEU A 922 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 957 through 959 removed outlier: 3.501A pdb=" N ASN A 973 " --> pdb=" O GLU A 969 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLN A 978 " --> pdb=" O GLU A 994 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLU A 994 " --> pdb=" O GLN A 978 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 331 through 336 removed outlier: 3.546A pdb=" N SER A 331 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 333 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 351 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 335 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 349 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 79 through 82 removed outlier: 3.645A pdb=" N ILE B 81 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 180 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLN B 134 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN B 134 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA B 124 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLY B 136 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 122 " --> pdb=" O GLY B 136 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THR B 138 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE B 120 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.971A pdb=" N VAL B 157 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 143 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 160 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ILE B 141 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 368 through 370 Processing sheet with id= S, first strand: chain 'B' and resid 385 through 388 removed outlier: 4.475A pdb=" N ALA B 385 " --> pdb=" O THR B 403 " (cutoff:3.500A) 210 hydrogen bonds defined for protein. 591 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: 2.96 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1559 1.31 - 1.44: 2435 1.44 - 1.56: 5357 1.56 - 1.69: 0 1.69 - 1.82: 82 Bond restraints: 9433 Sorted by residual: bond pdb=" C15 Y70 B 502 " pdb=" N16 Y70 B 502 " ideal model delta sigma weight residual 1.372 1.483 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C6 Y70 B 502 " pdb=" N10 Y70 B 502 " ideal model delta sigma weight residual 1.343 1.453 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C17 Y70 B 502 " pdb=" N16 Y70 B 502 " ideal model delta sigma weight residual 1.383 1.489 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" N PRO A 825 " pdb=" CA PRO A 825 " ideal model delta sigma weight residual 1.469 1.530 -0.061 1.25e-02 6.40e+03 2.39e+01 bond pdb=" C5 Y70 B 502 " pdb=" C9 Y70 B 502 " ideal model delta sigma weight residual 1.459 1.542 -0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 9428 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.54: 236 106.54 - 113.46: 5196 113.46 - 120.38: 3306 120.38 - 127.30: 3990 127.30 - 134.21: 88 Bond angle restraints: 12816 Sorted by residual: angle pdb=" N PRO B 98 " pdb=" CA PRO B 98 " pdb=" CB PRO B 98 " ideal model delta sigma weight residual 103.25 111.06 -7.81 1.05e+00 9.07e-01 5.53e+01 angle pdb=" C ASP A 824 " pdb=" N PRO A 825 " pdb=" CA PRO A 825 " ideal model delta sigma weight residual 120.04 128.00 -7.96 1.08e+00 8.57e-01 5.43e+01 angle pdb=" C TRP A1073 " pdb=" N ARG A1074 " pdb=" CA ARG A1074 " ideal model delta sigma weight residual 122.29 114.11 8.18 1.56e+00 4.11e-01 2.75e+01 angle pdb=" C THR A1125 " pdb=" CA THR A1125 " pdb=" CB THR A1125 " ideal model delta sigma weight residual 115.79 110.12 5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" N ASP A1116 " pdb=" CA ASP A1116 " pdb=" C ASP A1116 " ideal model delta sigma weight residual 112.93 107.41 5.52 1.33e+00 5.65e-01 1.72e+01 ... (remaining 12811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.92: 5289 23.92 - 47.84: 312 47.84 - 71.77: 22 71.77 - 95.69: 15 95.69 - 119.61: 1 Dihedral angle restraints: 5639 sinusoidal: 2160 harmonic: 3479 Sorted by residual: dihedral pdb=" CA GLY B 69 " pdb=" C GLY B 69 " pdb=" N ARG B 70 " pdb=" CA ARG B 70 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA VAL B 80 " pdb=" C VAL B 80 " pdb=" N ILE B 81 " pdb=" CA ILE B 81 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA ILE B 152 " pdb=" C ILE B 152 " pdb=" N GLU B 153 " pdb=" CA GLU B 153 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1249 0.064 - 0.127: 208 0.127 - 0.191: 9 0.191 - 0.254: 6 0.254 - 0.318: 3 Chirality restraints: 1475 Sorted by residual: chirality pdb=" CA VAL B 182 " pdb=" N VAL B 182 " pdb=" C VAL B 182 " pdb=" CB VAL B 182 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA CYS A 725 " pdb=" N CYS A 725 " pdb=" C CYS A 725 " pdb=" CB CYS A 725 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL B 182 " pdb=" CA VAL B 182 " pdb=" CG1 VAL B 182 " pdb=" CG2 VAL B 182 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1472 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 724 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C ILE A 724 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE A 724 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS A 725 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 180 