Starting phenix.real_space_refine on Wed Feb 12 10:09:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jh5_36254/02_2025/8jh5_36254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jh5_36254/02_2025/8jh5_36254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jh5_36254/02_2025/8jh5_36254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jh5_36254/02_2025/8jh5_36254.map" model { file = "/net/cci-nas-00/data/ceres_data/8jh5_36254/02_2025/8jh5_36254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jh5_36254/02_2025/8jh5_36254.cif" } resolution = 3.7 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= 0.003 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5070 2.51 5 N 1266 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7734 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2957 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "C" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 893 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'NPS': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, B Time building chain proxies: 5.87, per 1000 atoms: 0.76 Number of scatterers: 7734 At special positions: 0 Unit cell: (106.7, 121, 96.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1342 8.00 N 1266 7.00 C 5070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " 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: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 8 sheets defined 48.6% alpha, 9.7% 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 3 through 13 removed outlier: 4.149A pdb=" N PHE A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 11 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 13 " --> pdb=" O HIS A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 30 removed outlier: 3.532A pdb=" N TYR A 18 " --> pdb=" O MET A 14 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 49 removed outlier: 4.120A pdb=" N ILE A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 43 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 removed outlier: 3.597A pdb=" N LEU A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 removed outlier: 4.010A pdb=" N LEU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.505A pdb=" N LEU A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.764A pdb=" N VAL A 137 " --> pdb=" O MET A 133 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.557A pdb=" N GLU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 474 removed outlier: 3.565A pdb=" N THR A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 474 " --> pdb=" O TRP A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.929A pdb=" N PHE A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.589A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.556A pdb=" N MET A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 529 " --> pdb=" O PHE A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 removed outlier: 3.657A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 removed outlier: 3.690A pdb=" N VAL A 554 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 575 Processing helix chain 'A' and resid 582 through 591 removed outlier: 3.636A pdb=" N ALA A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 608 removed outlier: 4.022A pdb=" N LEU A 598 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 621 removed outlier: 4.348A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 4.148A pdb=" N PHE B 7 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 30 removed outlier: 3.533A pdb=" N TYR B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 29 " --> pdb=" O TYR B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 4.120A pdb=" N ILE B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 43 " --> pdb=" O CYS B 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.597A pdb=" N LEU B 53 " --> pdb=" O PHE B 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 removed outlier: 4.009A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 116 through 123 removed outlier: 3.505A pdb=" N LEU B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.764A pdb=" N VAL B 137 " --> pdb=" O MET B 133 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.558A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 474 removed outlier: 3.566A pdb=" N THR B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 474 " --> pdb=" O TRP B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.929A pdb=" N PHE B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 486 " --> pdb=" O SER B 482 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS B 494 " --> pdb=" O LEU B 490 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 3.589A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 