Starting phenix.real_space_refine on Sun Jul 27 23:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oji_12952/07_2025/7oji_12952_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oji_12952/07_2025/7oji_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_12952/07_2025/7oji_12952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oji_12952/07_2025/7oji_12952.map" model { file = "/net/cci-nas-00/data/ceres_data/7oji_12952/07_2025/7oji_12952_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oji_12952/07_2025/7oji_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.78, per 1000 atoms: 0.85 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: 3.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.07 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: 3.43 Time building geometry restraints manager: 3.21 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: 63.900 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 31.860 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.150 ------------------------------------------------------------------------------- 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 9404 Z= 0.656 Angle : 1.079 18.833 12759 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 Details of bonding type rmsd hydrogen bonds : bond 0.15782 ( 512) hydrogen bonds : angle 5.82729 ( 1482) SS BOND : bond 0.00857 ( 3) SS BOND : angle 2.14928 ( 6) covalent geometry : bond 0.01242 ( 9401) covalent geometry : angle 1.07856 (12753) *********************** 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 : 2.215 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: 0.4294 time to fit residues: 108.9993 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 : 1.155 ------------------------------------------------------------------------------- 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: 0.8980 chunk 89 optimal weight: 2.9990 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: 0.8580 ------------------------------------------------------------------------------- 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 271 GLN B 436 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.117319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.101427 restraints weight = 16073.753| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.90 r_work: 0.3275 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9404 Z= 0.136 Angle : 0.584 11.424 12759 Z= 0.299 Chirality : 0.041 0.142 1467 Planarity : 0.004 0.032 1542 Dihedral : 10.719 87.341 1649 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.74 % Allowed : 8.71 % Favored : 89.55 % 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: 0.99 (0.26), residues: 1128 helix: 1.96 (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 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.011 0.001 PHE B 591 TYR 0.016 0.001 TYR A 282 ARG 0.003 0.000 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.04922 ( 512) hydrogen bonds : angle 3.90907 ( 1482) SS BOND : bond 0.01181 ( 3) SS BOND : angle 2.01548 ( 6) covalent geometry : bond 0.00287 ( 9401) covalent geometry : angle 0.58268 (12753) *********************** 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 : 1.182 Fit side-chains REVERT: A 131 MET cc_start: 0.8115 (tpp) cc_final: 0.7819 (tpp) REVERT: A 226 LEU cc_start: 0.8467 (pp) cc_final: 0.8242 (pp) REVERT: A 446 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7930 (mt-10) REVERT: B 102 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 595 LEU cc_start: 0.5873 (OUTLIER) cc_final: 0.5549 (tt) outliers start: 17 outliers final: 7 residues processed: 109 average time/residue: 0.2193 time to fit residues: 35.0454 Evaluate side-chains 85 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.933 ------------------------------------------------------------------------------- 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 102 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 595 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 82 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 96 optimal weight: 0.0370 chunk 68 optimal weight: 9.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095639 restraints weight = 16531.650| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.94 r_work: 0.3175 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9404 Z= 0.175 Angle : 0.547 7.739 12759 Z= 0.283 Chirality : 0.041 0.131 1467 Planarity : 0.003 0.035 1542 Dihedral : 10.138 88.424 1645 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.05 % Allowed : 10.25 % Favored : 87.70 % 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: 1.14 (0.26), residues: 1128 helix: 2.09 (0.20), residues: 694 sheet: -0.69 (0.51), residues: 76 loop : -1.69 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 379 HIS 0.004 0.001 HIS A 40 PHE 0.011 0.001 PHE A 182 TYR 0.020 0.001 TYR A 282 ARG 0.003 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.05022 ( 512) hydrogen bonds : angle 3.65470 ( 1482) SS BOND : bond 0.00611 ( 3) SS BOND : angle 2.19750 ( 6) covalent geometry : bond 0.00415 ( 9401) covalent geometry : angle 0.54530 (12753) *********************** 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 106 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.948 Fit side-chains REVERT: A 71 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8096 (mmp) REVERT: A 131 MET cc_start: 0.8273 (tpp) cc_final: 0.7947 (tpp) REVERT: A 446 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 125 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8976 (p) REVERT: B 233 LYS cc_start: 0.8711 (tptm) cc_final: 0.8491 (ttmt) REVERT: B 614 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8925 (mp) outliers start: 20 outliers final: 9 residues processed: 99 average time/residue: 0.1777 time to fit residues: 26.4369 Evaluate side-chains 90 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 243 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 125 VAL 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 92 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 375 HIS B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094126 restraints weight = 16414.442| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.92 r_work: 0.3156 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.004 0.036 9404 Z= 0.174 Angle : 0.546 10.005 12759 Z= 0.279 Chirality : 0.041 0.133 1467 Planarity : 0.003 0.033 1542 Dihedral : 10.173 88.031 1645 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.36 % Allowed : 11.27 % 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: 1.18 (0.26), residues: 1128 helix: 2.07 (0.20), residues: 696 sheet: -0.55 (0.52), residues: 76 loop : -1.59 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.016 0.001 PHE A 385 TYR 0.011 0.001 TYR B 336 ARG 0.002 0.000 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 512) hydrogen bonds : angle 3.54848 ( 1482) SS BOND : bond 0.01342 ( 3) SS BOND : angle 2.62466 ( 6) covalent geometry : bond 0.00410 ( 9401) covalent geometry : angle 0.54295 (12753) *********************** 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: 23 poor density : 82 time to evaluate : 0.943 Fit side-chains REVERT: A 131 MET cc_start: 0.8313 (tpp) cc_final: 0.7991 (tpp) REVERT: A 226 LEU cc_start: 0.8533 (pp) cc_final: 0.8272 (pp) REVERT: B 525 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8671 (mp) outliers start: 23 outliers final: 11 residues processed: 96 average time/residue: 0.1739 time to fit residues: 25.1872 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 : 0.925 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 617 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 457 HIS B 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.094139 restraints weight = 16463.883| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.95 r_work: 0.3149 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9404 Z= 0.116 Angle : 0.490 7.901 12759 Z= 0.251 Chirality : 0.038 0.136 1467 Planarity : 0.003 0.030 1542 Dihedral : 9.926 88.194 1645 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.36 % Allowed : 11.48 % Favored : 86.17 % 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: 1.44 (0.26), residues: 1128 helix: 2.26 (0.20), residues: 696 sheet: -0.41 (0.54), residues: 76 loop : -1.46 (0.35), residues: 356 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 0.008 0.001 PHE A 385 TYR 0.010 0.001 TYR A 336 ARG 0.001 0.000 ARG B 236 Details of bonding type rmsd hydrogen bonds : bond 0.04159 ( 512) hydrogen bonds : angle 3.37173 ( 1482) SS BOND : bond 0.00603 ( 3) SS BOND : angle 1.63932 ( 6) covalent geometry : bond 0.00261 ( 9401) covalent geometry : angle 0.48899 (12753) *********************** 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 109 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 1.673 Fit side-chains REVERT: A 131 MET cc_start: 0.8353 (tpp) cc_final: 0.8037 (tpp) REVERT: A 226 LEU cc_start: 0.8547 (pp) cc_final: 0.7982 (mm) REVERT: A 385 PHE cc_start: 0.7183 (t80) cc_final: 0.6844 (t80) REVERT: A 386 LYS cc_start: 0.8657 (mttm) cc_final: 0.8411 (mttt) REVERT: B 525 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8646 (mp) REVERT: B 604 ASN cc_start: 0.6493 (OUTLIER) cc_final: 0.5258 (t0) REVERT: B 614 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8925 (mp) outliers start: 23 outliers final: 11 residues processed: 102 average time/residue: 0.2035 time to fit residues: 32.1282 Evaluate side-chains 92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 604 ASN 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 55 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.094512 restraints weight = 16483.092| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.93 r_work: 0.3172 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9404 Z= 0.132 Angle : 0.499 9.356 12759 Z= 0.255 Chirality : 0.039 0.135 1467 Planarity : 0.003 0.030 1542 Dihedral : 9.818 89.077 1645 