Starting phenix.real_space_refine on Sun Dec 29 17:06:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9co0_45768/12_2024/9co0_45768.cif Found real_map, /net/cci-nas-00/data/ceres_data/9co0_45768/12_2024/9co0_45768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9co0_45768/12_2024/9co0_45768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9co0_45768/12_2024/9co0_45768.map" model { file = "/net/cci-nas-00/data/ceres_data/9co0_45768/12_2024/9co0_45768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9co0_45768/12_2024/9co0_45768.cif" } resolution = 3.3 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= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 235 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 6801 2.51 5 N 1848 2.21 5 O 2084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10766 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5042 Classifications: {'peptide': 634} Link IDs: {'PTRANS': 25, 'TRANS': 608} Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2576 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 11, 'TRANS': 332} Chain breaks: 2 Chain: "C" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 370 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 7, 'TRANS': 45} Chain: "D" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1661 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 685 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Unusual residues: {'ACY': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'TRANS': 14, None: 1} Not linked: pdbres="ACY F 0 " pdbres="PHE F 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Unusual residues: {'ACY': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'TRANS': 14, None: 1} Not linked: pdbres="ACY G 0 " pdbres="PHE G 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Unusual residues: {'ACY': 1} Classifications: {'peptide': 15, 'undetermined': 1} Link IDs: {'TRANS': 14, None: 1} Not linked: pdbres="ACY I 0 " pdbres="PHE I 1 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACY:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.35, per 1000 atoms: 0.59 Number of scatterers: 10766 At special positions: 0 Unit cell: (103.14, 112.734, 140.318, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 2084 8.00 N 1848 7.00 C 6801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.02 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 16 sheets defined 22.5% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.112A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 removed outlier: 3.779A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.667A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.793A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.603A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.861A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 691 through 695 Processing helix chain 'A' and resid 726 through 731 removed outlier: 4.309A pdb=" N ASN A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.906A pdb=" N TYR C 65 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'D' and resid 33 through 46 removed outlier: 4.654A pdb=" N THR D 38 " --> pdb=" O GLU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 4.157A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 97 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.528A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 240 Processing helix chain 'E' and resid 41 through 46 Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.527A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 274 removed outlier: 4.694A pdb=" N LEU A 268 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU A 337 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLY A 270 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 339 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU A 272 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL A 341 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N SER A 274 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 334 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 376 removed outlier: 