529 removed outlier: 3.556A pdb=" N MET B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 528 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN B 529 " --> pdb=" O PHE B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 removed outlier: 3.657A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 556 removed outlier: 3.689A pdb=" N VAL B 554 " --> pdb=" O VAL B 550 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 575 Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.636A pdb=" N ALA B 588 " --> pdb=" O PRO B 584 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 590 " --> pdb=" O VAL B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 608 removed outlier: 4.022A pdb=" N LEU B 598 " --> pdb=" O HIS B 594 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 603 " --> pdb=" O SER B 599 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 608 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 621 removed outlier: 4.348A pdb=" N LEU B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.563A pdb=" N GLN C 7 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA4, first strand: chain 'C' and resid 51 through 56 removed outlier: 6.623A pdb=" N TRP C 40 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA C 54 " --> pdb=" O MET C 38 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET C 38 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 41 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 99 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 11 removed outlier: 3.563A pdb=" N GLN D 7 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 15 through 16 Processing sheet with id=AA7, first strand: chain 'D' and resid 51 through 56 removed outlier: 6.623A pdb=" N TRP D 40 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA D 54 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET D 38 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 41 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR D 99 " --> pdb=" O TYR D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 109 removed outlier: 6.534A pdb=" N TRP D 107 " --> pdb=" O ALA B 194 " (cutoff:3.500A) 257 hydrogen bonds defined for protein. 750 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: 2.03 Time building geometry restraints manager: 2.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1178 1.30 - 1.43: 2126 1.43 - 1.55: 4515 1.55 - 1.68: 3 1.68 - 1.81: 100 Bond restraints: 7922 Sorted by residual: bond pdb=" CA ASN A 112 " pdb=" C ASN A 112 " ideal model delta sigma weight residual 1.526 1.438 0.087 1.30e-02 5.92e+03 4.52e+01 bond pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 1.526 1.438 0.087 1.30e-02 5.92e+03 4.52e+01 bond pdb=" CA PHE A 585 " pdb=" C PHE A 585 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.37e-02 5.33e+03 3.55e+01 bond pdb=" CA PHE B 585 " pdb=" C PHE B 585 " ideal model delta sigma weight residual 1.524 1.443 0.081 1.37e-02 5.33e+03 3.46e+01 bond pdb=" C PHE B 585 " pdb=" O PHE B 585 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.28e-02 6.10e+03 2.82e+01 ... (remaining 7917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 10722 4.60 - 9.21: 44 9.21 - 13.81: 2 13.81 - 18.41: 0 18.41 - 23.02: 4 Bond angle restraints: 10772 Sorted by residual: angle pdb=" O NPS A 701 " pdb=" C15 NPS A 701 " pdb=" OXT NPS A 701 " ideal model delta sigma weight residual 126.82 103.80 23.02 3.00e+00 1.11e-01 5.89e+01 angle pdb=" O NPS B 701 " pdb=" C15 NPS B 701 " pdb=" OXT NPS B 701 " ideal model delta sigma weight residual 126.82 103.82 23.00 3.00e+00 1.11e-01 5.88e+01 angle pdb=" O NPS B 701 " pdb=" C15 NPS B 701 " pdb=" C14 NPS B 701 " ideal model delta sigma weight residual 116.41 138.94 -22.53 3.00e+00 1.11e-01 5.64e+01 angle pdb=" O NPS A 701 " pdb=" C15 NPS A 701 " pdb=" C14 NPS A 701 " ideal model delta sigma weight residual 116.41 138.92 -22.51 3.00e+00 1.11e-01 5.63e+01 angle pdb=" N PHE A 585 " pdb=" CA PHE A 585 " pdb=" C PHE A 585 " ideal model delta sigma weight residual 112.45 104.66 7.79 1.39e+00 5.18e-01 3.14e+01 ... (remaining 10767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 4439 14.88 - 29.76: 147 29.76 - 44.64: 69 44.64 - 59.51: 6 59.51 - 74.39: 2 Dihedral angle restraints: 4663 sinusoidal: 1803 harmonic: 2860 Sorted by residual: dihedral pdb=" CA ILE D 35 " pdb=" C ILE D 35 " pdb=" N THR D 36 " pdb=" CA THR D 36 " ideal model delta harmonic sigma weight residual -180.00 -141.45 -38.55 0 5.00e+00 4.00e-02 5.95e+01 dihedral pdb=" CA ILE C 35 " pdb=" C ILE C 35 " pdb=" N THR C 36 " pdb=" CA THR C 36 " ideal model delta harmonic sigma weight residual -180.00 -141.46 -38.54 0 5.00e+00 4.00e-02 5.94e+01 dihedral