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.46 % Allowed : 12.50 % Favored : 85.04 % 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: 1.58 (0.26), residues: 1128 helix: 2.36 (0.20), residues: 690 sheet: -0.23 (0.56), residues: 76 loop : -1.35 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.010 0.001 PHE B 495 TYR 0.009 0.001 TYR A 336 ARG 0.001 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 512) hydrogen bonds : angle 3.34136 ( 1482) SS BOND : bond 0.00517 ( 3) SS BOND : angle 1.52186 ( 6) covalent geometry : bond 0.00304 ( 9401) covalent geometry : angle 0.49764 (12753) *********************** 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: 24 poor density : 80 time to evaluate : 1.077 Fit side-chains REVERT: A 131 MET cc_start: 0.8286 (tpp) cc_final: 0.7956 (tpp) REVERT: A 385 PHE cc_start: 0.7342 (t80) cc_final: 0.7112 (t80) REVERT: B 525 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8650 (mp) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.2024 time to fit residues: 30.0104 Evaluate side-chains 92 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 243 HIS Chi-restraints excluded: chain A residue 283 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 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 451 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 617 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.093617 restraints weight = 16736.428| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.96 r_work: 0.3156 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9404 Z= 0.154 Angle : 0.517 10.073 12759 Z= 0.263 Chirality : 0.040 0.146 1467 Planarity : 0.003 0.029 1542 Dihedral : 9.772 87.996 1645 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.25 % Allowed : 12.60 % Favored : 85.14 % 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: 1.56 (0.26), residues: 1128 helix: 2.32 (0.20), residues: 696 sheet: -0.07 (0.56), residues: 76 loop : -1.40 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.006 0.001 HIS B 243 PHE 0.012 0.001 PHE A 506 TYR 0.010 0.001 TYR B 336 ARG 0.001 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 512) hydrogen bonds : angle 3.36171 ( 1482) SS BOND : bond 0.00476 ( 3) SS BOND : angle 1.58605 ( 6) covalent geometry : bond 0.00363 ( 9401) covalent geometry : angle 0.51559 (12753) *********************** 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 : 1.108 Fit side-chains REVERT: A 131 MET cc_start: 0.8331 (tpp) cc_final: 0.7974 (tpp) REVERT: A 385 PHE cc_start: 0.7457 (t80) cc_final: 0.7228 (t80) REVERT: B 525 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8659 (mp) outliers start: 22 outliers final: 17 residues processed: 95 average time/residue: 0.2008 time to fit residues: 29.1855 Evaluate side-chains 93 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.321 ------------------------------------------------------------------------------- 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 243 HIS Chi-restraints excluded: chain A residue 283 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 A residue 620 ASP 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 617 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.111212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.094605 restraints weight = 16886.694| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.93 r_work: 0.3164 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9404 Z= 0.119 Angle : 0.495 10.727 12759 Z= 0.251 Chirality : 0.038 0.140 1467 Planarity : 0.003 0.028 1542 Dihedral : 9.600 87.782 1645 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.36 % Allowed : 12.81 % Favored : 84.84 % 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: 1.68 (0.26), residues: 1128 helix: 2.40 (0.20), residues: 696 sheet: 0.12 (0.57), residues: 76 loop : -1.37 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.007 0.001 PHE A 506 TYR 0.010 0.001 TYR A 336 ARG 0.002 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 512) hydrogen bonds : angle 3.27861 ( 1482) SS BOND : bond 0.00807 ( 3) SS BOND : angle 1.67155 ( 6) covalent geometry : bond 0.00269 ( 9401) covalent geometry : angle 0.49384 (12753) *********************** 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 108 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.963 Fit side-chains REVERT: A 131 MET cc_start: 0.8282 (tpp) cc_final: 0.7983 (tpp) REVERT: B 525 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8657 (mp) REVERT: B 604 ASN cc_start: 0.6683 (OUTLIER) cc_final: 0.5544 (t0) outliers start: 23 outliers final: 16 residues processed: 100 average time/residue: 0.1813 time to fit residues: 27.1625 Evaluate side-chains 98 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 243 HIS Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 525 LEU 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 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 604 ASN Chi-restraints excluded: chain B residue 617 