4.560A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.570A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N TYR A 454 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLY A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE A 426 " --> pdb=" O PHE F 13 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG F 8 " --> pdb=" O HIS F 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 5.005A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.966A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.959A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.069A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.589A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.514A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.059A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 290 through 292 removed outlier: 4.056A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.521A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.139A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 4.281A pdb=" N ASN E 71 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 2 through 4 489 hydrogen bonds defined for protein. 1344 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: 3.69 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3463 1.34 - 1.46: 1881 1.46 - 1.57: 5605 1.57 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 11010 Sorted by residual: bond pdb=" N ASN A 681 " pdb=" CA ASN A 681 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.48e+00 bond pdb=" C ACY G 0 " pdb=" O ACY G 0 " ideal model delta sigma weight residual 1.248 1.285 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C ACY F 0 " pdb=" O ACY F 0 " ideal model delta sigma weight residual 1.248 1.284 -0.036 2.00e-02 2.50e+03 3.28e+00 bond pdb=" C ACY I 0 " pdb=" O ACY I 0 " ideal model delta sigma weight residual 1.248 1.284 -0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" CB ASP A 582 " pdb=" CG ASP A 582 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.79e+00 ... (remaining 11005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 14470 1.75 - 3.50: 402 3.50 - 5.25: 54 5.25 - 7.00: 21 7.00 - 8.75: 2 Bond angle restraints: 14949 Sorted by residual: angle pdb=" N VAL B 357 " pdb=" CA VAL B 357 " pdb=" C VAL B 357 " ideal model delta sigma weight residual 113.53 109.91 3.62 9.80e-01 1.04e+00 1.37e+01 angle pdb=" C SER A 680 " pdb=" N ASN A 681 " pdb=" CA ASN A 681 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C HIS G 5 " pdb=" N LYS G 6 " pdb=" CA LYS G 6 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 angle pdb=" N GLN D 54 " pdb=" CA GLN D 54 " pdb=" CB GLN D 54 " ideal model delta sigma weight residual 110.16 114.77 -4.61 1.48e+00 4.57e-01 9.68e+00 angle pdb=" CA LYS G 6 " pdb=" CB LYS G 6 " pdb=" CG LYS G 6 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.63e+00 ... (remaining 14944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5970 17.75 - 35.49: 375 35.49 - 53.24: 70 53.24 - 70.99: 22 70.99 - 88.74: 13 Dihedral angle restraints: 6450 sinusoidal: 2526 harmonic: 3924 Sorted by residual: dihedral pdb=" CA CYS A 700 " pdb=" C CYS A 700 " pdb=" N LYS A 701 " pdb=" CA LYS A 701 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA CYS A 690 " pdb=" C CYS A 690 " pdb=" N ALA A 691 " pdb=" CA ALA A 691 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual 93.00 123.52 -30.52 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 6447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1226 0.052 - 0.105: 303 0.105 - 0.157: 68 0.157 - 0.209: 4 0.209 - 0.261: 1 Chirality restraints: 1602 Sorted by residual: chirality pdb=" CB ILE F 4 " pdb=" CA ILE F 4 " pdb=" CG1 ILE F 4 " pdb=" CG2 ILE F 4 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE G 4 " pdb=" CA ILE G 4 " pdb=" CG1 ILE G 4 " pdb=" CG2 ILE G 4 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CA ASN A 681 " pdb=" N ASN A 681 " pdb=" C ASN A 681 " pdb=" CB ASN A 681 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 1599 not shown) Planarity restraints: 1961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN D 99 " 0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO D 100 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 