pdb=" C ASN B 112 " pdb=" N ASN B 112 " pdb=" CA ASN B 112 " pdb=" CB ASN B 112 " ideal model delta harmonic sigma weight residual -122.60 -112.35 -10.25 0 2.50e+00 1.60e-01 1.68e+01 ... (remaining 4660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 614 0.035 - 0.070: 446 0.070 - 0.106: 123 0.106 - 0.141: 43 0.141 - 0.176: 20 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CB VAL B 557 " pdb=" CA VAL B 557 " pdb=" CG1 VAL B 557 " pdb=" CG2 VAL B 557 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CB VAL A 557 " pdb=" CA VAL A 557 " pdb=" CG1 VAL A 557 " pdb=" CG2 VAL A 557 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.63e-01 chirality pdb=" CB VAL D 6 " pdb=" CA VAL D 6 " pdb=" CG1 VAL D 6 " pdb=" CG2 VAL D 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 1243 not shown) Planarity restraints: 1320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 584 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C PRO B 584 " -0.049 2.00e-02 2.50e+03 pdb=" O PRO B 584 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE B 585 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 584 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C PRO A 584 " 0.049 2.00e-02 2.50e+03 pdb=" O PRO A 584 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 585 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 551 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO B 552 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 552 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 552 " -0.030 5.00e-02 4.00e+02 ... (remaining 1317 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 39 2.60 - 3.18: 6048 3.18 - 3.75: 10893 3.75 - 4.33: 15235 4.33 - 4.90: 24874 Nonbonded interactions: 57089 Sorted by model distance: nonbonded pdb=" SG CYS D 26 " pdb=" SG CYS D 100 " model vdw 2.031 3.760 nonbonded pdb=" NH2 ARG A 547 " pdb=" O ALA A 576 " model vdw 2.319 3.120 nonbonded pdb=" NH2 ARG B 547 " pdb=" O ALA B 576 " model vdw 2.319 3.120 nonbonded pdb=" NH2 ARG D 101 " pdb=" OE2 GLU B 191 " model vdw 2.344 3.120 nonbonded pdb=" ND2 ASN B 43 " pdb=" OG SER B 521 " model vdw 2.371 3.120 ... (remaining 57084 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.840 Find NCS groups from input model: 0.140 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: 27.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 : 0.006 0.090 7922 Z= 0.401 Angle : 0.965 23.015 10772 Z= 0.481 Chirality : 0.053 0.176 1246 Planarity : 0.007 0.053 1320 Dihedral : 9.929 74.392 2820 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -5.76 (0.20), residues: 976 helix: -4.77 (0.08), residues: 512 sheet: -1.41 (0.42), residues: 166 loop : -2.85 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 37 HIS 0.004 0.001 HIS A 9 PHE 0.022 0.002 PHE B 585 TYR 0.022 0.002 TYR C 56 ARG 0.003 0.001 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 ASN cc_start: 0.8810 (t0) cc_final: 0.8567 (t0) REVERT: A 196 ILE cc_start: 0.8605 (mt) cc_final: 0.8127 (mt) REVERT: A 468 MET cc_start: 0.8521 (mmm) cc_final: 0.8308 (mmm) REVERT: A 499 MET cc_start: 0.8561 (ttp) cc_final: 0.8353 (ttp) REVERT: A 519 MET cc_start: 0.8565 (mmt) cc_final: 0.8362 (mmm) REVERT: A 538 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7328 (tmt170) REVERT: A 575 GLN cc_start: 0.8996 (pp30) cc_final: 0.8721 (pp30) REVERT: A 599 SER cc_start: 0.9165 (p) cc_final: 0.8964 (p) REVERT: A 615 LEU cc_start: 0.8924 (tp) cc_final: 0.8673 (tp) REVERT: C 51 TRP cc_start: 0.7421 (m-10) cc_final: 0.7029 (m100) REVERT: C 76 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6818 (ttp-110) REVERT: D 42 ARG cc_start: 0.8649 (ptp-110) cc_final: 0.8426 (ptm160) REVERT: D 76 ARG cc_start: 0.7233 (ttp-170) cc_final: 0.6552 (ttp-170) REVERT: B 62 ASN cc_start: 0.8811 (t0) cc_final: 0.8568 (t0) REVERT: B 196 ILE cc_start: 0.8627 (mt) cc_final: 0.8156 (mt) REVERT: B 468 MET cc_start: 0.8523 (mmm) cc_final: 0.8295 (mmm) REVERT: B 499 MET cc_start: 0.8558 (ttp) cc_final: 0.8351 (ttp) REVERT: B 519 MET cc_start: 0.8552 (mmt) cc_final: 0.8292 (mmm) REVERT: B 615 LEU cc_start: 0.8936 (tp) cc_final: 0.8690 (tp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2554 time to fit residues: 74.6064 Evaluate side-chains 157 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 38 optimal weight: 50.0000 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 56 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 HIS A 43 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 HIS C 7 GLN B 9 HIS B 43 ASN B 127 ASN ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.146354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.098586 restraints weight = 12464.