Starting phenix.real_space_refine on Tue Mar 11 20:31:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t23_40979/03_2025/8t23_40979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t23_40979/03_2025/8t23_40979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t23_40979/03_2025/8t23_40979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t23_40979/03_2025/8t23_40979.map" model { file = "/net/cci-nas-00/data/ceres_data/8t23_40979/03_2025/8t23_40979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t23_40979/03_2025/8t23_40979.cif" } resolution = 3.87 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= -0.001 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4121 2.51 5 N 1075 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6451 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4904 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Chain: "B" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1467 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 11, 'TRANS': 173} Chain breaks: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.15, per 1000 atoms: 0.80 Number of scatterers: 6451 At special positions: 0 Unit cell: (103.23, 75.48, 135.42, 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 37 16.00 O 1218 8.00 N 1075 7.00 C 4121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.02 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " BETA1-6 " NAG H 1 " - " FUC H 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 53 " " NAG B 601 " - " ASN B 343 " " NAG G 1 " - " ASN A 322 " " NAG H 1 " - " ASN A 216 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 906.0 milliseconds 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 45.6% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.534A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU A 38 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 66 through 83 removed outlier: 3.646A pdb=" N THR A 82 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR A 83 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.610A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 4.873A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N MET A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.616A pdb=" N GLY A 147 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 157 through 163 removed outlier: 4.367A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.577A pdb=" N LEU A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 219 through 223 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 236 through 248 removed outlier: 4.855A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 removed outlier: 3.973A pdb=" N TYR A 252 " --> pdb=" O MET A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 252' Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.388A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.956A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 382 Processing helix chain 'A' and resid 383 through 386 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 413 removed outlier: 3.628A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 446 through 452 removed outlier: 4.238A pdb=" N THR A 449 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 450 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Proline residue: A 451 - end of helix No H-bonds generated for 'chain 'A' and resid 446 through 452' Processing helix chain 'A' and resid 453 through 464 removed outlier: 4.725A pdb=" N ARG A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 removed outlier: 4.026A pdb=" N GLU A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 6.677A pdb=" N PHE A 504 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS A 505 " --> pdb=" O ALA A 502 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 506 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 507 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 523 removed outlier: 3.646A pdb=" N GLN A 522 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 547 through 555 removed outlier: 3.946A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.840A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.536A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.588A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.008A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.941A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 396 through 403 removed outlier: 3.898A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) 173 hydrogen bonds defined for protein. 