408 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO A 409 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 48 " -0.023 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP D 48 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP D 48 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 48 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 48 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 48 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP D 48 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 48 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 48 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 48 " -0.004 2.00e-02 2.50e+03 ... (remaining 1958 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1091 2.76 - 3.29: 10504 3.29 - 3.83: 18022 3.83 - 4.36: 20922 4.36 - 4.90: 37001 Nonbonded interactions: 87540 Sorted by model distance: nonbonded pdb=" OG1 THR A 615 " pdb=" OG1 THR A 633 " model vdw 2.219 3.040 nonbonded pdb=" NE2 GLN D 40 " pdb=" OD2 ASP D 74 " model vdw 2.279 3.120 nonbonded pdb=" OG SER A 778 " pdb=" O GLY A 781 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR B 166 " pdb=" OD1 ASN B 168 " model vdw 2.298 3.040 nonbonded pdb=" OD1 ASN A 463 " pdb=" OH TYR I 11 " model vdw 2.304 3.040 ... (remaining 87535 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 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.440 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.003 0.040 11010 Z= 0.201 Angle : 0.692 8.746 14949 Z= 0.376 Chirality : 0.047 0.261 1602 Planarity : 0.006 0.096 1961 Dihedral : 13.259 88.735 3957 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 (0.23), residues: 1346 helix: 0.92 (0.31), residues: 260 sheet: 0.11 (0.26), residues: 394 loop : -0.02 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP D 48 HIS 0.004 0.001 HIS I 5 PHE 0.022 0.001 PHE A 802 TYR 0.021 0.002 TYR A 229 ARG 0.013 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.382 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9482 (mt) cc_final: 0.9254 (mp) REVERT: A 229 TYR cc_start: 0.8975 (t80) cc_final: 0.8744 (t80) REVERT: A 325 MET cc_start: 0.7825 (ppp) cc_final: 0.7484 (tmm) REVERT: A 583 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7721 (ttp80) REVERT: A 729 TYR cc_start: 0.7177 (m-10) cc_final: 0.6755 (m-10) REVERT: B 273 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7591 (mtm110) REVERT: B 290 ILE cc_start: 0.8883 (tp) cc_final: 0.8583 (tp) REVERT: B 368 GLN cc_start: 0.8300 (tm-30) cc_final: 0.8002 (tm-30) REVERT: D 93 ASP cc_start: 0.8562 (t70) cc_final: 0.8259 (t0) REVERT: D 109 MET cc_start: 0.8310 (mmt) cc_final: 0.7842 (mmt) REVERT: F 12 TRP cc_start: 0.7914 (m-90) cc_final: 0.7619 (m100) REVERT: I 8 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7310 (mtm180) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2216 time to fit residues: 68.5478 Evaluate side-chains 182 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 0.0270 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN B 62 ASN F 5 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11010 Z= 0.207 Angle : 0.565 7.602 14949 Z= 0.306 Chirality : 0.045 0.194 1602 Planarity : 0.005 0.062 1961 Dihedral : 4.407 16.678 1504 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.49 % Allowed : 6.84 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1346 helix: 1.18 (0.31), residues: 264 sheet: 0.05 (0.25), residues: 421 loop : 0.11 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 48 HIS 0.003 0.001 HIS A 533 PHE 0.018 0.001 PHE A 440 TYR 0.032 0.001 TYR A 550 ARG 0.006 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9517 (mt) cc_final: 0.9212 (mp) REVERT: A 314 ARG cc_start: 0.8214 (mtm110) cc_final: 0.7972 (ttm170) REVERT: A 319 TYR cc_start: 0.8216 (m-80) cc_final: 0.8016 (m-80) REVERT: A 323 GLN cc_start: 0.7742 (pm20) cc_final: 0.7455 (pm20) REVERT: A 546 TRP cc_start: 0.7096 (m100) cc_final: 0.6290 (m100) REVERT: A 729 TYR cc_start: 0.7162 (m-10) cc_final: 0.6811 (m-10) REVERT: A 777 MET cc_start: 0.8415 (mmm) cc_final: 0.8196 (mmt) REVERT: B 127 