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ALA B 180 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA B 180 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS B 181 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A1022 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A1023 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1023 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1023 " 0.027 5.00e-02 4.00e+02 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2123 2.79 - 3.32: 8340 3.32 - 3.85: 14296 3.85 - 4.37: 16146 4.37 - 4.90: 28807 Nonbonded interactions: 69712 Sorted by model distance: nonbonded pdb=" ND2 ASN B 351 " pdb=" O TYR B 355 " model vdw 2.266 2.520 nonbonded pdb=" OE1 GLU A 213 " pdb=" OG SER A 236 " model vdw 2.267 2.440 nonbonded pdb=" N ASN A 826 " pdb=" OD1 ASN A 826 " model vdw 2.277 2.520 nonbonded pdb=" ND2 ASN A 36 " pdb=" OD1 ASN A1034 " model vdw 2.309 2.520 nonbonded pdb=" OE2 GLU A 72 " pdb=" NH2 ARG A 103 " model vdw 2.329 2.520 ... (remaining 69707 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 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: 1.090 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: 3.320 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.340 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 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 0.111 9433 Z= 0.270 Angle : 0.654 10.247 12816 Z= 0.377 Chirality : 0.049 0.318 1475 Planarity : 0.004 0.048 1648 Dihedral : 14.706 119.609 3395 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.06 % Favored : 92.35 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.23 (0.24), residues: 1190 helix: -0.36 (0.42), residues: 164 sheet: -1.30 (0.29), residues: 352 loop : -1.89 (0.22), residues: 674 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 1.034 Fit side-chains outliers start: 13 outliers final: 2 residues processed: 168 average time/residue: 0.2028 time to fit residues: 49.2036 Evaluate side-chains 122 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0948 time to fit residues: 1.9240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 50 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 chunk 108 optimal weight: 2.9990 overall best weight: 1.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9433 Z= 0.260 Angle : 0.571 5.829 12816 Z= 0.294 Chirality : 0.044 0.144 1475 Planarity : 0.004 0.044 1648 Dihedral : 5.280 100.154 1288 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.89 % Favored : 92.69 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.06 (0.24), residues: 1190 helix: -0.18 (0.43), residues: 163 sheet: -1.24 (0.26), residues: 382 loop : -1.76 (0.23), residues: 645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.131 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 128 average time/residue: 0.1954 time to fit residues: 36.7392 Evaluate side-chains 121 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0870 time to fit residues: 2.7005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN B 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9433 Z= 0.212 Angle : 0.530 8.447 12816 Z= 0.272 Chirality : 0.043 0.148 1475 Planarity : 0.003 0.043 1648 Dihedral : 5.162 97.895 1288 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.30 % Favored : 93.28 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.99 (0.24), residues: 1190 helix: 0.06 (0.44), residues: 158 sheet: -1.30 (0.26), residues: 376 loop : -1.67 (0.23), residues: 656 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.150 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 135 average time/residue: 0.2043 time to fit residues: 40.4855 Evaluate side-chains 127 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0932 time to fit residues: 3.3461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 796 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 9433 Z= 0.387 Angle : 0.615 7.228 12816 Z= 0.318 Chirality : 0.045 0.138 1475 Planarity : 0.004 0.047 1648 Dihedral : 5.448 98.137 1288 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.24 % Favored : 91.34 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.07 (0.24), residues: 1190 helix: -0.03 (0.44), residues: 158 sheet: -1.35 (0.27), residues: 363 loop : -1.73 (0.23), residues: 669 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.052 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 131 average time/residue: 0.1886 time to fit residues: 36.8100 Evaluate side-chains 124 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0925 time to fit residues: 2.4388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 9433 Z= 0.235 Angle : 0.551 9.951 12816 Z= 0.280 Chirality : 0.043 0.138 1475 Planarity : 0.003 0.048 1648 Dihedral : 5.207 96.861 1288 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.89 % Favored : 92.77 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.97 (0.24), residues: 1190 helix: -0.00 (0.43), residues: 158 sheet: -1.29 (0.26), residues: 375 loop : -1.63 (0.23), residues: 657 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.116 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 140 average time/residue: 0.1908 time to fit residues: 39.3969 Evaluate side-chains 131 