Starting phenix.real_space_refine on Sun Dec 29 04:37:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oji_12952/12_2024/7oji_12952_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oji_12952/12_2024/7oji_12952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oji_12952/12_2024/7oji_12952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oji_12952/12_2024/7oji_12952.map" model { file = "/net/cci-nas-00/data/ceres_data/7oji_12952/12_2024/7oji_12952_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oji_12952/12_2024/7oji_12952_trim.cif" } resolution = 3.4 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= 0.005 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 58 5.16 5 C 5997 2.51 5 N 1483 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9195 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4453 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain breaks: 3 Chain: "B" Number of atoms: 4453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4453 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain breaks: 3 Chain: "A" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'ATP': 1, 'CLR': 2, 'PLC': 1, 'TTC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 1, 'CLR': 2, 'PLC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.01, per 1000 atoms: 0.76 Number of scatterers: 9195 At special positions: 0 Unit cell: (100.98, 91.74, 128.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 8 15.00 O 1649 8.00 N 1483 7.00 C 5997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.02 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " 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 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 923.0 milliseconds 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 64.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 116 through 119 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 169 Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.828A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.607A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.398A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.577A pdb=" N ILE A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.500A pdb=" N LYS A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.623A pdb=" N GLN A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 413 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 441 through 451 removed outlier: 3.525A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.510A pdb=" N TYR A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 498 removed outlier: 3.612A pdb=" N MET A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) Proline residue: A 485 - end of helix removed outlier: 4.757A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 529 Processing helix chain 'A' and resid 533 through 550 removed outlier: 3.880A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.529A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 removed outlier: 3.649A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 601 removed outlier: 3.918A pdb=" N ASN A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.542A pdb=" N TYR A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 650 removed outlier: 5.124A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 153 through 169 Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.829A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.606A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 281 removed outlier: 4.399A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.576A pdb=" N ILE B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.500A pdb=" N LYS B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 390 removed outlier: 3.623A pdb=" N GLN B 376 " --> pdb=" O SER B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 413 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 441 through 451 removed outlier: 3.525A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 465 through 477 removed outlier: 3.510A pdb=" N TYR B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 498 removed outlier: 3.612A pdb=" N MET B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) Proline residue: B 485 - end of helix removed outlier: 4.757A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 529 Processing helix chain 'B' and resid 533 through 550 removed outlier: 3.880A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.528A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 587 removed outlier: 3.649A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 601 removed outlier: 3.918A pdb=" N ASN B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.542A pdb=" N TYR B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 removed outlier: 5.123A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 71 removed outlier: 6.719A pdb=" N TYR A 44 