Starting phenix.real_space_refine on Fri Jun 6 18:50:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7svr_25452/06_2025/7svr_25452.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svr_25452/06_2025/7svr_25452.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/cci-nas-00/data/ceres_data/7svr_25452/06_2025/7svr_25452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svr_25452/06_2025/7svr_25452.map" model { file = "/net/cci-nas-00/data/ceres_data/7svr_25452/06_2025/7svr_25452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svr_25452/06_2025/7svr_25452.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 5046 2.51 5 N 1375 2.21 5 O 1390 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7841 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1134, 7713 Classifications: {'peptide': 1134} Incomplete info: {'truncation_to_alanine': 403} Link IDs: {'PTRANS': 28, 'TRANS': 1105} Chain breaks: 6 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1433 Unresolved non-hydrogen angles: 1826 Unresolved non-hydrogen dihedrals: 1188 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 7, 'TYR:plan': 13, 'ASN:plan1': 14, 'TRP:plan': 6, 'ASP:plan': 22, 'PHE:plan': 21, 'GLU:plan': 35, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 747 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 95 Classifications: {'peptide': 19} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'TRANS': 18} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'VX8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.71, per 1000 atoms: 0.73 Number of scatterers: 7841 At special positions: 0 Unit cell: (103, 118.45, 112.27, 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) S 28 16.00 F 2 9.00 O 1390 8.00 N 1375 7.00 C 5046 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.0 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 6 sheets defined 70.5% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.529A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 46 through 64 removed outlier: 4.187A pdb=" N GLU A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 77 through 103 removed outlier: 4.310A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.503A pdb=" N ALA A 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 108 " --> pdb=" O ILE A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 138 through 165 removed outlier: 3.593A pdb=" N LEU A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 176 through 187 removed outlier: 4.057A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASN A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 3.620A pdb=" N GLU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 202 through 220 removed outlier: 3.969A pdb=" N LEU A 206 " --> pdb=" O TRP A 202 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 267 removed outlier: 3.842A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 277 through 329 removed outlier: 4.837A pdb=" N THR A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 333 through 349 removed outlier: 3.547A pdb=" N PHE A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL A 345 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 376 removed outlier: 3.749A pdb=" N GLN A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 549 through 563 Processing helix chain 'A' and resid 573 through 577 removed outlier: 4.283A pdb=" N TYR A 577 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.850A pdb=" N ALA A 613 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 645 removed outlier: 3.937A pdb=" N MET A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 854 Processing helix chain 'A' and resid 856 through 886 removed outlier: 4.001A pdb=" N ILE A 860 " --> pdb=" O HIS A 856 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 861 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 916 Processing helix chain 'A' and resid 916 through 921 removed outlier: 4.126A pdb=" N VAL A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 928 removed outlier: 3.940A pdb=" N LEU A 926 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 927 " --> pdb=" O ALA A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 957 removed outlier: 3.698A pdb=" N VAL A 938 " --> pdb=" O GLY A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 965 Processing helix chain 'A' and resid 969 through 974 removed outlier: 4.081A pdb=" N LEU A 973 " --> pdb=" O ALA A 969 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 969 through 974' Processing helix chain 'A' and resid 978 through 1012 removed outlier: 5.055A pdb=" N LEU A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) Proline residue: A 988 - end of helix removed outlier: 3.608A pdb=" N LEU A1011 " --> pdb=" O VAL A1007 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN A1012 " --> pdb=" O VAL A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1061 removed outlier: 3.560A pdb=" N ALA A1018 " --> pdb=" O TYR A1014 " (cutoff:3.500A) Proline