468 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: 1.42 Time building geometry restraints manager: 1.72 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: 2064 1.34 - 1.46: 1660 1.46 - 1.58: 2852 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6635 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" CB PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.92e+00 bond pdb=" CG PRO A 389 " pdb=" CD PRO A 389 " ideal model delta sigma weight residual 1.503 1.431 0.072 3.40e-02 8.65e+02 4.45e+00 bond pdb=" CA LYS A 441 " pdb=" CB LYS A 441 " ideal model delta sigma weight residual 1.526 1.559 -0.033 1.70e-02 3.46e+03 3.83e+00 bond pdb=" N PRO A 389 " pdb=" CA PRO A 389 " ideal model delta sigma weight residual 1.469 1.444 0.024 1.28e-02 6.10e+03 3.66e+00 ... (remaining 6630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 8877 3.35 - 6.69: 118 6.69 - 10.04: 10 10.04 - 13.38: 4 13.38 - 16.73: 3 Bond angle restraints: 9012 Sorted by residual: angle pdb=" CA PRO A 389 " pdb=" N PRO A 389 " pdb=" CD PRO A 389 " ideal model delta sigma weight residual 112.00 95.27 16.73 1.40e+00 5.10e-01 1.43e+02 angle pdb=" C ALA A 212 " pdb=" N ASP A 213 " pdb=" CA ASP A 213 " ideal model delta sigma weight residual 122.35 132.59 -10.24 1.46e+00 4.69e-01 4.92e+01 angle pdb=" N PRO A 389 " pdb=" CD PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 103.20 94.54 8.66 1.50e+00 4.44e-01 3.33e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 113.71 108.86 4.85 9.50e-01 1.11e+00 2.61e+01 angle pdb=" CA LEU A 45 " pdb=" CB LEU A 45 " pdb=" CG LEU A 45 " ideal model delta sigma weight residual 116.30 132.29 -15.99 3.50e+00 8.16e-02 2.09e+01 ... (remaining 9007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.55: 3535 23.55 - 47.09: 388 47.09 - 70.64: 62 70.64 - 94.19: 10 94.19 - 117.74: 6 Dihedral angle restraints: 4001 sinusoidal: 1708 harmonic: 2293 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 168.30 -75.30 1 1.00e+01 1.00e-02 7.16e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 167.32 -74.32 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.83 48.17 1 1.00e+01 1.00e-02 3.20e+01 ... (remaining 3998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 828 0.077 - 0.154: 113 0.154 - 0.231: 3 0.231 - 0.308: 1 0.308 - 0.385: 1 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 216 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CB VAL A 318 " pdb=" CA VAL A 318 " pdb=" CG1 VAL A 318 " pdb=" CG2 VAL A 318 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 943 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.144 5.00e-02 4.00e+02 2.00e-01 6.39e+01 pdb=" N PRO A 389 " -0.344 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.113 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 168 " -0.017 2.00e-02 2.50e+03 1.96e-02 9.57e+00 pdb=" CG TRP A 168 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 168 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 168 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 168 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 168 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 168 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 168 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 168 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 168 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 564 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO A 565 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " 0.039 5.00e-02 4.00e+02 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 191 2.69 - 3.24: 6608 3.24 - 3.79: 9892 3.79 - 