Starting phenix.real_space_refine (version: dev) on Wed Feb 22 19:42:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/02_2023/7q2x_13783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/02_2023/7q2x_13783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/02_2023/7q2x_13783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/02_2023/7q2x_13783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/02_2023/7q2x_13783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q2x_13783/02_2023/7q2x_13783_updated.pdb" } resolution = 3.0 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= 0.007 sd= 0.059 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 Process input model Symmetric amino acids flipped Residue "A GLU 1113": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18240 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3413 Classifications: {'peptide': 431} Link IDs: {'PTRANS': 12, 'TRANS': 418} Chain breaks: 1 Chain: "B" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3102 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2279 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 283} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 7906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7906 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 966} Chain breaks: 10 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 756 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "G" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.29, per 1000 atoms: 0.56 Number of scatterers: 18240 At special positions: 0 Unit cell: (121.98, 147.66, 161.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 91 16.00 P 76 15.00 Mg 2 11.99 F 6 9.00 O 3633 8.00 N 3057 7.00 C 11373 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D1059 " - pdb=" SG CYS D1071 " distance=2.88 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: 7.69 Conformation dependent library (CDL) restraints added in 2.5 seconds 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 9 sheets defined 60.2% alpha, 6.7% beta 36 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain 'A' and resid 38 through 48 removed outlier: 3.929A pdb=" N LEU A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 124 through 134 removed outlier: 3.870A pdb=" N VAL A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.623A pdb=" N ALA A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 227 Proline residue: A 205 - end of helix removed outlier: 3.985A pdb=" N ARG A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 977 removed outlier: 4.074A pdb=" N LYS A 974 " --> pdb=" O GLN A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1047 removed outlier: 3.835A pdb=" N GLU A1027 " --> pdb=" O GLU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1065 No H-bonds generated for 'chain 'A' and resid 1063 through 1065' Processing helix chain 'A' and resid 1086 through 1103 Processing helix chain 'A' and resid 1120 through 1131 Processing helix chain 'A' and resid 1146 through 1149 No H-bonds generated for 'chain 'A' and resid 1146 through 1149' Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.925A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 209 Processing helix chain 'B' and resid 279 through 288 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 335 through 349 removed outlier: 4.302A pdb=" N LEU B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1247 through 1286 Processing helix chain 'B' and resid 1301 through 1304 No H-bonds generated for 'chain 'B' and resid 1301 through 1304' Processing helix chain 'B' and resid 1325 through 1342 Processing helix chain 'B' and resid 1359 through 1371 Processing helix chain 'B' and resid 1385 through 1389 Processing helix chain 'C' and resid 23 through 40 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 72 through 105 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 276 through 287 Processing helix chain 'C' and resid 300 through 310 removed outlier: 4.004A pdb=" N ARG C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 322 removed outlier: 4.425A pdb=" N ASP C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 668 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 705 through 710 removed outlier: 3.718A pdb=" N ASP C 710 " --> pdb=" O ASP C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 726 Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 27 through 40 removed outlier: 4.151A pdb=" N VAL D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 51 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 67 through 91 Processing helix chain 'D' and resid 105 through 127 Processing helix chain 'D' and resid 154 through 176 Processing helix chain 'D' and resid 186 through 205 removed outlier: 3.545A pdb=" N PHE D 196 " --> pdb=" O PHE D 192 " (cutoff:3.500A) Proline residue: D 199 - end of helix removed outlier: 3.805A pdb=" N GLU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 211 Processing helix chain 'D' and resid 213 through 229 Processing helix chain 'D' and resid 235 through 246 Processing helix chain 'D' and resid 251 through 263 Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 289 through 304 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 313 through 321 removed outlier: 4.006A pdb=" N THR D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 344 removed outlier: 3.577A pdb=" N ALA D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'D' and resid 353 through 367 removed outlier: 3.748A pdb=" N