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7960 (mm-30) REVERT: B 170 GLN cc_start: 0.6478 (pt0) cc_final: 0.6006 (pm20) REVERT: B 343 GLU cc_start: 0.7669 (tp30) cc_final: 0.7390 (tp30) REVERT: B 368 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8137 (tm-30) REVERT: D 93 ASP cc_start: 0.8654 (t70) cc_final: 0.8356 (t0) REVERT: D 112 ARG cc_start: 0.8071 (ttp-170) cc_final: 0.7627 (ttp-170) REVERT: D 183 GLU cc_start: 0.7776 (tt0) cc_final: 0.7560 (tt0) REVERT: F 12 TRP cc_start: 0.8052 (m-90) cc_final: 0.7695 (m100) REVERT: I 7 ARG cc_start: 0.7450 (tpp-160) cc_final: 0.7236 (mmm-85) outliers start: 17 outliers final: 13 residues processed: 208 average time/residue: 0.2332 time to fit residues: 68.3603 Evaluate side-chains 197 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 90 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 0.0870 chunk 130 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN C 51 HIS E 54 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11010 Z= 0.163 Angle : 0.536 7.612 14949 Z= 0.287 Chirality : 0.044 0.186 1602 Planarity : 0.004 0.052 1961 Dihedral : 4.213 14.667 1504 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.40 % Allowed : 10.69 % Favored : 87.91 % 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: 0.50 (0.23), residues: 1346 helix: 1.34 (0.32), residues: 264 sheet: 0.18 (0.26), residues: 422 loop : 0.15 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 48 HIS 0.003 0.001 HIS A 533 PHE 0.028 0.001 PHE A 238 TYR 0.023 0.001 TYR D 184 ARG 0.005 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.9518 (mt) cc_final: 0.9216 (mp) REVERT: A 323 GLN cc_start: 0.7708 (pm20) cc_final: 0.7381 (mp10) REVERT: A 729 TYR cc_start: 0.7192 (m-10) cc_final: 0.6936 (m-10) REVERT: B 170 GLN cc_start: 0.6548 (pt0) cc_final: 0.5972 (pm20) REVERT: B 368 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8103 (tm-30) REVERT: D 93 ASP cc_start: 0.8647 (t70) cc_final: 0.8358 (t0) REVERT: D 98 LEU cc_start: 0.9208 (tp) cc_final: 0.8982 (tt) REVERT: F 12 TRP cc_start: 0.8056 (m-90) cc_final: 0.7848 (m100) REVERT: I 7 ARG cc_start: 0.7509 (tpp-160) cc_final: 0.7301 (mmm-85) outliers start: 16 outliers final: 11 residues processed: 212 average time/residue: 0.2291 time to fit residues: 69.6603 Evaluate side-chains 196 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 62 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 115 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11010 Z= 0.265 Angle : 0.563 7.458 14949 Z= 0.303 Chirality : 0.045 0.187 1602 Planarity : 0.004 0.052 1961 Dihedral : 4.376 18.447 1504 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.28 % Allowed : 11.66 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1346 helix: 1.37 (0.32), residues: 264 sheet: 0.08 (0.25), residues: 420 loop : 0.16 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 48 HIS 0.003 0.001 HIS A 533 PHE 0.025 0.001 PHE A 238 TYR 0.022 0.001 TYR D 184 ARG 0.005 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 1.190 Fit side-chains REVERT: A 247 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8230 (pt) REVERT: A 323 GLN cc_start: 0.7625 (pm20) cc_final: 0.7226 (mp10) REVERT: A 338 ARG cc_start: 0.8244 (mtp-110) cc_final: 0.8042 (mtp-110) REVERT: A 729 TYR cc_start: 0.7308 (m-10) cc_final: 0.7077 (m-10) REVERT: A 805 ASN cc_start: 0.8361 (t0) cc_final: 0.8109 (t0) REVERT: B 170 GLN cc_start: 0.6893 (pt0) cc_final: 0.6540 (pm20) REVERT: B 343 GLU cc_start: 0.7693 (tp30) cc_final: 0.7428 (tp30) REVERT: B 352 GLU cc_start: 0.7115 (tp30) cc_final: 0.6901 (tp30) REVERT: B 368 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8186 (tm-30) REVERT: D 48 TRP cc_start: 0.8434 (m-10) cc_final: 0.8207 (m-10) REVERT: D 93 ASP cc_start: 0.8664 (t70) cc_final: 0.8402 (t0) REVERT: D 98 LEU cc_start: 0.9153 (tp) cc_final: 0.8918 (tt) REVERT: F 12 TRP cc_start: 0.8115 (m-90) cc_final: 0.7785 (m100) REVERT: I 7 ARG cc_start: 0.7579 (tpp-160) cc_final: 0.7245 (mmm-85) outliers start: 26 outliers final: 15 residues processed: 197 average time/residue: 0.2266 time to fit residues: 64.3622 Evaluate side-chains 187 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 