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0884 time to fit residues: 2.8939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.7319 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 9433 Z= 0.309 Angle : 0.574 8.155 12816 Z= 0.293 Chirality : 0.044 0.137 1475 Planarity : 0.004 0.050 1648 Dihedral : 5.274 96.941 1288 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.24 % Favored : 91.43 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.02 (0.24), residues: 1190 helix: 0.03 (0.43), residues: 158 sheet: -1.37 (0.26), residues: 377 loop : -1.66 (0.23), residues: 655 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.188 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 131 average time/residue: 0.2133 time to fit residues: 40.5486 Evaluate side-chains 128 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0975 time to fit residues: 3.5308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 96 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.0270 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9433 Z= 0.176 Angle : 0.520 7.818 12816 Z= 0.264 Chirality : 0.043 0.137 1475 Planarity : 0.003 0.044 1648 Dihedral : 4.999 95.520 1288 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.30 % Favored : 93.36 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.87 (0.24), residues: 1190 helix: 0.22 (0.44), residues: 153 sheet: -1.24 (0.27), residues: 375 loop : -1.59 (0.23), residues: 662 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 1.156 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 126 average time/residue: 0.1989 time to fit residues: 37.3171 Evaluate side-chains 123 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1038 time to fit residues: 2.2298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 0.0170 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 HIS A1005 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 9433 Z= 0.163 Angle : 0.519 8.115 12816 Z= 0.262 Chirality : 0.043 0.137 1475 Planarity : 0.003 0.044 1648 Dihedral : 4.866 94.850 1288 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.72 % Favored : 92.94 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.77 (0.24), residues: 1190 helix: 0.21 (0.44), residues: 155 sheet: -1.14 (0.27), residues: 374 loop : -1.53 (0.23), residues: 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 118 time to evaluate : 1.169 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 118 average time/residue: 0.2130 time to fit residues: 36.6974 Evaluate side-chains 117 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0905 time to fit residues: 2.0790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 30.0000 chunk 68 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 9433 Z= 0.398 Angle : 0.619 11.673 12816 Z= 0.317 Chirality : 0.045 0.140 1475 Planarity : 0.004 0.053 1648 Dihedral : 5.319 96.169 1288 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.99 % Favored : 90.67 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.00 (0.24), residues: 1190 helix: -0.06 (0.43), residues: 160 sheet: -1.31 (0.27), residues: 373 loop : -1.65 (0.23), residues: 657 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.115 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 117 average time/residue: 0.2021 time to fit residues: 34.5967 Evaluate side-chains 116 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1033 time to fit residues: 1.8313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 0.0070 chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9433 Z= 0.175 Angle : 0.543 11.544 12816 Z= 0.273 Chirality : 0.043 0.138 1475 Planarity : 0.003 0.046 1648 Dihedral : 4.998 94.455 1288 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.64 % Favored : 93.03 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.86 (0.24), residues: 1190 helix: 0.15 (0.43), residues: 155 sheet: -1.26 (0.27), residues: 365 loop : -1.55 (0.23), residues: 670 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 1.181 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 119 average time/residue: 0.2228 time to fit residues: 38.5585 Evaluate side-chains 115 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1096 time to fit residues: 1.9157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN B 351 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.190251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.151431 restraints weight = 10702.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148008 restraints weight = 19974.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.148255 restraints weight = 16584.943| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9433 Z= 0.232 Angle : 0.553 11.242 12816 Z= 0.279 Chirality : 0.043 0.134 1475 Planarity : 0.003 0.046 1648 Dihedral : 5.036 94.575 1288 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.82 % Favored : 91.85 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.86 (0.24), residues: 1190 helix: 0.20 (0.44), residues: 154 sheet: -1.20 (0.27), residues: 369 loop : -1.61 (0.23), residues: 667 =============================================================================== Job complete usr+sys time: 1764.40 seconds wall clock time: 33 minutes 4.80 seconds (1984.80 seconds total)