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N SER A 65 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE A 42 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 67 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS A 40 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY A 69 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER A 38 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 6.245A pdb=" N LEU A 207 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N SER A 241 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 209 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLY A 74 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE A 240 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN A 76 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 71 removed outlier: 6.719A pdb=" N TYR B 44 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER B 65 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE B 42 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 67 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N HIS B 40 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY B 69 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER B 38 " --> pdb=" O GLY B 69 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 121 through 124 removed outlier: 6.245A pdb=" N LEU B 207 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N SER B 241 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 209 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY B 74 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N PHE B 240 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN B 76 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1414 1.31 - 1.44: 2486 1.44 - 1.57: 5370 1.57 - 1.69: 37 1.69 - 1.82: 94 Bond restraints: 9401 Sorted by residual: bond pdb=" C5 ATP A 705 " pdb=" N7 ATP A 705 " ideal model delta sigma weight residual 1.387 1.524 -0.137 1.00e-02 1.00e+04 1.88e+02 bond pdb=" C5 ATP B 704 " pdb=" N7 ATP B 704 " ideal model delta sigma weight residual 1.387 1.524 -0.137 1.00e-02 1.00e+04 1.86e+02 bond pdb=" C6 ATP B 704 " pdb=" N6 ATP B 704 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.10e-02 8.26e+03 1.06e+02 bond pdb=" C6 ATP A 705 " pdb=" N6 ATP A 705 " ideal model delta sigma weight residual 1.337 1.449 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" C4 ATP B 704 " pdb=" N9 ATP B 704 " ideal model delta sigma weight residual 1.374 1.272 0.102 1.00e-02 1.00e+04 1.04e+02 ... (remaining 9396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 12590 3.77 - 7.53: 109 7.53 - 11.30: 38 11.30 - 15.07: 9 15.07 - 18.83: 7 Bond angle restraints: 12753 Sorted by residual: angle pdb=" PB ATP B 704 " pdb=" O3B ATP B 704 " pdb=" PG ATP B 704 " ideal model delta sigma weight residual 139.87 121.04 18.83 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP A 705 " pdb=" O3B ATP A 705 " pdb=" PG ATP A 705 " ideal model delta sigma weight residual 139.87 122.31 17.56 1.00e+00 1.00e+00 3.08e+02 angle pdb=" C4 ATP B 704 " pdb=" N9 ATP B 704 " pdb=" C8 ATP B 704 " ideal model delta sigma weight residual 105.72 121.81 -16.09 1.00e+00 1.00e+00 2.59e+02 angle pdb=" C4 ATP A 705 " pdb=" N9 ATP A 705 " pdb=" C8 ATP A 705 " ideal model delta sigma weight residual 105.72 121.70 -15.98 1.00e+00 1.00e+00 2.55e+02 angle pdb=" PA ATP B 704 " pdb=" O3A ATP B 704 " pdb=" PB ATP B 704 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 ... (remaining 12748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.49: 5503 21.49 - 42.97: 274 42.97 - 64.46: 32 64.46 - 85.94: 9 85.94 - 107.43: 4 Dihedral angle restraints: 5822 sinusoidal: 2526 harmonic: 3296 Sorted by residual: dihedral pdb=" CA HIS B 283 " pdb=" C HIS B 283 " pdb=" N CYS B 284 " pdb=" CA CYS B 284 " ideal model delta harmonic sigma weight residual -180.00 -146.86 -33.14 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA HIS A 283 " pdb=" C HIS A 283 " pdb=" N CYS A 284 " pdb=" CA CYS A 284 " ideal model delta harmonic sigma weight residual -180.00 -146.92 -33.08 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA VAL B 493 " pdb=" C VAL B 493 " pdb=" N TYR B 494 " pdb=" CA TYR B 494 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.323: 1461 0.323 - 0.647: 4 0.647 - 0.970: 0 0.970 - 1.294: 0 1.294 - 1.617: 2 Chirality restraints: 1467 Sorted by residual: chirality pdb=" CG LEU B 595 " pdb=" CB LEU B 595 " pdb=" CD1 LEU B 595 " pdb=" CD2 LEU B 595 " both_signs ideal model delta sigma weight residual False -2.59 -0.97 -1.62 2.00e-01 2.50e+01 6.54e+01 chirality pdb=" CG LEU A 595 " pdb=" CB LEU A 595 " pdb=" CD1 LEU A 595 " pdb=" CD2 LEU A 595 " both_signs ideal model delta sigma weight residual False -2.59 -0.97 -1.62 2.00e-01 2.50e+01 6.52e+01 chirality pdb=" C21 TTC A 701 " pdb=" C16 TTC A 701 " pdb=" C20 TTC A 701 " pdb=" O24 TTC A 701 " both_signs ideal model delta