0.0870 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11010 Z= 0.204 Angle : 0.543 8.270 14949 Z= 0.289 Chirality : 0.044 0.186 1602 Planarity : 0.004 0.045 1961 Dihedral : 4.245 15.227 1504 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.45 % Allowed : 12.80 % Favored : 84.75 % 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: 0.49 (0.23), residues: 1346 helix: 1.53 (0.32), residues: 264 sheet: 0.04 (0.25), residues: 423 loop : 0.16 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 48 HIS 0.002 0.001 HIS F 5 PHE 0.030 0.001 PHE A 238 TYR 0.023 0.001 TYR D 184 ARG 0.006 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.205 Fit side-chains REVERT: A 193 LEU cc_start: 0.9474 (mt) cc_final: 0.9201 (mp) REVERT: A 247 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8148 (pt) REVERT: A 323 GLN cc_start: 0.7633 (pm20) cc_final: 0.7227 (mp10) REVERT: A 338 ARG cc_start: 0.8277 (mtp-110) cc_final: 0.8020 (mtp-110) REVERT: A 552 MET cc_start: 0.8943 (mmm) cc_final: 0.8724 (mmm) REVERT: A 729 TYR cc_start: 0.7185 (m-10) cc_final: 0.6970 (m-10) REVERT: A 805 ASN cc_start: 0.8395 (t0) cc_final: 0.8175 (t0) REVERT: B 170 GLN cc_start: 0.6799 (pt0) cc_final: 0.6454 (pm20) REVERT: B 352 GLU cc_start: 0.7185 (tp30) cc_final: 0.6662 (tm-30) REVERT: B 368 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8161 (tm-30) REVERT: D 93 ASP cc_start: 0.8613 (t70) cc_final: 0.8336 (t0) REVERT: D 98 LEU cc_start: 0.9125 (tp) cc_final: 0.8882 (tt) REVERT: F 12 TRP cc_start: 0.8083 (m-90) cc_final: 0.7758 (m100) REVERT: I 7 ARG cc_start: 0.7570 (tpp-160) cc_final: 0.7230 (mmm-85) outliers start: 28 outliers final: 17 residues processed: 200 average time/residue: 0.2312 time to fit residues: 66.1840 Evaluate side-chains 195 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN E 54 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11010 Z= 0.217 Angle : 0.553 7.471 14949 Z= 0.294 Chirality : 0.044 0.202 1602 Planarity : 0.004 0.044 1961 Dihedral : 4.218 15.473 1504 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.80 % Allowed : 13.23 % Favored : 83.96 % 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: 0.47 (0.23), residues: 1346 helix: 1.57 (0.32), residues: 264 sheet: 0.02 (0.25), residues: 422 loop : 0.14 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 48 HIS 0.002 0.001 HIS A 533 PHE 0.029 0.001 PHE A 238 TYR 0.022 0.001 TYR D 184 ARG 0.005 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.132 Fit side-chains REVERT: A 247 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8167 (pt) REVERT: A 323 GLN cc_start: 0.7611 (pm20) cc_final: 0.7195 (mp10) REVERT: A 338 ARG cc_start: 0.8274 (mtp-110) cc_final: 0.7899 (mtm110) REVERT: A 552 MET cc_start: 0.8914 (mmm) cc_final: 0.8658 (mmm) REVERT: B 170 GLN cc_start: 0.6847 (pt0) cc_final: 0.6515 (pm20) REVERT: B 230 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7524 (tp-100) REVERT: B 343 GLU cc_start: 0.7760 (tp30) cc_final: 0.7423 (tp30) REVERT: B 352 GLU cc_start: 0.7182 (tp30) cc_final: 0.6891 (tp30) REVERT: B 368 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8154 (tm-30) REVERT: D 93 ASP cc_start: 0.8618 (t70) cc_final: 0.8356 (t0) REVERT: D 98 LEU cc_start: 0.9098 (tp) cc_final: 0.8852 (tt) REVERT: F 12 TRP cc_start: 0.8078 (m-90) cc_final: 0.7751 (m100) REVERT: I 7 ARG cc_start: 0.7578 (tpp-160) cc_final: 0.7366 (mpt-90) outliers start: 32 outliers final: 20 residues processed: 203 average time/residue: 0.2197 time to fit residues: 64.0728 Evaluate side-chains 194 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 0.0010 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN B 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11010 Z= 0.200 Angle : 0.555 7.939 14949 Z= 0.292 Chirality : 0.044 0.201 1602 Planarity : 0.004 0.040 1961 Dihedral : 4.233 18.322 1504 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.63 % Allowed : 13.94 % Favored : 83.44 % 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: 0.42 (0.23), residues: 1346 helix: 1.58 (0.32), residues: 264 sheet: -0.13 (0.25), residues: 433 loop : 0.17 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 