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.101580 restraints weight = 6622.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103446 restraints weight = 4474.518| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7922 Z= 0.376 Angle : 0.709 6.467 10772 Z= 0.366 Chirality : 0.046 0.144 1246 Planarity : 0.006 0.047 1320 Dihedral : 5.749 34.352 1084 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.62 % Allowed : 10.63 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -4.65 (0.22), residues: 976 helix: -3.48 (0.14), residues: 502 sheet: -0.87 (0.44), residues: 158 loop : -3.18 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 144 HIS 0.004 0.001 HIS A 9 PHE 0.028 0.002 PHE A 128 TYR 0.026 0.002 TYR C 56 ARG 0.007 0.001 ARG B 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 196 ILE cc_start: 0.8493 (mt) cc_final: 0.8133 (mt) REVERT: A 468 MET cc_start: 0.8840 (mmm) cc_final: 0.8436 (mmm) REVERT: A 517 MET cc_start: 0.7918 (mmm) cc_final: 0.7465 (ttm) REVERT: A 519 MET cc_start: 0.8689 (mmt) cc_final: 0.8471 (mmm) REVERT: A 538 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7209 (tmt170) REVERT: C 51 TRP cc_start: 0.7316 (m-10) cc_final: 0.6989 (m100) REVERT: C 76 ARG cc_start: 0.7302 (ttp-170) cc_final: 0.6592 (ttm110) REVERT: C 107 TRP cc_start: 0.7697 (m100) cc_final: 0.7411 (m100) REVERT: D 42 ARG cc_start: 0.8673 (ptp-110) cc_final: 0.8385 (ptp-110) REVERT: D 76 ARG cc_start: 0.7285 (ttp-170) cc_final: 0.5920 (ttp-110) REVERT: B 195 GLU cc_start: 0.7399 (tp30) cc_final: 0.7168 (tm-30) REVERT: B 196 ILE cc_start: 0.8474 (mt) cc_final: 0.7994 (mt) REVERT: B 468 MET cc_start: 0.8820 (mmm) cc_final: 0.8410 (mmm) REVERT: B 517 MET cc_start: 0.8041 (mmm) cc_final: 0.7630 (ttm) REVERT: B 519 MET cc_start: 0.8593 (mmt) cc_final: 0.8113 (mmt) REVERT: B 538 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7207 (tmt170) outliers start: 30 outliers final: 20 residues processed: 200 average time/residue: 0.1991 time to fit residues: 53.3258 Evaluate side-chains 169 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 47 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: B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.101411 restraints weight = 12487.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.104528 restraints weight = 6504.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.106602 restraints weight = 4335.745| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7922 Z= 0.187 Angle : 0.584 7.098 10772 Z= 0.294 Chirality : 0.042 0.135 1246 Planarity : 0.005 0.037 1320 Dihedral : 5.136 31.861 1084 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.02 % Allowed : 12.68 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.24), residues: 976 helix: -2.30 (0.19), residues: 494 sheet: -0.47 (0.44), residues: 142 loop : -2.67 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 37 HIS 0.002 0.000 HIS B 203 PHE 0.020 0.001 PHE A 128 TYR 0.022 0.002 TYR C 56 ARG 0.004 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8750 (p) REVERT: A 468 MET cc_start: 0.8868 (mmm) cc_final: 0.8215 (mmm) REVERT: A 517 MET cc_start: 0.7837 (mmm) cc_final: 0.7380 (ttm) REVERT: A 538 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7243 (tmt170) REVERT: A 616 TYR cc_start: 0.8386 (m-80) cc_final: 0.8006 (m-80) REVERT: C 51 TRP cc_start: 0.7286 (m-10) cc_final: 0.6805 (m-90) REVERT: C 76 ARG cc_start: 0.7067 (ttp-170) cc_final: 0.6635 (ttm170) REVERT: C 87 MET cc_start: 0.8771 (mmm) cc_final: 0.8401 (mmp) REVERT: D 42 ARG cc_start: 0.8641 (ptp-110) cc_final: 0.8418 (ptp-110) REVERT: D 71 ARG cc_start: 0.5175 (ttp-110) cc_final: 0.4841 (ttp-170) REVERT: D 76 ARG cc_start: 0.7405 (ttp-170) cc_final: 0.5875 (ttp-110) REVERT: B 168 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8757 (p) REVERT: B 196 ILE cc_start: 0.8505 (mt) cc_final: 0.8031 (mt) REVERT: B 468 MET cc_start: 0.8848 (mmm) cc_final: 0.8176 (mmm) REVERT: B 517 MET cc_start: 0.7957 (mmm) cc_final: 0.7320 (ttm) REVERT: B 519 MET cc_start: 0.8598 (mmt) cc_final: 0.8397 (mmm) REVERT: B 538 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7181 (tmt170) outliers start: 25 outliers final: 16 residues processed: 169 average time/residue: 0.2172 time to fit residues: 48.6549 Evaluate side-chains 159 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 64 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.148328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.100117 restraints weight = 12368.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.103172 restraints weight = 6498.