residue: A1021 - end of helix removed outlier: 4.027A pdb=" N ALA A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN A1035 " --> pdb=" O ALA A1031 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR A1036 " --> pdb=" O TYR A1032 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Proline residue: A1050 - end of helix Processing helix chain 'A' and resid 1061 through 1069 Processing helix chain 'A' and resid 1070 through 1120 removed outlier: 3.801A pdb=" N PHE A1074 " --> pdb=" O ARG A1070 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1139 removed outlier: 4.138A pdb=" N ASN A1138 " --> pdb=" O THR A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1168 removed outlier: 4.385A pdb=" N ARG A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER A1159 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A1160 " --> pdb=" O LEU A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1257 Processing helix chain 'A' and resid 1278 through 1283 Processing helix chain 'A' and resid 1299 through 1305 removed outlier: 3.529A pdb=" N ASP A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1321 Processing helix chain 'A' and resid 1324 through 1330 removed outlier: 3.933A pdb=" N GLN A1330 " --> pdb=" O SER A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1344 removed outlier: 3.995A pdb=" N CYS A1344 " --> pdb=" O VAL A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1362 removed outlier: 4.275A pdb=" N SER A1362 " --> pdb=" O ARG A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1376 removed outlier: 3.954A pdb=" N HIS A1375 " --> pdb=" O GLU A1371 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A1376 " --> pdb=" O PRO A1372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1371 through 1376' Processing helix chain 'A' and resid 1377 through 1391 removed outlier: 3.588A pdb=" N GLN A1390 " --> pdb=" O ARG A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 removed outlier: 4.152A pdb=" N MET A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1429 through 1434 Processing helix chain 'B' and resid 9 through 18 removed outlier: 4.140A pdb=" N UNK B 13 " --> pdb=" O UNK B 9 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N UNK B 15 " --> pdb=" O UNK B 11 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N UNK B 16 " --> pdb=" O UNK B 12 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 448 removed outlier: 7.091A pdb=" N PHE A 446 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU A 395 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE A 448 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL A 393 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 600 through 603 removed outlier: 3.625A pdb=" N LEU A 602 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 453 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N LEU A 617 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA A 455 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N LEU A 619 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE A 616 " --> pdb=" O TYR A 627 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR A 627 " --> pdb=" O ILE A 616 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE A 618 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 488 through 491 removed outlier: 6.686A pdb=" N SER A 489 " --> pdb=" O LEU A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1230 through 1234 removed outlier: 5.565A pdb=" N ILE A1230 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU A1215 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU A1264 " --> pdb=" O LEU A1215 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA A1217 " --> pdb=" O ASN A1262 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASN A1262 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1240 through 1241 Processing sheet with id=AA6, first strand: chain 'A' and resid 1286 through 1289 removed outlier: 3.636A pdb=" N ILE A1289 " --> pdb=" O LEU A1368 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1509 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: 2.59 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1283 1.31 - 1.44: 2064 1.44 - 1.56: 4571 1.56 - 1.68: 0 1.68 - 1.81: 50 Bond restraints: 7968 Sorted by residual: bond pdb=" C12 VX8 A1501 " pdb=" N2 VX8 A1501 " ideal model delta sigma weight residual 1.359 1.468 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C11 VX8 A1501 " pdb=" N2 VX8 A1501 " ideal model delta sigma weight residual 1.397 1.467 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C3 VX8 A1501 " pdb=" C4 VX8 A1501 " ideal model delta sigma weight residual 1.482 1.548 -0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C13 VX8 A1501 " pdb=" C14 VX8 A1501 " ideal model delta sigma weight residual 1.494 1.544 -0.050 2.00e-02 2.50e+03 6.19e+00 bond pdb=" C16 VX8 A1501 " pdb=" O5 VX8 A1501 " ideal model delta sigma weight residual 1.368 1.416 -0.048 2.00e-02 2.50e+03 5.88e+00 ... (remaining 7963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 10848 4.42 - 8.85: 26 8.85 - 13.27: 2 13.27 - 17.69: 0 17.69 - 22.11: 1 Bond angle restraints: 10877 Sorted by residual: angle pdb=" C14 VX8 A1501 " pdb=" C13 VX8 A1501 " pdb=" C22 VX8 A1501 " ideal model delta sigma weight residual 117.72 139.83 -22.11 3.00e+00 1.11e-01 5.43e+01 angle pdb=" C11 VX8 A1501 " pdb=" N2 VX8 A1501 " pdb=" C12 VX8 A1501 " ideal model delta sigma weight residual 127.44 115.04 12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" N ARG A 104 " pdb=" CA ARG A 104 " pdb=" C ARG A 104 " ideal model delta sigma weight residual 114.31 109.71 4.60 1.29e+00 6.01e-01 1.27e+01 angle pdb=" C12 VX8 A1501 " pdb=" C13 VX8 A1501 " pdb=" C14 VX8 A1501 " ideal model delta sigma weight residual 117.71 107.49 10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" N VAL A 956 " pdb=" CA VAL A 956 " pdb=" C VAL A 956 " ideal model delta sigma weight residual 112.90 109.82 3.08 9.60e-01 1.09e+00 1.03e+01 ... (remaining 10872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.27: 4570 30.27 - 60.54: 94 60.54 - 90.81: 7 90.81 - 121.08: 3 121.08 - 151.35: 3 Dihedral angle restraints: 4677 sinusoidal: 1341 harmonic: 3336 Sorted by residual: dihedral pdb=" C12 VX8 A1501 " pdb=" C13 VX8 A1501 " pdb=" C21 VX8 A1501 " pdb=" C22 VX8 A1501 " ideal model delta sinusoidal sigma weight residual 253.58 102.23 151.35 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" C16 VX8 A1501 " pdb=" C20 VX8 A1501 " pdb=" O5 VX8 A1501 " pdb=" F2 VX8 A1501 " ideal model delta sinusoidal sigma weight residual 236.98 101.86 135.12 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" C17 VX8 A1501 " pdb=" C20 VX8 A1501 " pdb=" O4 VX8 A1501 " pdb=" F2 VX8 A1501 " ideal model delta sinusoidal sigma weight residual 122.94 -101.99 -135.07 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 4674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1326 0.122 - 0.244: 6 0.244 - 0.366: 0 0.366 - 0.488: 0 0.488 - 0.610: 1 Chirality restraints: 1333 Sorted by residual: chirality pdb=" C13 VX8 A1501 " pdb=" C12 VX8 A1501 " pdb=" C14 VX8 A1501 " pdb=" C22 VX8 A1501 " both_signs ideal model delta sigma weight residual True 1.48 0.87 0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CA HIS A 139 " pdb=" N HIS A 139 " pdb=" C HIS A 139 " pdb=" CB HIS A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE A1289 " pdb=" N ILE A1289 " pdb=" C ILE A1289 " pdb=" CB ILE A1289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 1330 not shown) Planarity restraints: 1386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 286 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C GLU A 286 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU A 286 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN A 287 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 350 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C VAL A 350 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 350 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 351 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 959 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 960 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 960 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 960 " -0.019 5.00e-02 4.00e+02 ... (remaining 1383 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1350 2.76 - 3.29: 8013 3.29 - 3.83: 12496 3.83 - 4.36: 13030 4.36 - 4.90: 22783 Nonbonded interactions: 57672 Sorted by model distance: nonbonded pdb=" O ILE A1015 " pdb=" OG1 THR A1019 " model vdw 2.223 3.040 nonbonded pdb=" NH2 ARG A 153 " pdb=" OD2 ASP A 192 " model vdw 2.243 3.120 nonbonded pdb=" O LEU A 850 " pdb=" OG1 THR A 854 " model vdw 2.312 3.040 nonbonded pdb=" OG SER A 313 " pdb=" NH1 ARG A 347 " model vdw 2.314 3.120 nonbonded pdb=" O PRO A 67 " pdb=" NE2 GLN A 372 " model vdw 2.325 3.120 ... (remaining 57667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.620 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.220 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 0.109 7968 Z= 0.218 Angle : 0.799 22.113 10877 Z= 0.456 Chirality : 0.045 0.610 1333 Planarity : 0.003 0.034 1386 Dihedral : 14.298 151.349 2509 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.24), residues: 1120 helix: -0.49 (0.19), residues: 680 sheet: -4.59 (0.46), residues: 49 loop : -2.48 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 19 HIS 0.003 0.001 HIS A 147 PHE 0.019 0.002 PHE A 224 TYR 0.017 0.002 TYR A1092 ARG 0.005 0.001 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.15086 ( 515) hydrogen bonds : angle 6.43504 ( 1509) covalent geometry : bond 0.00422 ( 7968) covalent geometry : angle 0.79916 (10877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 CYS cc_start: 0.6869 (m) cc_final: 0.6626 (t) REVERT: A 129 LEU cc_start: 0.8837 (mm) cc_final: 0.8456 (tt) REVERT: A 265 MET cc_start: 0.8656 (tmm) cc_final: 0.8399 (tmm) REVERT: A 1164 PHE cc_start: 0.7750 (m-80) cc_final: 0.7513 (m-80) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1680 time to fit residues: 26.9266 Evaluate side-chains 79 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 58 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 949 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.119659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108574 restraints weight = 21305.