48 HIS 0.002 0.000 HIS A 533 PHE 0.032 0.001 PHE A 238 TYR 0.022 0.001 TYR D 184 ARG 0.005 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 GLN cc_start: 0.7586 (pm20) cc_final: 0.7175 (mp10) REVERT: A 338 ARG cc_start: 0.8255 (mtp-110) cc_final: 0.7889 (mtm110) REVERT: A 421 ARG cc_start: 0.6541 (ptp90) cc_final: 0.6253 (ptp-170) REVERT: A 552 MET cc_start: 0.8920 (mmm) cc_final: 0.8685 (mmm) REVERT: A 729 TYR cc_start: 0.7093 (m-10) cc_final: 0.6742 (m-10) REVERT: A 805 ASN cc_start: 0.8294 (t0) cc_final: 0.8038 (t0) REVERT: B 170 GLN cc_start: 0.6821 (pt0) cc_final: 0.6517 (pm20) REVERT: B 352 GLU cc_start: 0.7179 (tp30) cc_final: 0.6891 (tp30) REVERT: B 368 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8149 (tm-30) REVERT: D 93 ASP cc_start: 0.8602 (t70) cc_final: 0.8337 (t0) REVERT: D 98 LEU cc_start: 0.9104 (tp) cc_final: 0.8854 (tt) REVERT: F 12 TRP cc_start: 0.8060 (m-90) cc_final: 0.7729 (m100) REVERT: I 7 ARG cc_start: 0.7587 (tpp-160) cc_final: 0.7355 (mpt-90) outliers start: 30 outliers final: 22 residues processed: 190 average time/residue: 0.2290 time to fit residues: 62.3771 Evaluate side-chains 203 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11010 Z= 0.181 Angle : 0.566 8.633 14949 Z= 0.297 Chirality : 0.044 0.195 1602 Planarity : 0.004 0.037 1961 Dihedral : 4.170 17.596 1504 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.45 % Allowed : 14.46 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1346 helix: 1.62 (0.32), residues: 265 sheet: -0.06 (0.25), residues: 432 loop : 0.18 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 48 HIS 0.002 0.000 HIS F 5 PHE 0.033 0.001 PHE A 238 TYR 0.022 0.001 TYR D 184 ARG 0.005 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8057 (pt) REVERT: A 323 GLN cc_start: 0.7554 (pm20) cc_final: 0.7153 (mp10) REVERT: A 338 ARG cc_start: 0.8275 (mtp-110) cc_final: 0.7909 (mtm110) REVERT: A 536 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 552 MET cc_start: 0.8918 (mmm) cc_final: 0.8625 (mmm) REVERT: A 583 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7468 (ttp-170) REVERT: A 729 TYR cc_start: 0.7063 (m-10) cc_final: 0.6665 (m-10) REVERT: A 805 ASN cc_start: 0.8283 (t0) cc_final: 0.8001 (t0) REVERT: B 127 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7674 (mm-30) REVERT: B 170 GLN cc_start: 0.6712 (pt0) cc_final: 0.6470 (pm20) REVERT: B 343 GLU cc_start: 0.7764 (tp30) cc_final: 0.7413 (tp30) REVERT: B 352 GLU cc_start: 0.7203 (tp30) cc_final: 0.6927 (tp30) REVERT: B 368 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 93 ASP cc_start: 0.8593 (t70) cc_final: 0.8329 (t0) REVERT: D 98 LEU cc_start: 0.9097 (tp) cc_final: 0.8845 (tt) REVERT: F 12 TRP cc_start: 0.8051 (m-90) cc_final: 0.7718 (m100) REVERT: I 7 ARG cc_start: 0.7589 (tpp-160) cc_final: 0.7344 (mpt-90) outliers start: 28 outliers final: 22 residues processed: 200 average time/residue: 0.2289 time to fit residues: 65.6320 Evaluate side-chains 203 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11010 Z= 0.228 Angle : 0.587 8.935 14949 Z= 0.309 Chirality : 0.044 0.201 1602 Planarity : 0.004 0.042 1961 Dihedral : 4.247 19.367 1504 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.54 % Allowed : 14.11 % Favored : 83.35 % 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: 0.46 (0.23), residues: 1346 helix: 1.58 (0.32), residues: 265 sheet: -0.10 (0.25), residues: 431 loop : 0.20 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 48 HIS 0.002 0.000 HIS B 347 PHE 0.034 0.001 PHE A 238 TYR 0.022 0.001 TYR D 184 ARG 0.007 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8101 (pt) REVERT: A 323 GLN cc_start: 0.7565 (pm20) cc_final: 0.7156 (mp10) REVERT: A 338 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.7994 (mtp-110) REVERT: A 536 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8724 (mp) REVERT: A 552 MET cc_start: 0.8894 (mmm) cc_final: 0.8635 (mmm) REVERT: A 583 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7579 (ttp-170) REVERT: A 729 TYR cc_start: 0.7143 (m-10) cc_final: 0.6764 (m-10) REVERT: A 805 ASN cc_start: 0.8314 (t0) cc_final: 0.8058 (t0) REVERT: B 343 GLU cc_start: 0.7887 (tp30) cc_final: 0.7544 (tp30) REVERT: B 352 GLU cc_start: 0.7226 (tp30) cc_final: 0.6948 (tp30) REVERT: B 368 GLN cc_start: 0.8390 (tm-30) cc_final: 0.8117 (tm-30) REVERT: D 93 ASP cc_start: 0.8599 (t70) cc_final: 0.8326 (t0) REVERT: D 98 LEU cc_start: 0.9099 (tp) cc_final: 0.8842 (tt) REVERT: D 207 ASP cc_start: 0.8056 (p0) cc_final: 0.7781 (p0) REVERT: F 12 TRP cc_start: 0.8063 (m-90) cc_final: 0.7728 (m100) REVERT: I 7 ARG cc_start: 0.7579 (tpp-160) cc_final: 0.7323 (mpt-90) outliers start: 29 outliers final: 23 residues processed: 196 average time/residue: 0.2366 time to fit residues: 67.5594 Evaluate side-chains 206 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.0020 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 0.0050 chunk 105 optimal weight: 1.9990 chunk 10 optimal weight: 0.0170 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 0.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11010 Z= 0.186 Angle : 0.573 9.008 14949 Z= 0.302 Chirality : 0.044 0.197 1602 Planarity : 0.004 0.037 1961 Dihedral : 4.181 18.430 1504 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.28 % Allowed : 14.81 % Favored : 82.91 % 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: 0.50 (0.23), residues: 1346 helix: 1.69 (0.32), residues: 263 sheet: -0.07 (0.25), residues: 432 loop : 0.20 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 48 HIS 0.002 0.000 HIS B 347 PHE 0.034 0.001 PHE A 238 TYR 0.023 0.001 TYR D 184 ARG 0.008 0.000 ARG E 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8525 (mmt90) cc_final: 0.8210 (mmt90) REVERT: A 247 LEU cc_start: 0.8295 (pt) cc_final: 0.8025 (pt) REVERT: A 319 TYR cc_start: 0.8397 (m-80) cc_final: 0.8157 (m-80) REVERT: A 323 GLN cc_start: 0.7547 (pm20) cc_final: 0.7160 (mp10) REVERT: A 338 ARG cc_start: 0.8233 (mtp-110) cc_final: 0.7978 (mtp-110) REVERT: A 536 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8699 (mp) REVERT: A 552 MET cc_start: 0.8914 (mmm) cc_final: 0.8628 (mmm) REVERT: A 583 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7550 (ttp-170) REVERT: A 729 TYR cc_start: 0.7114 (m-10) cc_final: 0.6912 (m-10) REVERT: A 805 ASN cc_start: 0.8304 (t0) cc_final: 0.8039 (t0) REVERT: B 91 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7648 (tp30) REVERT: B 343 GLU cc_start: 0.7883 (tp30) cc_final: 0.7493 (tp30) REVERT: B 352 GLU cc_start: 0.7218 (tp30) cc_final: 0.6945 (tp30) REVERT: B 368 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8087 (tm-30) REVERT: D 93 ASP cc_start: 0.8594 (t70) cc_final: 0.8329 (t0) REVERT: D 98 LEU cc_start: 0.9076 (tp) cc_final: 0.8817 (tt) REVERT: D 207 ASP cc_start: 0.8073 (p0) cc_final: 0.7786 (p0) REVERT: F 12 TRP cc_start: 0.8051 (m-90) cc_final: 0.7719 (m100) REVERT: I 7 ARG cc_start: 0.7573 (tpp-160) cc_final: 0.7332 (mpt-90) outliers start: 26 outliers final: 23 residues processed: 197 average time/residue: 0.2278 time to fit residues: 64.4201 Evaluate side-chains 200 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 724 PHE Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 227 MET Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 102 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 = 0.3743 r_free = 0.3743 target = 0.136097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096368 restraints weight = 17679.354| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.68 r_work: 0.3043 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11010 Z= 0.254 Angle : 0.588 9.003 14949 Z= 0.310 Chirality : 0.045 0.192 1602 Planarity : 0.004 0.046 1961 Dihedral : 4.281 18.817 1504 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.45 % Allowed : 14.81 % Favored : 82.73 % 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: 0.44 (0.23), residues: 1346 helix: 1.64 (0.32), residues: 263 sheet: -0.10 (0.25), residues: 435 loop : 0.15 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 48 HIS 0.002 0.000 HIS B 64 PHE 0.036 0.001 PHE A 238 TYR 0.022 0.001 TYR D 184 ARG 0.008 0.000 ARG E 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2421.45 seconds wall clock time: 45 minutes 33.54 seconds (2733.54 seconds total)