sigma weight residual False -2.50 -2.98 0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 1464 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 TTC A 701 " 0.009 2.00e-02 2.50e+03 1.08e-02 6.46e+00 pdb=" C11 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C13 TTC A 701 " 0.009 2.00e-02 2.50e+03 pdb=" C14 TTC A 701 " 0.008 2.00e-02 2.50e+03 pdb=" C15 TTC A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C16 TTC A 701 " 0.019 2.00e-02 2.50e+03 pdb=" C17 TTC A 701 " 0.007 2.00e-02 2.50e+03 pdb=" C19 TTC A 701 " -0.007 2.00e-02 2.50e+03 pdb=" C2 TTC A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C21 TTC A 701 " -0.033 2.00e-02 2.50e+03 pdb=" C27 TTC A 701 " -0.022 2.00e-02 2.50e+03 pdb=" C3 TTC A 701 " 0.010 2.00e-02 2.50e+03 pdb=" C4 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C5 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C6 TTC A 701 " 0.004 2.00e-02 2.50e+03 pdb=" C7 TTC A 701 " -0.005 2.00e-02 2.50e+03 pdb=" C8 TTC A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C9 TTC A 701 " -0.002 2.00e-02 2.50e+03 pdb=" N10 TTC A 701 " -0.007 2.00e-02 2.50e+03 pdb=" N12 TTC A 701 " 0.006 2.00e-02 2.50e+03 pdb=" O18 TTC A 701 " -0.001 2.00e-02 2.50e+03 pdb=" O26 TTC A 701 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 211 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 212 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 211 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO B 212 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 212 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 212 " -0.020 5.00e-02 4.00e+02 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1825 2.77 - 3.30: 9201 3.30 - 3.83: 14441 3.83 - 4.37: 17140 4.37 - 4.90: 30112 Nonbonded interactions: 72719 Sorted by model distance: nonbonded pdb=" O GLY B 594 " pdb=" OG1 THR B 598 " model vdw 2.231 3.040 nonbonded pdb=" O GLY A 594 " pdb=" OG1 THR A 598 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP B 91 " pdb=" OH TYR B 123 " model vdw 2.297 3.040 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR A 123 " model vdw 2.298 3.040 nonbonded pdb=" O TYR B 336 " pdb=" OG SER B 339 " model vdw 2.312 3.040 ... (remaining 72714 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 'A' and (resid 34 through 654 or resid 702 through 703)) selection = (chain 'B' and (resid 34 through 654 or resid 702 through 703)) } 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=0.00 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: 4.440 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.820 Find NCS groups from input model: 0.400 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.012 0.195 9401 Z= 0.817 Angle : 1.079 18.833 12753 Z= 0.646 Chirality : 0.080 1.617 1467 Planarity : 0.004 0.037 1542 Dihedral : 12.846 107.428 3697 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.79 % Favored : 95.04 % Rotamer: Outliers : 0.41 % Allowed : 2.46 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.15 (0.24), residues: 1128 helix: 1.03 (0.19), residues: 672 sheet: -1.28 (0.50), residues: 82 loop : -1.91 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 379 HIS 0.004 0.001 HIS B 267 PHE 0.014 0.001 PHE A 448 TYR 0.014 0.002 TYR B 282 ARG 0.003 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 178 time to evaluate : 0.920 Fit side-chains REVERT: B 231 MET cc_start: 0.8750 (ttm) cc_final: 0.8520 (ttm) outliers start: 4 outliers final: 3 residues processed: 182 average time/residue: 0.2449 time to fit residues: 59.6812 Evaluate side-chains 92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 489 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 436 ASN B 436 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9401 Z= 0.191 Angle : 0.580 11.486 12753 Z= 0.296 Chirality : 0.041 0.167 1467 Planarity : 0.004 0.032 1542 Dihedral : 10.723 89.540 1649 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.74 % Allowed : 8.50 % Favored : 89.75 % 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: 1.00 (0.26), residues: 1128 helix: 1.97 (0.20), residues: 694 sheet: -0.86 (0.51), residues: 76 loop : -1.69 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE B 591 TYR 0.014 0.001 TYR A 282 ARG 0.003 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.042 Fit side-chains REVERT: A 131 MET cc_start: 0.7676 (tpp) cc_final: 0.7308 (tpp) REVERT: A 226 LEU cc_start: 0.8408 (pp) cc_final: 0.8176 (pp) REVERT: B 198 MET cc_start: 0.8536 (mtp) cc_final: 0.8332 (mtp) outliers start: 17 outliers final: 7 residues processed: 109 average time/residue: 0.2019 time to fit residues: 32.3879 Evaluate side-chains 83 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 592 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 271 GLN B 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9401 Z= 0.355 Angle : 0.611 7.806 12753 Z= 0.313 Chirality : 0.044 