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.105159 restraints weight = 4346.588| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7922 Z= 0.210 Angle : 0.584 7.567 10772 Z= 0.291 Chirality : 0.043 0.142 1246 Planarity : 0.004 0.033 1320 Dihedral : 4.987 31.013 1084 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.38 % Allowed : 12.56 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.25), residues: 976 helix: -1.69 (0.21), residues: 498 sheet: 1.05 (0.52), residues: 100 loop : -2.42 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 144 HIS 0.001 0.000 HIS B 203 PHE 0.017 0.001 PHE A 128 TYR 0.025 0.001 TYR D 56 ARG 0.003 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8737 (p) REVERT: A 468 MET cc_start: 0.8877 (mmm) cc_final: 0.8635 (mmm) REVERT: A 517 MET cc_start: 0.7808 (mmm) cc_final: 0.7419 (ttm) REVERT: A 538 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7325 (tmt170) REVERT: A 616 TYR cc_start: 0.8465 (m-80) cc_final: 0.8234 (m-80) REVERT: C 51 TRP cc_start: 0.7189 (m-10) cc_final: 0.6746 (m-90) REVERT: C 107 TRP cc_start: 0.7354 (m100) cc_final: 0.6952 (m100) REVERT: D 41 TYR cc_start: 0.7682 (p90) cc_final: 0.6716 (p90) REVERT: D 42 ARG cc_start: 0.8533 (ptp-110) cc_final: 0.8230 (ptm160) REVERT: B 168 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8745 (p) REVERT: B 195 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6483 (tm-30) REVERT: B 196 ILE cc_start: 0.8275 (mt) cc_final: 0.8032 (mt) REVERT: B 468 MET cc_start: 0.8877 (mmm) cc_final: 0.8626 (mmm) REVERT: B 517 MET cc_start: 0.8002 (mmm) cc_final: 0.7244 (ttm) REVERT: B 538 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7266 (tmt170) REVERT: B 616 TYR cc_start: 0.8441 (m-80) cc_final: 0.8186 (m-80) outliers start: 28 outliers final: 22 residues processed: 172 average time/residue: 0.2048 time to fit residues: 47.4849 Evaluate side-chains 166 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 562 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101853 restraints weight = 12411.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105002 restraints weight = 6563.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107122 restraints weight = 4430.286| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7922 Z= 0.164 Angle : 0.576 8.353 10772 Z= 0.282 Chirality : 0.042 0.145 1246 Planarity : 0.004 0.032 1320 Dihedral : 4.704 29.562 1084 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.50 % Allowed : 11.96 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.26), residues: 976 helix: -1.14 (0.22), residues: 496 sheet: -0.26 (0.45), residues: 140 loop : -2.25 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 37 HIS 0.001 0.000 HIS B 203 PHE 0.015 0.001 PHE A 128 TYR 0.025 0.001 TYR D 56 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 195 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6814 (tm-30) REVERT: A 468 MET cc_start: 0.8894 (mmm) cc_final: 0.8673 (mmm) REVERT: A 517 MET cc_start: 0.7812 (mmm) cc_final: 0.7539 (ttm) REVERT: A 538 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7290 (tmt170) REVERT: A 555 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7188 (tpp) REVERT: A 615 LEU cc_start: 0.8638 (tt) cc_final: 0.8368 (tt) REVERT: C 51 TRP cc_start: 0.7111 (m-10) cc_final: 0.6674 (m-90) REVERT: D 41 TYR cc_start: 0.7612 (p90) cc_final: 0.6592 (p90) REVERT: D 42 ARG cc_start: 0.8459 (ptp-110) cc_final: 0.8088 (ptm160) REVERT: B 168 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8674 (p) REVERT: B 195 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6417 (tm-30) REVERT: B 196 ILE cc_start: 0.8245 (mt) cc_final: 0.7971 (mt) REVERT: B 468 MET cc_start: 0.8894 (mmm) cc_final: 0.8669 (mmm) REVERT: B 538 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7236 (tmt170) REVERT: B 615 LEU cc_start: 0.8625 (tt) cc_final: 0.8356 (tt) outliers start: 29 outliers final: 22 residues processed: 169 average time/residue: 0.1940 time to fit residues: 44.5087 Evaluate side-chains 163 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 0.0980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.102607 restraints weight = 12299.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105765 restraints weight = 6435.