4.35: 12329 4.35 - 4.90: 18650 Nonbonded interactions: 47670 Sorted by model distance: nonbonded pdb=" OH TYR A 180 " pdb=" O THR A 496 " model vdw 2.136 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.226 3.040 nonbonded pdb=" O GLU A 166 " pdb=" OG SER A 170 " model vdw 2.228 3.040 nonbonded pdb=" O ARG A 305 " pdb=" NZ LYS A 309 " model vdw 2.233 3.120 nonbonded pdb=" NH2 ARG B 355 " pdb=" OD2 ASP B 398 " model vdw 2.239 3.120 ... (remaining 47665 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 'G' and resid 1) selection = (chain 'H' and resid 1) } 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: 5.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.570 Find NCS groups from input model: 0.070 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4948 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 : 0.005 0.149 6635 Z= 0.293 Angle : 1.004 16.729 9012 Z= 0.535 Chirality : 0.051 0.385 946 Planarity : 0.009 0.200 1164 Dihedral : 19.217 117.737 2511 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 0.59 % Allowed : 31.48 % Favored : 67.94 % 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: -3.06 (0.28), residues: 775 helix: -1.63 (0.31), residues: 257 sheet: 2.48 (1.14), residues: 24 loop : -2.66 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 168 HIS 0.008 0.001 HIS A 505 PHE 0.020 0.002 PHE B 338 TYR 0.015 0.001 TYR A 510 ARG 0.008 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6107 (mt) cc_final: 0.5829 (mm) REVERT: A 62 MET cc_start: 0.4429 (mpp) cc_final: 0.4108 (pmm) REVERT: A 123 MET cc_start: -0.0391 (tpt) cc_final: -0.0686 (tpt) REVERT: A 202 TYR cc_start: 0.7222 (m-10) cc_final: 0.6390 (t80) REVERT: A 379 ILE cc_start: 0.8955 (tt) cc_final: 0.8683 (mm) REVERT: A 382 ASP cc_start: 0.8908 (t70) cc_final: 0.8393 (p0) REVERT: A 408 MET cc_start: 0.3341 (mmp) cc_final: 0.2561 (mmm) REVERT: A 474 MET cc_start: -0.1394 (ptt) cc_final: -0.2041 (ptt) REVERT: A 497 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6257 (t80) REVERT: A 515 TYR cc_start: 0.6070 (m-80) cc_final: 0.5712 (m-80) REVERT: A 539 LEU cc_start: 0.6118 (tp) cc_final: 0.5859 (mp) outliers start: 4 outliers final: 1 residues processed: 127 average time/residue: 0.1858 time to fit residues: 31.2504 Evaluate side-chains 82 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 0.0770 chunk 23 optimal weight: 0.0010 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 overall best weight: 0.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.146761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.128114 restraints weight = 41088.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.129929 restraints weight = 33500.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.131113 restraints weight = 27884.165| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5100 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6635 Z= 0.202 Angle : 0.793 13.523 9012 Z= 0.397 Chirality : 0.051 0.497 946 Planarity : 0.006 0.067 1164 Dihedral : 11.621 106.110 982 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 4.25 % Allowed : 26.50 % Favored : 69.25 % 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: -2.68 (0.30), residues: 775 helix: -1.13 (0.33), residues: 252 sheet: 1.87 (1.14), residues: 24 loop : -2.47 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 168 HIS 0.006 0.001 HIS A 417 PHE 0.024 0.002 PHE B 490 TYR 0.017 0.001 TYR A 180 ARG 0.006 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.4924 (mpp) cc_final: 0.4695 (pmm) REVERT: A 92 ILE cc_start: 0.6941 (mm) cc_final: 0.6662 (mt) REVERT: A 203 TRP cc_start: 0.6350 (t-100) cc_final: 0.4743 (m-10) REVERT: A 211 TRP cc_start: 0.5337 (p90) cc_final: 0.2754 (m100) REVERT: A 252 TYR cc_start: 0.2728 (OUTLIER) cc_final: 0.1783 (p90) REVERT: A 279 TYR cc_start: 0.5445 (OUTLIER) cc_final: 0.4930 (m-10) REVERT: A 345 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7396 (t70) REVERT: A 376 MET cc_start: 0.8902 (tpt) cc_final: 0.8044 (ptp) REVERT: A 382 ASP cc_start: 0.9119 (t70) cc_final: 0.8464 (p0) REVERT: A 400 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 402 GLU cc_start: 0.6978 (mp0) cc_final: 0.6653 (mp0) REVERT: A 462 MET cc_start: 0.7180 (ppp) cc_final: 0.6819 (ppp) REVERT: A 474 MET cc_start: -0.1832 (ptt) cc_final: -0.2069 (ptt) REVERT: A 566 TRP cc_start: 0.7374 (p-90) cc_final: 0.6970 (p-90) REVERT: A 579 MET cc_start: 0.6568 (ppp) cc_final: 0.5329 (ppp) outliers start: 29 outliers final: 14 residues processed: 109 average time/residue: 0.1709 time to fit residues: 25.2477 Evaluate side-chains 93 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 18 optimal weight: 0.7980 chunk 51 optimal weight: 0.0010 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.0030 chunk 41 optimal weight: 0.0050 chunk 67 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.2410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 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 = 0.4578 r_free = 0.4578 target = 0.146544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.127928 restraints weight = 41308.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.129658 restraints weight = 34556.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.130663 restraints weight = 29171.193| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5200 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6635 Z= 0.183 Angle : 0.746 16.433 9012 Z= 0.368 Chirality : 0.050 0.515 946 Planarity : 0.006 0.065 1164 Dihedral : 10.807 102.328 980 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 4.10 % Allowed : 27.53 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.30), residues: 775 helix: -0.80 (0.34), residues: 243 sheet: 1.64 (1.06), residues: 24 loop : -2.41 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 211 HIS 0.008 0.001 HIS A 417 PHE 0.036 0.002 PHE A 72 TYR 0.014 0.001 TYR A 217 ARG 0.004 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: -0.0567 (OUTLIER) cc_final: -0.1270 (pttm) REVERT: A 93 ILE cc_start: 0.6787 (mm) cc_final: 0.6251 (pt) REVERT: A 123 MET cc_start: -0.0642 (tpt) cc_final: -0.1034 (tpt) REVERT: A 150 ASP cc_start: 0.9144 (p0) cc_final: 0.8157 (t0) REVERT: A 171 GLU cc_start: 0.8957 (pp20) cc_final: 0.8484 (pm20) REVERT: A 252 TYR cc_start: 0.2612 (OUTLIER) cc_final: 0.1737 (p90) REVERT: A 279 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.4962 (m-10) REVERT: A 345 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7528 (t70) REVERT: A 376 MET cc_start: 0.8995 (tpt) cc_final: 0.8045 (ptp) REVERT: A 381 TYR cc_start: 0.5723 (OUTLIER) cc_final: 0.4114 (p90) REVERT: A 382 ASP cc_start: 0.9147 (t70) cc_final: 0.8346 (p0) REVERT: A 400 PHE cc_start: 0.8366 (t80) cc_final: 0.7958 (t80) REVERT: A 462 MET cc_start: 0.7371 (ppp) cc_final: 0.6989 (ppp) REVERT: A 579 MET cc_start: 0.6719 (ppp) cc_final: 0.5918 (ppp) outliers start: 28 outliers final: 15 residues processed: 103 average time/residue: 0.2016 time to fit residues: 27.5773 Evaluate side-chains 92 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 5 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.0370 chunk 37 optimal weight: 4.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 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 = 0.4549 r_free = 0.4549 target = 0.143253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.124809 restraints weight = 41939.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.126518 restraints weight = 34849.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.127823 restraints weight = 28578.913| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6635 Z= 0.198 Angle : 0.743 11.754 9012 Z= 0.369 Chirality : 0.049 0.515 946 Planarity : 0.006 0.064 1164 Dihedral : 10.201 92.794 980 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 4.69 % Allowed : 27.82 % Favored : 67.50 % 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: -2.37 (0.30), residues: 775 helix: -0.90 (0.35), residues: 247 sheet: 1.72 (1.08), residues: 24 loop : -2.23 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 168 HIS 0.009 0.001 HIS A 555 PHE 0.031 0.002 PHE