PHE D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 394 through 408 removed outlier: 3.970A pdb=" N LYS D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 427 Processing helix chain 'D' and resid 441 through 456 Processing helix chain 'D' and resid 518 through 551 Processing helix chain 'D' and resid 556 through 571 Processing helix chain 'D' and resid 577 through 587 removed outlier: 3.851A pdb=" N HIS D 586 " --> pdb=" O LYS D 582 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU D 587 " --> pdb=" O LYS D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 611 Processing helix chain 'D' and resid 621 through 637 Processing helix chain 'D' and resid 641 through 656 Processing helix chain 'D' and resid 663 through 675 removed outlier: 4.007A pdb=" N ALA D 675 " --> pdb=" O ILE D 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 713 removed outlier: 3.851A pdb=" N ALA D 713 " --> pdb=" O MET D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 719 Processing helix chain 'D' and resid 722 through 728 Processing helix chain 'D' and resid 732 through 736 removed outlier: 3.757A pdb=" N LYS D 736 " --> pdb=" O ALA D 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 732 through 736' Processing helix chain 'D' and resid 738 through 749 Processing helix chain 'D' and resid 765 through 780 removed outlier: 4.450A pdb=" N VAL D 770 " --> pdb=" O GLU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 802 removed outlier: 3.665A pdb=" N TYR D 789 " --> pdb=" O ASN D 786 " (cutoff:3.500A) Proline residue: D 790 - end of helix removed outlier: 4.544A pdb=" N GLU D 793 " --> pdb=" O PRO D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 806 through 820 Processing helix chain 'D' and resid 839 through 874 removed outlier: 3.554A pdb=" N GLU D 874 " --> pdb=" O LYS D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 922 Processing helix chain 'D' and resid 933 through 945 Proline residue: D 938 - end of helix Processing helix chain 'D' and resid 947 through 950 No H-bonds generated for 'chain 'D' and resid 947 through 950' Processing helix chain 'D' and resid 953 through 967 Processing helix chain 'D' and resid 971 through 986 Proline residue: D 979 - end of helix Processing helix chain 'D' and resid 991 through 1006 Processing helix chain 'D' and resid 1009 through 1012 No H-bonds generated for 'chain 'D' and resid 1009 through 1012' Processing helix chain 'D' and resid 1015 through 1023 Processing helix chain 'D' and resid 1028 through 1043 Processing helix chain 'D' and resid 1053 through 1061 removed outlier: 3.826A pdb=" N CYS D1059 " --> pdb=" O GLU D1055 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU D1060 " --> pdb=" O MET D1056 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP D1061 " --> pdb=" O ALA D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1065 through 1077 removed outlier: 4.285A pdb=" N MET D1070 " --> pdb=" O GLY D1066 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N CYS D1071 " --> pdb=" O ILE D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1099 removed outlier: 4.055A pdb=" N ALA D1084 " --> pdb=" O LYS D1081 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE D1085 " --> pdb=" O ASP D1082 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE D1090 " --> pdb=" O ASN D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1117 removed outlier: 3.853A pdb=" N LYS D1109 " --> pdb=" O GLU D1105 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE D1117 " --> pdb=" O PHE D1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 1123 through 1136 removed outlier: 3.814A pdb=" N ARG D1136 " --> pdb=" O VAL D1132 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1146 Processing helix chain 'D' and resid 1149 through 1153 Processing helix chain 'D' and resid 1159 through 1167 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.975A pdb=" N VAL A 82 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU A 6 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N THR A 80 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE A 8 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER A 78 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR A 115 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1165 through 1169 Processing sheet with id= C, first strand: chain 'A' and resid 1051 through 1057 Processing sheet with id= D, first strand: chain 'B' and resid 153 through 156 Processing sheet with id= E, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= F, first strand: chain 'B' and resid 1403 through 1410 removed outlier: 7.572A pdb=" N PHE B 180 " --> pdb=" O GLN B1393 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N VAL B1395 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 182 " --> pdb=" O VAL B1395 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N VAL B1397 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL B 184 " --> pdb=" O VAL B1397 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N LYS B1399 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE B1378 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL B 183 " --> pdb=" O PHE B1378 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B1380 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLY B 185 " --> pdb=" O VAL B1380 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= H, first strand: chain 'B' and resid 1290 through 1295 Processing sheet with id= I, first strand: chain 'C' and resid 730 through 733 934 hydrogen bonds defined for protein. 