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.110727 restraints weight = 11170.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.112019 restraints weight = 6875.236| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7968 Z= 0.128 Angle : 0.563 7.312 10877 Z= 0.294 Chirality : 0.040 0.152 1333 Planarity : 0.004 0.066 1386 Dihedral : 10.901 147.087 1235 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.84 % Allowed : 7.77 % Favored : 91.39 % 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: -0.62 (0.25), residues: 1120 helix: 0.72 (0.20), residues: 707 sheet: -4.20 (0.50), residues: 49 loop : -2.08 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.009 0.001 HIS A 199 PHE 0.019 0.001 PHE A 224 TYR 0.013 0.001 TYR A 161 ARG 0.004 0.001 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 515) hydrogen bonds : angle 4.58982 ( 1509) covalent geometry : bond 0.00254 ( 7968) covalent geometry : angle 0.56264 (10877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.7900 (m-30) cc_final: 0.7539 (t0) REVERT: A 129 LEU cc_start: 0.8957 (mm) cc_final: 0.8420 (tt) REVERT: A 1137 MET cc_start: 0.7943 (tpp) cc_final: 0.7678 (tpp) outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.1673 time to fit residues: 26.9188 Evaluate side-chains 90 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 878 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 0.0020 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.119051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.107981 restraints weight = 21725.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.110112 restraints weight = 11691.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.111360 restraints weight = 7278.329| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7968 Z= 0.125 Angle : 0.520 6.703 10877 Z= 0.271 Chirality : 0.040 0.178 1333 Planarity : 0.003 0.051 1386 Dihedral : 10.860 147.082 1235 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.36 % Allowed : 12.33 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1120 helix: 1.02 (0.20), residues: 725 sheet: -4.01 (0.55), residues: 44 loop : -2.09 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 79 HIS 0.007 0.001 HIS A 199 PHE 0.013 0.001 PHE A 131 TYR 0.017 0.001 TYR A 89 ARG 0.002 0.000 ARG A1158 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 515) hydrogen bonds : angle 4.18900 ( 1509) covalent geometry : bond 0.00266 ( 7968) covalent geometry : angle 0.51972 (10877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.7930 (m-30) cc_final: 0.7465 (t0) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 0.2010 time to fit residues: 31.5458 Evaluate side-chains 97 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 28 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.115670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104438 restraints weight = 21796.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106512 restraints weight = 11729.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.107922 restraints weight = 7422.727| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7968 Z= 0.183 Angle : 0.587 6.675 10877 Z= 0.303 Chirality : 0.042 0.170 1333 Planarity : 0.004 0.050 1386 Dihedral : 11.058 147.569 1235 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.04 % Allowed : 16.39 % Favored : 80.57 % 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: -0.32 (0.26), residues: 1120 helix: 0.95 (0.20), residues: 716 sheet: -3.61 (0.55), residues: 55 loop : -2.05 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 79 HIS 0.006 0.001 HIS A 199 PHE 0.025 0.001 PHE A1164 TYR 0.026 0.002 TYR A 89 ARG 0.007 0.001 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 515) hydrogen bonds : angle 4.37327 ( 1509) covalent geometry : bond 0.00412 ( 7968) covalent geometry : angle 0.58749 (10877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8025 (m-30) cc_final: 0.7560 (t0) outliers start: 18 outliers final: 11 residues processed: 99 average time/residue: 0.1556 time to fit residues: 22.8808 Evaluate side-chains 91 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 110 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.118309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.107067 restraints weight = 21243.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.109198 restraints weight = 11398.