A 452 TYR 0.014 0.002 TYR A 41 ARG 0.007 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7009 (mm) cc_final: 0.6376 (pt) REVERT: A 252 TYR cc_start: 0.3158 (OUTLIER) cc_final: 0.2284 (p90) REVERT: A 279 TYR cc_start: 0.5846 (OUTLIER) cc_final: 0.4880 (m-10) REVERT: A 323 MET cc_start: -0.0231 (mmt) cc_final: -0.0462 (mmt) REVERT: A 345 HIS cc_start: 0.8291 (OUTLIER) cc_final: 0.7769 (t70) REVERT: A 376 MET cc_start: 0.8966 (tpt) cc_final: 0.7988 (ptp) REVERT: A 462 MET cc_start: 0.7528 (ppp) cc_final: 0.7061 (ppp) REVERT: A 497 TYR cc_start: 0.7170 (t80) cc_final: 0.6785 (t80) REVERT: A 579 MET cc_start: 0.6670 (ppp) cc_final: 0.5247 (tpp) REVERT: B 484 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6535 (tm-30) REVERT: B 486 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6427 (t80) outliers start: 32 outliers final: 22 residues processed: 100 average time/residue: 0.1923 time to fit residues: 25.5503 Evaluate side-chains 97 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.0020 chunk 48 optimal weight: 0.0000 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.0570 chunk 17 optimal weight: 0.0470 chunk 74 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 46 optimal weight: 0.0370 overall best weight: 0.0266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.145836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.127172 restraints weight = 41490.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.128809 restraints weight = 34502.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.129857 restraints weight = 29152.045| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5372 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6635 Z= 0.168 Angle : 0.723 17.833 9012 Z= 0.351 Chirality : 0.048 0.474 946 Planarity : 0.005 0.062 1164 Dihedral : 8.476 81.319 980 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 4.39 % Allowed : 28.70 % Favored : 66.91 % 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: -2.30 (0.30), residues: 775 helix: -0.90 (0.34), residues: 255 sheet: 1.89 (1.04), residues: 24 loop : -2.18 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 566 HIS 0.016 0.002 HIS A 79 PHE 0.042 0.002 PHE A 72 TYR 0.008 0.001 TYR A 41 ARG 0.002 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.6930 (mm) cc_final: 0.6343 (pt) REVERT: A 171 GLU cc_start: 0.9109 (pp20) cc_final: 0.8695 (pm20) REVERT: A 203 TRP cc_start: 0.6578 (t-100) cc_final: 0.4829 (m-10) REVERT: A 252 TYR cc_start: 0.2813 (OUTLIER) cc_final: 0.2398 (p90) REVERT: A 279 TYR cc_start: 0.5895 (OUTLIER) cc_final: 0.4901 (m-10) REVERT: A 323 MET cc_start: -0.0422 (mmt) cc_final: -0.0625 (mmt) REVERT: A 376 MET cc_start: 0.9007 (tpt) cc_final: 0.7937 (ptp) REVERT: A 381 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.4117 (p90) REVERT: A 382 ASP cc_start: 0.9107 (t0) cc_final: 0.8286 (p0) REVERT: A 462 MET cc_start: 0.7504 (ppp) cc_final: 0.7114 (ppp) REVERT: A 579 MET cc_start: 0.6643 (ppp) cc_final: 0.5102 (tpp) REVERT: B 486 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6619 (t80) outliers start: 30 outliers final: 19 residues processed: 98 average time/residue: 0.1912 time to fit residues: 24.8992 Evaluate side-chains 95 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 83 TYR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 37 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 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 = 0.4512 r_free = 0.4512 target = 0.139499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.121454 restraints weight = 41936.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.123046 restraints weight = 33548.