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 0.0040 chunk 3 optimal weight: 0.0980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093953 restraints weight = 16649.061| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.94 r_work: 0.3142 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9404 Z= 0.105 Angle : 0.486 11.106 12759 Z= 0.246 Chirality : 0.038 0.136 1467 Planarity : 0.003 0.028 1542 Dihedral : 9.452 89.190 1645 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.84 % Allowed : 13.52 % 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: 1.83 (0.26), residues: 1128 helix: 2.53 (0.20), residues: 690 sheet: 0.28 (0.58), residues: 76 loop : -1.30 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 379 HIS 0.006 0.001 HIS A 283 PHE 0.022 0.001 PHE B 432 TYR 0.009 0.001 TYR A 336 ARG 0.002 0.000 ARG A 193 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 512) hydrogen bonds : angle 3.22127 ( 1482) SS BOND : bond 0.00605 ( 3) SS BOND : angle 1.53738 ( 6) covalent geometry : bond 0.00233 ( 9401) covalent geometry : angle 0.48491 (12753) *********************** 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 100 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.083 Fit side-chains REVERT: A 131 MET cc_start: 0.8342 (tpp) cc_final: 0.8083 (tpp) REVERT: A 287 TYR cc_start: 0.7438 (m-80) cc_final: 0.7100 (m-80) REVERT: B 525 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8654 (mp) REVERT: B 604 ASN cc_start: 0.6715 (OUTLIER) cc_final: 0.5568 (t0) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.1861 time to fit residues: 26.5041 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 : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 525 LEU 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 Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 617 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.0370 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094930 restraints weight = 16850.960| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.95 r_work: 0.3142 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9404 Z= 0.107 Angle : 0.484 11.476 12759 Z= 0.244 Chirality : 0.038 0.137 1467 Planarity : 0.003 0.028 1542 Dihedral : 9.245 86.939 1645 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.05 % Allowed : 13.22 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.26), residues: 1128 helix: 2.48 (0.20), residues: 696 sheet: 0.41 (0.59), residues: 76 loop : -1.34 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.006 0.001 HIS A 283 PHE 0.021 0.001 PHE B 432 TYR 0.009 0.001 TYR A 336 ARG 0.002 0.000 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 512) hydrogen bonds : angle 3.18011 ( 1482) SS BOND : bond 0.00568 ( 3) SS BOND : angle 1.47677 ( 6) covalent geometry : bond 0.00243 ( 9401) covalent geometry : angle 0.48343 (12753) ********************** 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 102 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.952 Fit side-chains REVERT: A 131 MET cc_start: 0.8318 (tpp) cc_final: 0.8075 (tpp) REVERT: A 287 TYR cc_start: 0.7469 (m-80) cc_final: 0.7136 (m-80) REVERT: A 652 LYS cc_start: 0.8715 (mmtm) cc_final: 0.8279 (mptt) REVERT: B 525 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8653 (mp) REVERT: B 604 ASN cc_start: 0.6750 (OUTLIER) cc_final: 0.5681 (t0) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.1740 time to fit residues: 25.1208 Evaluate side-chains 96 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 178 VAL 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 Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 617 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 0.0010 chunk 10 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.108231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.091545 restraints weight = 16850.193| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.95 r_work: 0.3113 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 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 = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9404 Z= 0.189 Angle : 0.560 11.728 12759 Z= 0.283 Chirality : 0.041 0.136 1467 Planarity : 0.003 0.028 1542 Dihedral : 9.441 86.848 1645 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.36 % Allowed : 13.32 % 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: 1.71 (0.26), residues: 1128 helix: 2.38 (0.20), residues: 696 sheet: 0.31 (0.67), residues: 50 loop : -1.20 (0.34), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 379 HIS 0.007 0.001 HIS A 155 PHE 0.021 0.002 PHE B 432 TYR 0.011 0.001 TYR A 336 ARG 0.002 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 512) hydrogen bonds : angle 3.35983 ( 1482) SS BOND : bond 0.00698 ( 3) SS BOND : angle 1.98047 ( 6) covalent geometry : bond 0.00451 ( 9401) covalent geometry : angle 0.55798 (12753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6013.77 seconds wall clock time: 107 minutes 44.52 seconds (6464.52 seconds total)