0.135 1467 Planarity : 0.004 0.037 1542 Dihedral : 10.411 89.242 1645 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.25 % Allowed : 10.25 % Favored : 87.50 % 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: 0.92 (0.25), residues: 1128 helix: 1.90 (0.19), residues: 694 sheet: -0.76 (0.51), residues: 76 loop : -1.74 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 379 HIS 0.005 0.002 HIS B 630 PHE 0.012 0.002 PHE B 506 TYR 0.016 0.001 TYR A 282 ARG 0.002 0.000 ARG B 426 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.035 Fit side-chains REVERT: A 131 MET cc_start: 0.7976 (tpp) cc_final: 0.7566 (tpp) REVERT: A 226 LEU cc_start: 0.8501 (pp) cc_final: 0.8204 (pp) REVERT: B 614 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8657 (mp) outliers start: 22 outliers final: 11 residues processed: 99 average time/residue: 0.1925 time to fit residues: 28.4366 Evaluate side-chains 89 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.3980 chunk 77 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS B 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9401 Z= 0.169 Angle : 0.505 10.087 12753 Z= 0.260 Chirality : 0.039 0.183 1467 Planarity : 0.003 0.032 1542 Dihedral : 10.086 88.885 1645 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.25 % Allowed : 11.68 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1128 helix: 2.14 (0.20), residues: 696 sheet: -0.46 (0.53), residues: 76 loop : -1.54 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.005 0.001 HIS A 457 PHE 0.010 0.001 PHE B 591 TYR 0.011 0.001 TYR A 336 ARG 0.002 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 1.088 Fit side-chains REVERT: A 131 MET cc_start: 0.7886 (tpp) cc_final: 0.7534 (tpp) REVERT: A 226 LEU cc_start: 0.8466 (pp) cc_final: 0.8179 (pp) REVERT: A 386 LYS cc_start: 0.8468 (mttm) cc_final: 0.8264 (mttt) REVERT: B 525 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8440 (mp) outliers start: 22 outliers final: 11 residues processed: 98 average time/residue: 0.1828 time to fit residues: 26.9686 Evaluate side-chains 87 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 457 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9401 Z= 0.274 Angle : 0.546 9.306 12753 Z= 0.279 Chirality : 0.040 0.145 1467 Planarity : 0.003 0.032 1542 Dihedral : 10.070 88.647 1645 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.15 % Allowed : 11.48 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.26), residues: 1128 helix: 2.17 (0.20), residues: 694 sheet: -0.40 (0.55), residues: 76 loop : -1.52 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE B 495 TYR 0.011 0.001 TYR A 336 ARG 0.001 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.001 Fit side-chains REVERT: A 131 MET cc_start: 0.8031 (tpp) cc_final: 0.7616 (tpp) REVERT: A 226 LEU cc_start: 0.8509 (pp) cc_final: 0.7940 (mm) REVERT: B 468 SER cc_start: 0.8863 (m) cc_final: 0.8649 (t) REVERT: B 525 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8430 (mp) REVERT: B 614 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8643 (mp) outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 0.1858 time to fit residues: 25.6207 Evaluate side-chains 87 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 614 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 283 HIS B 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9401 Z= 0.273 Angle : 0.536 9.468 12753 Z= 0.276 Chirality : 0.040 0.152 1467 Planarity : 0.003 0.032 1542 Dihedral : 9.906 88.336 1645 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.56 % Allowed : 11.68 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1128 helix: 2.20 (0.20), residues: 694 sheet: -0.28 (0.56), residues: 76 loop : -1.46 (0.35), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.008 0.001 HIS A 155 PHE 0.010 0.001 PHE A 448 TYR 0.010 0.001 TYR B 336 ARG 0.003 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.185 Fit side-chains REVERT: A 131 MET cc_start: 0.8086 (tpp) cc_final: 0.7617 (tpp) REVERT: A 226 LEU cc_start: 0.8522 (pp) cc_final: 0.7969 (mm) REVERT: B 468 SER cc_start: 0.8858 (m) cc_final: 0.8652 (t) REVERT: B 525 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8430 (mp) outliers start: 25 outliers final: 13 residues processed: 93 average time/residue: 0.2231 time to fit residues: 32.4837 Evaluate side-chains 91 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 109 optimal weight: 0.0170 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9401 Z= 0.202 Angle : 0.516 10.104 12753 Z= 0.263 Chirality : 0.039 0.135 1467 Planarity : 0.003 0.030 1542 Dihedral : 9.725 88.142 1645 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.25 % Allowed : 12.19 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1128 helix: 2.27 (0.20), residues: 696 sheet: -0.09 (0.57), residues: 76 loop : -1.40 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.014 