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.123923 restraints weight = 28289.949| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 6635 Z= 0.244 Angle : 0.790 13.929 9012 Z= 0.394 Chirality : 0.050 0.521 946 Planarity : 0.006 0.070 1164 Dihedral : 7.867 60.943 980 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 4.10 % Allowed : 29.43 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.30), residues: 775 helix: -0.90 (0.34), residues: 250 sheet: 1.66 (0.96), residues: 27 loop : -2.23 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 566 HIS 0.013 0.002 HIS A 345 PHE 0.027 0.002 PHE A 72 TYR 0.018 0.002 TYR B 351 ARG 0.007 0.001 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7244 (mm) cc_final: 0.6634 (pt) REVERT: A 171 GLU cc_start: 0.9103 (pp20) cc_final: 0.8724 (pm20) REVERT: A 211 TRP cc_start: 0.6067 (p90) cc_final: 0.5628 (p90) REVERT: A 249 MET cc_start: 0.5770 (mmm) cc_final: 0.5443 (mmt) REVERT: A 252 TYR cc_start: 0.4399 (OUTLIER) cc_final: 0.3732 (p90) REVERT: A 279 TYR cc_start: 0.6161 (OUTLIER) cc_final: 0.4936 (m-10) REVERT: A 381 TYR cc_start: 0.5702 (OUTLIER) cc_final: 0.4012 (p90) REVERT: A 462 MET cc_start: 0.7507 (ppp) cc_final: 0.7165 (ppp) REVERT: A 477 TRP cc_start: 0.5289 (m100) cc_final: 0.5005 (m-10) REVERT: A 497 TYR cc_start: 0.7210 (t80) cc_final: 0.6907 (t80) REVERT: A 579 MET cc_start: 0.7033 (ppp) cc_final: 0.6515 (ppp) REVERT: B 486 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6571 (t80) outliers start: 28 outliers final: 21 residues processed: 99 average time/residue: 0.1996 time to fit residues: 25.8274 Evaluate side-chains 94 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 0.0870 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 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 = 0.4533 r_free = 0.4533 target = 0.140895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.122564 restraints weight = 41769.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.124322 restraints weight = 33826.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.125363 restraints weight = 28206.598| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6635 Z= 0.183 Angle : 0.743 18.837 9012 Z= 0.363 Chirality : 0.048 0.491 946 Planarity : 0.005 0.065 1164 Dihedral : 7.142 53.580 980 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 4.83 % Allowed : 29.43 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.30), residues: 775 helix: -0.87 (0.33), residues: 256 sheet: 1.80 (0.98), residues: 27 loop : -2.18 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 566 HIS 0.006 0.001 HIS A 555 PHE 0.025 0.002 PHE A 452 TYR 0.012 0.002 TYR B 351 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.9046 (pp20) cc_final: 0.8736 (pm20) REVERT: A 249 MET cc_start: 0.5594 (mmm) cc_final: 0.5373 (mmt) REVERT: A 252 TYR cc_start: 0.4058 (OUTLIER) cc_final: 0.3379 (p90) REVERT: A 279 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.4754 (m-10) REVERT: A 376 MET cc_start: 0.8815 (tpt) cc_final: 0.7882 (ptp) REVERT: A 381 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.3929 (p90) REVERT: A 462 MET cc_start: 0.7543 (ppp) cc_final: 0.7271 (ppp) REVERT: A 464 PHE cc_start: 0.2478 (OUTLIER) cc_final: -0.0876 (t80) REVERT: A 477 TRP cc_start: 0.5189 (m100) cc_final: 0.4988 (m-10) REVERT: A 497 TYR cc_start: 0.6834 (t80) cc_final: 0.6534 (t80) REVERT: A 579 MET cc_start: 0.7116 (ppp) cc_final: 0.6562 (ppp) REVERT: B 486 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6633 (t80) outliers start: 33 outliers final: 26 residues processed: 100 average time/residue: 0.2076 time to fit residues: 27.1260 Evaluate side-chains 97 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 12 optimal weight: 0.0270 chunk 29 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 56 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.140905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.122520 restraints weight = 41684.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.124481 restraints weight = 33367.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.125445 restraints weight = 27867.956| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6635 Z= 0.176 Angle : 0.717 17.496 9012 Z= 0.356 Chirality : 0.048 0.502 946 Planarity : 0.005 0.064 1164 Dihedral : 6.628 53.069 980 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 5.12 % Allowed : 30.01 % Favored : 64.86 % 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: -2.24 (0.30), residues: 775 helix: -0.80 (0.34), residues: 250 sheet: 1.82 (0.99), residues: 27 loop : -2.18 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 566 HIS 0.014 0.002 HIS A 79 PHE 0.023 0.002 PHE A 452 TYR 0.015 0.001 TYR A 202 ARG 0.007 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1550 Ramachandran restraints generated. 