2649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 7.03 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3160 1.33 - 1.45: 4673 1.45 - 1.57: 10517 1.57 - 1.69: 148 1.69 - 1.81: 153 Bond restraints: 18651 Sorted by residual: bond pdb=" BE BEF A2002 " pdb=" F2 BEF A2002 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" BE BEF B2002 " pdb=" F2 BEF B2002 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" BE BEF B2002 " pdb=" F1 BEF B2002 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.59e+00 ... (remaining 18646 not shown) Histogram of bond angle deviations from ideal: 99.69 - 107.00: 794 107.00 - 114.31: 11230 114.31 - 121.61: 9472 121.61 - 128.92: 3797 128.92 - 136.23: 136 Bond angle restraints: 25429 Sorted by residual: angle pdb=" F2 BEF A2002 " pdb=" BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 119.96 107.49 12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" F2 BEF B2002 " pdb=" BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 119.96 107.58 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N PRO A 158 " pdb=" CA PRO A 158 " pdb=" CB PRO A 158 " ideal model delta sigma weight residual 103.30 99.74 3.56 1.12e+00 7.97e-01 1.01e+01 angle pdb=" F1 BEF A2002 " pdb=" BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 120.12 110.99 9.13 3.00e+00 1.11e-01 9.26e+00 angle pdb=" F1 BEF B2002 " pdb=" BE BEF B2002 " pdb=" F3 BEF B2002 " ideal model delta sigma weight residual 120.12 110.99 9.13 3.00e+00 1.11e-01 9.25e+00 ... (remaining 25424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 10734 35.96 - 71.93: 442 71.93 - 107.89: 19 107.89 - 143.85: 1 143.85 - 179.82: 3 Dihedral angle restraints: 11199 sinusoidal: 5052 harmonic: 6147 Sorted by residual: dihedral pdb=" C5' ADP B2001 " pdb=" O5' ADP B2001 " pdb=" PA ADP B2001 " pdb=" O2A ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 101.82 -161.81 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP B2001 " pdb=" O3A ADP B2001 " pdb=" PA ADP B2001 " pdb=" PB ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 85.28 -145.28 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP B2001 " pdb=" O3A ADP B2001 " pdb=" PB ADP B2001 " pdb=" PA ADP B2001 " ideal model delta sinusoidal sigma weight residual -60.00 69.77 -129.78 1 2.00e+01 2.50e-03 3.94e+01 ... (remaining 11196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2057 0.032 - 0.063: 625 0.063 - 0.095: 195 0.095 - 0.127: 80 0.127 - 0.159: 6 Chirality restraints: 2963 Sorted by residual: chirality pdb=" CA THR D 186 " pdb=" N THR D 186 " pdb=" C THR D 186 " pdb=" CB THR D 186 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE C 731 " pdb=" N ILE C 731 " pdb=" C ILE C 731 " pdb=" CB ILE C 731 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 2960 not shown) Planarity restraints: 2951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 305 " 0.065 5.00e-02 4.00e+02 9.79e-02 1.53e+01 pdb=" N PRO D 306 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO D 306 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 306 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 312 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.57e+00 pdb=" N PRO B 313 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B1345 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO B1346 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B1346 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1346 " -0.028 5.00e-02 4.00e+02 ... (remaining 2948 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 154 2.61 - 3.18: 15992 3.18 - 3.75: 29288 3.75 - 4.33: 38824 4.33 - 4.90: 63004 Nonbonded interactions: 147262 Sorted by model distance: nonbonded pdb=" F1 BEF B2002 " pdb="MG MG B2003 " model vdw 2.035 2.120 nonbonded pdb=" O2B ADP A2001 " pdb="MG MG A2003 " model vdw 2.063 2.170 nonbonded pdb=" OG SER B 192 " pdb="MG MG B2003 " model vdw 2.085 2.170 nonbonded pdb=" OE1 GLN B 302 " pdb="MG MG B2003 " model vdw 2.133 2.170 nonbonded pdb=" OG SER A 39 " pdb="MG MG A2003 " model vdw 2.143 2.170 ... (remaining 147257 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 Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 76 5.49 5 Mg 2 5.21 5 S 91 5.16 5 Be 2 3.05 5 C 11373 2.51 5 N 3057 2.21 5 O 3633 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 2.790 Check model and map are aligned: 0.280 Process input model: 53.010 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 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 : 0.002 0.084 18651 Z= 0.144 Angle : 0.546 12.467 25429 Z= 0.285 Chirality : 0.037 0.159 2963 Planarity : 0.004 0.098 2951 Dihedral : 17.413 179.817 7176 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.11 % 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: 2.57 (0.19), residues: 2054 helix: 2.71 (0.15), residues: 1260 sheet: 1.48 (0.39), residues: 180 loop : -0.44 (0.24), residues: 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 438 time to evaluate : 2.041 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 438 average time/residue: 1.3071 time to fit residues: 641.5943 Evaluate side-chains 386 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 2.061 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 106 GLN B 171 GLN B 266 ASN B 307 ASN C 307 ASN C 653 ASN C 725 ASN C 738 ASN D 70 GLN D 83 ASN D 163 GLN ** D 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 GLN ** D 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1062 