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.110501 restraints weight = 7079.820| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7968 Z= 0.121 Angle : 0.532 8.104 10877 Z= 0.270 Chirality : 0.040 0.138 1333 Planarity : 0.003 0.053 1386 Dihedral : 10.893 146.335 1235 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.21 % Allowed : 16.55 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1120 helix: 1.19 (0.20), residues: 729 sheet: -3.33 (0.57), residues: 54 loop : -1.93 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 79 HIS 0.005 0.001 HIS A 199 PHE 0.020 0.001 PHE A1164 TYR 0.038 0.002 TYR A 247 ARG 0.010 0.001 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 515) hydrogen bonds : angle 4.04573 ( 1509) covalent geometry : bond 0.00259 ( 7968) covalent geometry : angle 0.53192 (10877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.7957 (m-30) cc_final: 0.7523 (t0) REVERT: A 243 MET cc_start: 0.6429 (mmp) cc_final: 0.6219 (mmp) REVERT: A 1046 GLU cc_start: 0.7951 (pp20) cc_final: 0.7201 (mt-10) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 0.1550 time to fit residues: 25.0641 Evaluate side-chains 98 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 53 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.114827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103441 restraints weight = 21820.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105440 restraints weight = 12088.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.106620 restraints weight = 7757.323| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7968 Z= 0.201 Angle : 0.616 6.873 10877 Z= 0.317 Chirality : 0.042 0.174 1333 Planarity : 0.004 0.047 1386 Dihedral : 11.042 146.556 1235 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.38 % Allowed : 20.44 % Favored : 76.18 % 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: -0.30 (0.26), residues: 1120 helix: 0.94 (0.20), residues: 726 sheet: -3.55 (0.59), residues: 55 loop : -2.09 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 79 HIS 0.006 0.001 HIS A 199 PHE 0.025 0.002 PHE A1164 TYR 0.020 0.002 TYR A 89 ARG 0.004 0.001 ARG A 851 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 515) hydrogen bonds : angle 4.38860 ( 1509) covalent geometry : bond 0.00453 ( 7968) covalent geometry : angle 0.61636 (10877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8058 (m-30) cc_final: 0.7638 (t0) REVERT: A 1137 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7379 (ttm) outliers start: 20 outliers final: 15 residues processed: 103 average time/residue: 0.1635 time to fit residues: 24.6872 Evaluate side-chains 97 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1169 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.117616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105931 restraints weight = 21584.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108072 restraints weight = 11652.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.109328 restraints weight = 7292.956| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7968 Z= 0.113 Angle : 0.541 9.046 10877 Z= 0.270 Chirality : 0.040 0.198 1333 Planarity : 0.003 0.040 1386 Dihedral : 10.777 146.088 1235 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.70 % Allowed : 21.11 % Favored : 76.18 % 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: 0.21 (0.26), residues: 1120 helix: 1.30 (0.20), residues: 727 sheet: -3.28 (0.61), residues: 54 loop : -1.84 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 79 HIS 0.004 0.001 HIS A 199 PHE 0.017 0.001 PHE A1164 TYR 0.023 0.001 TYR A 89 ARG 0.004 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 515) hydrogen bonds : angle 3.99240 ( 1509) covalent geometry : bond 0.00240 ( 7968) covalent geometry : angle 0.54073 (10877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8025 (m-30) cc_final: 0.7582 (t0) REVERT: A 92 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8434 (mm-30) REVERT: A 162 LYS cc_start: 0.8797 (tptt) cc_final: 0.8543 (tttm) REVERT: A 1137 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7400 (ttm) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 0.1631 time to fit residues: 24.6603 Evaluate side-chains 98 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1137 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.113723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.102316 restraints weight = 22318.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.104304 restraints weight = 12428.