0.002 HIS B 243 PHE 0.008 0.001 PHE A 432 TYR 0.011 0.001 TYR A 336 ARG 0.002 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.005 Fit side-chains REVERT: A 226 LEU cc_start: 0.8510 (pp) cc_final: 0.7960 (mm) REVERT: B 243 HIS cc_start: 0.7853 (OUTLIER) cc_final: 0.7525 (t-90) REVERT: B 468 SER cc_start: 0.8827 (m) cc_final: 0.8617 (t) REVERT: B 525 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8462 (mp) outliers start: 22 outliers final: 16 residues processed: 94 average time/residue: 0.1948 time to fit residues: 27.4323 Evaluate side-chains 94 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 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 283 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9401 Z= 0.167 Angle : 0.495 10.667 12753 Z= 0.251 Chirality : 0.038 0.136 1467 Planarity : 0.003 0.029 1542 Dihedral : 9.547 87.731 1645 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.25 % Allowed : 13.11 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1128 helix: 2.38 (0.20), residues: 696 sheet: 0.06 (0.59), residues: 76 loop : -1.36 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.012 0.001 HIS A 283 PHE 0.011 0.001 PHE A 506 TYR 0.010 0.001 TYR A 336 ARG 0.002 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.803 Fit side-chains REVERT: A 131 MET cc_start: 0.7898 (tpp) cc_final: 0.7498 (tpp) REVERT: A 226 LEU cc_start: 0.8501 (pp) cc_final: 0.7954 (mm) REVERT: B 468 SER cc_start: 0.8806 (m) cc_final: 0.8600 (t) REVERT: B 525 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8447 (mp) outliers start: 22 outliers final: 17 residues processed: 95 average time/residue: 0.1819 time to fit residues: 26.0926 Evaluate side-chains 94 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9401 Z= 0.313 Angle : 0.560 10.962 12753 Z= 0.284 Chirality : 0.041 0.140 1467 Planarity : 0.003 0.029 1542 Dihedral : 9.691 87.939 1645 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.46 % Allowed : 13.22 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 1128 helix: 2.28 (0.20), residues: 694 sheet: -0.11 (0.70), residues: 50 loop : -1.26 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.020 0.002 HIS A 283 PHE 0.014 0.001 PHE B 432 TYR 0.012 0.001 TYR A 282 ARG 0.001 0.000 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.961 Fit side-chains REVERT: A 131 MET cc_start: 0.7957 (tpp) cc_final: 0.7530 (tpp) REVERT: A 226 LEU cc_start: 0.8543 (pp) cc_final: 0.7998 (mm) REVERT: B 468 SER cc_start: 0.8857 (m) cc_final: 0.8643 (t) REVERT: B 525 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8421 (mp) outliers start: 24 outliers final: 18 residues processed: 94 average time/residue: 0.1908 time to fit residues: 26.5358 Evaluate side-chains 94 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9401 Z= 0.185 Angle : 0.499 11.682 12753 Z= 0.251 Chirality : 0.038 0.136 1467 Planarity : 0.003 0.029 1542 Dihedral : 9.343 86.706 1645 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.84 % Allowed : 14.04 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.26), residues: 1128 helix: 2.40 (0.20), residues: 696 sheet: 0.08 (0.71), residues: 50 loop : -1.17 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 379 HIS 0.006 0.001 HIS A 283 PHE 0.012 0.001 PHE B 432 TYR 0.010 0.001 TYR A 336 ARG 0.002 0.000 ARG B 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2256 Ramachandran restraints generated. 1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 1.090 Fit side-chains REVERT: A 131 MET cc_start: 0.7861 (tpp) cc_final: 0.7553 (tpp) REVERT: A 226 LEU cc_start: 0.8510 (pp) cc_final: 0.7971 (mm) REVERT: A 287 TYR cc_start: 0.7370 (m-80) cc_final: 0.7101 (m-80) REVERT: A 652 LYS cc_start: 0.8454 (mmtm) cc_final: 0.8140 (mptt) REVERT: B 468 SER cc_start: 0.8793 (m) cc_final: 0.8576 (t) REVERT: B 525 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8467 (mp) outliers start: 18 outliers final: 15 residues processed: 90 average time/residue: 0.1948 time to fit residues: 26.2410 Evaluate side-chains 92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091556 restraints weight = 16829.730| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.95 r_work: 0.3126 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9401 Z= 0.290 Angle : 0.546 11.387 12753 Z= 0.276 Chirality : 0.040 0.139 1467 Planarity : 0.003 0.029 1542 Dihedral : 9.426 86.554 1645 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.84 % Allowed : 13.93 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1128 helix: 2.33 (0.20), residues: 696 sheet: -0.00 (0.70), residues: 50 loop : -1.22 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 379 HIS 0.015 0.002 HIS A 283 PHE 0.013 0.001 PHE B 432 TYR 0.011 0.001 TYR A 282 ARG 0.001 0.000 ARG B 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.70 seconds wall clock time: 39 minutes 28.20 seconds (2368.20 seconds total)