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 18651 Z= 0.362 Angle : 0.699 10.390 25429 Z= 0.363 Chirality : 0.045 0.195 2963 Planarity : 0.005 0.063 2951 Dihedral : 18.541 176.261 2941 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 3.42 % 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 (0.18), residues: 2054 helix: 2.14 (0.14), residues: 1268 sheet: 1.09 (0.39), residues: 183 loop : -0.64 (0.23), residues: 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 524 time to evaluate : 2.246 Fit side-chains revert: symmetry clash outliers start: 65 outliers final: 18 residues processed: 548 average time/residue: 1.3208 time to fit residues: 808.2436 Evaluate side-chains 488 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 470 time to evaluate : 2.001 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 9 residues processed: 11 average time/residue: 0.4555 time to fit residues: 9.4324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 chunk 210 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 132 GLN A1138 GLN B1283 GLN C 314 GLN C 660 ASN C 743 ASN D 163 GLN D 232 GLN ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 ASN D 781 ASN D 852 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 18651 Z= 0.177 Angle : 0.544 9.478 25429 Z= 0.281 Chirality : 0.038 0.182 2963 Planarity : 0.003 0.053 2951 Dihedral : 18.237 176.170 2941 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 3.47 % 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: 2.20 (0.18), residues: 2054 helix: 2.44 (0.14), residues: 1253 sheet: 1.19 (0.39), residues: 181 loop : -0.55 (0.23), residues: 620 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 472 time to evaluate : 2.052 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 24 residues processed: 496 average time/residue: 1.3613 time to fit residues: 753.1727 Evaluate side-chains 477 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 453 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 13 residues processed: 13 average time/residue: 0.9586 time to fit residues: 17.5129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A1138 GLN A1153 ASN B 211 GLN B1283 GLN B1393 GLN C 660 ASN ** D 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 610 GLN D 634 ASN ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 781 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 18651 Z= 0.299 Angle : 0.615 12.589 25429 Z= 0.316 Chirality : 0.042 0.178 2963 Planarity : 0.004 0.054 2951 Dihedral : 18.321 172.504 2941 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 4.47 % 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: 1.96 (0.18), residues: 2054 helix: 2.26 (0.14), residues: 1254 sheet: 0.94 (0.39), residues: 181 loop : -0.62 (0.23), residues: 619 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 500 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 31 residues processed: 535 average time/residue: 1.4073 time to fit residues: 840.3658 Evaluate side-chains 504 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 473 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 14 average time/residue: 0.7518 time to fit residues: 15.5055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 chunk 52 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 132 GLN A 142 ASN A 221 GLN A1138 GLN B1393 GLN C 653 ASN C 738 ASN D 178 ASN D 237 GLN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 946 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18651 Z= 0.158 Angle : 0.554 11.996 25429 Z= 0.284 Chirality : 0.038 0.164 2963 Planarity : 0.003 0.055 2951 Dihedral : 18.215 174.991 2941 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 3.89 % 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: 2.16 (0.19), residues: 2054 helix: 2.43 (0.14), residues: 1256 sheet: 0.92 (0.39), residues: 181 loop : -0.55 (0.24), residues: 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 467 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 23 residues processed: 503 average time/residue: 1.3930 time to fit residues: 781.4467 Evaluate side-chains 474 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 451 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 14 residues processed: 10 average time/residue: 0.8269 time to fit residues: 12.6412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 132 GLN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 972 ASN A1022 ASN A1138 GLN A1153 ASN B 265 ASN B1393 GLN ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 738 ASN D 162 ASN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.057 18651 Z= 0.429 Angle : 0.701 13.638 25429 Z= 0.356 Chirality : 0.045 0.219 2963 Planarity : 0.004 0.057 2951 Dihedral : 18.417 171.166 2941 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 4.