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.105487 restraints weight = 7965.512| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7968 Z= 0.248 Angle : 0.688 9.066 10877 Z= 0.350 Chirality : 0.044 0.187 1333 Planarity : 0.004 0.048 1386 Dihedral : 11.103 146.525 1235 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.55 % Allowed : 21.62 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.26), residues: 1120 helix: 0.87 (0.20), residues: 726 sheet: -3.62 (0.63), residues: 54 loop : -2.12 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.007 0.001 HIS A 199 PHE 0.023 0.002 PHE A1164 TYR 0.028 0.002 TYR A 89 ARG 0.003 0.001 ARG A 289 Details of bonding type rmsd hydrogen bonds : bond 0.05197 ( 515) hydrogen bonds : angle 4.56481 ( 1509) covalent geometry : bond 0.00559 ( 7968) covalent geometry : angle 0.68819 (10877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8103 (m-30) cc_final: 0.7659 (t0) outliers start: 21 outliers final: 19 residues processed: 98 average time/residue: 0.1536 time to fit residues: 22.9115 Evaluate side-chains 101 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 917 TYR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 995 ILE Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 103 optimal weight: 0.0670 chunk 35 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.117636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105993 restraints weight = 21947.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.108075 restraints weight = 11798.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.109538 restraints weight = 7431.991| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7968 Z= 0.113 Angle : 0.560 8.578 10877 Z= 0.277 Chirality : 0.040 0.326 1333 Planarity : 0.003 0.040 1386 Dihedral : 10.754 146.031 1235 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.69 % Allowed : 23.99 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1120 helix: 1.39 (0.20), residues: 727 sheet: -3.33 (0.66), residues: 53 loop : -1.79 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 79 HIS 0.004 0.001 HIS A 199 PHE 0.014 0.001 PHE A1164 TYR 0.028 0.001 TYR A 89 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 515) hydrogen bonds : angle 3.99068 ( 1509) covalent geometry : bond 0.00243 ( 7968) covalent geometry : angle 0.56009 (10877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8045 (m-30) cc_final: 0.7578 (t0) outliers start: 10 outliers final: 9 residues processed: 96 average time/residue: 0.1557 time to fit residues: 22.6024 Evaluate side-chains 94 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 89 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 100 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 37 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.104119 restraints weight = 21849.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.106207 restraints weight = 11745.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.107505 restraints weight = 7449.094| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7968 Z= 0.152 Angle : 0.591 8.394 10877 Z= 0.293 Chirality : 0.041 0.258 1333 Planarity : 0.003 0.042 1386 Dihedral : 10.811 146.033 1235 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.36 % Allowed : 22.97 % Favored : 74.66 % 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: 0.31 (0.26), residues: 1120 helix: 1.37 (0.20), residues: 728 sheet: -3.32 (0.67), residues: 53 loop : -1.80 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 79 HIS 0.005 0.001 HIS A 199 PHE 0.016 0.001 PHE A1164 TYR 0.026 0.002 TYR A 89 ARG 0.002 0.000 ARG A 933 Details of bonding type rmsd hydrogen bonds : bond 0.04370 ( 515) hydrogen bonds : angle 4.07315 ( 1509) covalent geometry : bond 0.00346 ( 7968) covalent geometry : angle 0.59127 (10877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8060 (m-30) cc_final: 0.7639 (t0) outliers start: 14 outliers final: 13 residues processed: 95 average time/residue: 0.1543 time to fit residues: 22.0384 Evaluate side-chains 97 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 925 THR Chi-restraints excluded: chain A residue 1109 ILE Chi-restraints excluded: chain A residue 1112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 75 optimal weight: 0.0670 chunk 106 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.118620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106612 restraints weight = 21565.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108859 restraints weight = 11296.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.110401 restraints weight = 6980.916| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7968 Z= 0.107 Angle : 0.550 8.532 10877 Z= 0.269 Chirality : 0.039 0.261 1333 Planarity : 0.003 0.038 1386 Dihedral : 10.670 145.969 1235 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.20 % Allowed : 23.31 % Favored : 74.49 % 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: 0.68 (0.27), residues: 1120 helix: 1.64 (0.20), residues: 728 sheet: -4.09 (0.70), residues: 43 loop : -1.51 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 79 HIS 0.004 0.001 HIS A 199 PHE 0.013 0.001 PHE A1164 TYR 0.026 0.001 TYR A 89 ARG 0.002 0.000 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 515) hydrogen bonds : angle 3.81596 ( 1509) covalent geometry : bond 0.00227 ( 7968) covalent geometry : angle 0.55012 (10877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.52 seconds wall clock time: 41 minutes 18.85 seconds (2478.85 seconds total)