775 Oldfield, 0 Emsley, 775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.7191 (mm) cc_final: 0.6556 (pt) REVERT: A 171 GLU cc_start: 0.9021 (pp20) cc_final: 0.8743 (pm20) REVERT: A 252 TYR cc_start: 0.4183 (OUTLIER) cc_final: 0.3584 (p90) REVERT: A 279 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.4725 (m-10) REVERT: A 376 MET cc_start: 0.8898 (tpt) cc_final: 0.8078 (ptp) REVERT: A 381 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.3709 (p90) REVERT: A 462 MET cc_start: 0.7498 (ppp) cc_final: 0.7280 (ppp) REVERT: A 464 PHE cc_start: 0.2182 (OUTLIER) cc_final: -0.1160 (t80) REVERT: A 579 MET cc_start: 0.7285 (ppp) cc_final: 0.6766 (ppp) REVERT: B 486 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6664 (t80) outliers start: 35 outliers final: 26 residues processed: 98 average time/residue: 0.1953 time to fit residues: 25.2602 Evaluate side-chains 95 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 TYR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.6498 > 50: distance: 47 - 57: 34.188 distance: 57 - 58: 43.369 distance: 58 - 59: 36.801 distance: 58 - 61: 48.107 distance: 59 - 60: 49.719 distance: 59 - 68: 14.424 distance: 60 - 92: 13.541 distance: 61 - 62: 8.377 distance: 62 - 63: 67.217 distance: 62 - 64: 62.817 distance: 63 - 65: 60.598 distance: 64 - 66: 54.312 distance: 65 - 67: 40.576 distance: 66 - 67: 41.476 distance: 68 - 69: 58.283 distance: 69 - 70: 49.279 distance: 69 - 72: 59.133 distance: 70 - 71: 43.576 distance: 70 - 77: 42.702 distance: 71 - 103: 49.172 distance: 72 - 73: 37.613 distance: 73 - 74: 40.234 distance: 74 - 75: 37.496 distance: 74 - 76: 40.723 distance: 77 - 78: 58.154 distance: 77 - 83: 19.907 distance: 78 - 79: 30.671 distance: 78 - 81: 18.988 distance: 79 - 80: 4.141 distance: 79 - 84: 39.871 distance: 81 - 82: 44.597 distance: 82 - 83: 20.111 distance: 84 - 85: 33.426 distance: 85 - 86: 57.127 distance: 85 - 88: 52.644 distance: 86 - 92: 35.830 distance: 87 - 124: 18.568 distance: 88 - 89: 40.551 distance: 89 - 90: 32.537 distance: 89 - 91: 45.630 distance: 92 - 93: 16.010 distance: 93 - 94: 46.080 distance: 93 - 96: 40.097 distance: 94 - 95: 41.694 distance: 94 - 103: 56.144 distance: 95 - 132: 41.295 distance: 96 - 97: 41.378 distance: 97 - 99: 23.327 distance: 98 - 100: 10.146 distance: 99 - 101: 43.639 distance: 100 - 102: 35.378 distance: 101 - 102: 24.413 distance: 103 - 104: 15.838 distance: 104 - 105: 37.285 distance: 104 - 107: 44.167 distance: 105 - 106: 26.891 distance: 105 - 110: 21.522 distance: 107 - 108: 14.353 distance: 107 - 109: 62.430 distance: 110 - 111: 7.789 distance: 111 - 112: 33.141 distance: 111 - 114: 30.953 distance: 112 - 113: 24.169 distance: 112 - 124: 16.211 distance: 114 - 115: 16.356 distance: 115 - 116: 13.874 distance: 115 - 117: 8.388 distance: 116 - 118: 19.647 distance: 117 - 119: 5.911 distance: 117 - 120: 4.103 distance: 118 - 119: 3.549 distance: 119 - 121: 4.223 distance: 120 - 122: 7.873 distance: 121 - 123: 4.997 distance: 122 - 123: 5.225 distance: 124 - 125: 25.377 distance: 125 - 126: 22.560 distance: 125 - 128: 19.183 distance: 126 - 127: 11.044 distance: 126 - 132: 57.444 distance: 128 - 129: 23.035 distance: 129 - 130: 6.405 distance: 129 - 131: 18.929 distance: 132 - 133: 16.615 distance: 133 - 134: 46.803 distance: 133 - 136: 51.383 distance: 134 - 135: 47.180 distance: 134 - 141: 14.605 distance: 136 - 137: 21.236 distance: 137 - 138: 29.000 distance: 138 - 139: 14.708 distance: 139 - 140: 12.573 distance: 141 - 142: 16.070 distance: 142 - 143: 29.095 distance: 142 - 145: 39.150 distance: 143 - 144: 51.156 distance: 143 - 150: 32.018 distance: 146 - 147: 37.991 distance: 147 - 148: 15.168 distance: 147 - 149: 28.441