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.56 (0.18), residues: 2054 helix: 1.94 (0.14), residues: 1262 sheet: 0.58 (0.39), residues: 183 loop : -0.76 (0.24), residues: 609 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 508 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 43 residues processed: 548 average time/residue: 1.3752 time to fit residues: 842.4765 Evaluate side-chains 540 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 497 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 23 residues processed: 24 average time/residue: 0.6532 time to fit residues: 22.3327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 129 GLN A 132 GLN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 265 ASN B1385 ASN B1393 GLN C 725 ASN D 111 HIS D 229 ASN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 852 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 18651 Z= 0.228 Angle : 0.613 12.267 25429 Z= 0.311 Chirality : 0.040 0.189 2963 Planarity : 0.004 0.056 2951 Dihedral : 18.341 170.961 2941 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.18), residues: 2054 helix: 2.13 (0.14), residues: 1258 sheet: 0.56 (0.39), residues: 181 loop : -0.74 (0.24), residues: 615 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 490 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 37 residues processed: 523 average time/residue: 1.3945 time to fit residues: 814.0698 Evaluate side-chains 512 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 475 time to evaluate : 1.903 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 23 residues processed: 18 average time/residue: 0.4916 time to fit residues: 14.3183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 101 optimal weight: 0.0050 chunk 19 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 139 ASN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1153 ASN B 132 ASN B1385 ASN B1392 GLN B1393 GLN C 292 GLN ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 18651 Z= 0.245 Angle : 0.632 12.950 25429 Z= 0.319 Chirality : 0.040 0.216 2963 Planarity : 0.004 0.057 2951 Dihedral : 18.350 174.945 2941 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 3.31 % 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: 1.70 (0.18), residues: 2054 helix: 2.11 (0.14), residues: 1265 sheet: 0.43 (0.39), residues: 183 loop : -0.78 (0.24), residues: 606 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 490 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 38 residues processed: 518 average time/residue: 1.4341 time to fit residues: 830.0785 Evaluate side-chains 521 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 483 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 24 residues processed: 19 average time/residue: 0.7138 time to fit residues: 19.2751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 265 ASN B1272 ASN B1385 ASN B1392 GLN B1393 GLN C 725 ASN D 229 ASN ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 18651 Z= 0.248 Angle : 0.651 13.796 25429 Z= 0.326 Chirality : 0.040 0.169 2963 Planarity : 0.004 0.056 2951 Dihedral : 18.293 178.064 2941 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 3.05 % 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 (0.18), residues: 2054 helix: 2.12 (0.14), residues: 1257 sheet: 0.42 (0.39), residues: 183 loop : -0.78 (0.23), residues: 614 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 482 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 40 residues processed: 510 average time/residue: 1.4059 time to fit residues: 798.2575 Evaluate side-chains 518 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 478 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 26 residues processed: 17 average time/residue: 0.5795 time to fit residues: 15.3885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.0040 chunk 124 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 169 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B1272 ASN B1322 ASN ** B1385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1392 GLN B1393 GLN ** C 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN D 923 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 18651 Z= 0.229 Angle : 0.665 15.443 25429 Z= 0.334 Chirality : 0.040 0.186 2963 Planarity : 0.004 0.056 2951 Dihedral : 18.225 170.916 2941 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 2.52 % 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 (0.19), residues: 2054 helix: 2.15 (0.15), residues: 1261 sheet: 0.40 (0.39), residues: 181 loop : -0.77 (0.24), residues: 612 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4108 Ramachandran restraints generated. 2054 Oldfield, 0 Emsley, 2054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 480 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 507 average time/residue: 1.4211 time to fit residues: 802.3257 Evaluate side-chains 506 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 474 time to evaluate : 1.999 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 10 average time/residue: 0.4694 time to fit residues: 9.0363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.7980 chunk 52 optimal weight: 0.0270 chunk 156 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 125 GLN A1138 GLN A1153 ASN B 211 GLN B1272 ASN B1322 ASN B1392 GLN B1393 GLN C 725 ASN D 111 HIS ** D 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN D 923 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.153464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.125106 restraints weight = 24648.683| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.68 r_work: 0.3357 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 18651 Z= 0.192 Angle : 0.655 16.918 25429 Z= 0.327 Chirality : 0.040 0.183 2963 Planarity : 0.004 0.056 2951 Dihedral : 18.120 171.015 2941 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.19), residues: 2054 helix: 2.19 (0.15), residues: 1263 sheet: 0.38 (0.39), residues: 181 loop : -0.73 (0.24), residues: 610 =============================================================================== Job complete usr+sys time: 10339.60 seconds wall clock time: 181 minutes 51.98 seconds (10911.98 seconds total)