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.107855 restraints weight = 4286.306| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7922 Z= 0.145 Angle : 0.561 7.770 10772 Z= 0.272 Chirality : 0.041 0.133 1246 Planarity : 0.004 0.032 1320 Dihedral : 4.479 28.291 1084 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.78 % Allowed : 13.53 % Favored : 83.70 % 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: -1.65 (0.27), residues: 976 helix: -0.65 (0.23), residues: 490 sheet: -0.18 (0.45), residues: 140 loop : -1.98 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 37 HIS 0.001 0.000 HIS B 203 PHE 0.013 0.001 PHE A 128 TYR 0.024 0.001 TYR C 56 ARG 0.002 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 195 GLU cc_start: 0.7152 (tm-30) cc_final: 0.6824 (tm-30) REVERT: A 538 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7249 (tmt170) REVERT: A 555 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7139 (tpp) REVERT: C 51 TRP cc_start: 0.7069 (m-10) cc_final: 0.6696 (m-90) REVERT: D 41 TYR cc_start: 0.7661 (p90) cc_final: 0.6785 (p90) REVERT: D 42 ARG cc_start: 0.8543 (ptp-110) cc_final: 0.8150 (ptm160) REVERT: B 168 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 195 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6563 (tm-30) REVERT: B 519 MET cc_start: 0.8580 (mmt) cc_final: 0.8272 (mmt) REVERT: B 538 ARG cc_start: 0.7648 (mtt180) cc_final: 0.7195 (tmt170) outliers start: 23 outliers final: 19 residues processed: 163 average time/residue: 0.1949 time to fit residues: 43.0467 Evaluate side-chains 158 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.148231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099004 restraints weight = 12469.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102093 restraints weight = 6651.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.104051 restraints weight = 4506.134| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7922 Z= 0.245 Angle : 0.611 9.187 10772 Z= 0.297 Chirality : 0.043 0.141 1246 Planarity : 0.004 0.032 1320 Dihedral : 4.650 27.873 1084 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.35 % Allowed : 13.04 % Favored : 82.61 % 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: -1.53 (0.27), residues: 976 helix: -0.51 (0.23), residues: 492 sheet: -0.11 (0.45), residues: 140 loop : -2.01 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.002 0.001 HIS A 176 PHE 0.014 0.001 PHE A 128 TYR 0.021 0.001 TYR C 56 ARG 0.002 0.000 ARG A 475 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.840 Fit side-chains REVERT: A 168 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8698 (p) REVERT: A 195 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 196 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8703 (mp) REVERT: A 538 ARG cc_start: 0.7698 (mtt180) cc_final: 0.7286 (tmt170) REVERT: A 555 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7178 (tpp) REVERT: A 615 LEU cc_start: 0.8637 (tt) cc_final: 0.8408 (tt) REVERT: C 49 ARG cc_start: 0.8361 (ptp-170) cc_final: 0.7868 (ptm160) REVERT: C 51 TRP cc_start: 0.6997 (m-10) cc_final: 0.6654 (m-90) REVERT: D 41 TYR cc_start: 0.7511 (p90) cc_final: 0.6297 (p90) REVERT: D 42 ARG cc_start: 0.8470 (ptp-110) cc_final: 0.8028 (ptm160) REVERT: D 49 ARG cc_start: 0.8454 (ptm160) cc_final: 0.8238 (ptm160) REVERT: D 87 MET cc_start: 0.7991 (mmm) cc_final: 0.7522 (mmm) REVERT: B 168 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8697 (p) REVERT: B 538 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7271 (tmt170) REVERT: B 615 LEU cc_start: 0.8634 (tt) cc_final: 0.8409 (tt) outliers start: 36 outliers final: 27 residues processed: 166 average time/residue: 0.1971 time to fit residues: 43.9262 Evaluate side-chains 168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 0.0980 chunk 80 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101396 restraints weight = 12447.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104522 restraints weight = 6470.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106670 restraints weight = 4320.282| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7922 Z= 0.155 Angle : 0.583 8.690 10772 Z= 0.280 Chirality : 0.042 0.142 1246 Planarity : 0.004 0.032 1320 Dihedral : 4.439 27.389 1084 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.14 % Allowed : 14.37 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.27), residues: 976 helix: -0.17 (0.24), residues: 496 sheet: 0.00 (0.46), residues: 140 loop : -1.87 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 37 HIS 0.001 0.000 HIS B 203 PHE 0.012 0.001 PHE A 128 TYR 0.021 0.001 TYR B 617 ARG 0.002 0.000 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.847 Fit side-chains REVERT: A 168 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8569 (p) REVERT: A 195 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6951 (tm-30) REVERT: A 196 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8687 (mp) REVERT: A 538 ARG cc_start: 0.7655 (mtt180) cc_final: 0.7270 (tmt170) REVERT: A 555 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7006 (tpp) REVERT: A 615 LEU cc_start: 0.8525 (tt) cc_final: 0.7333 (mp) REVERT: C 49 ARG cc_start: 0.8358 (ptp-170) cc_final: 0.7824 (ptm160) REVERT: C 51 TRP cc_start: 0.6907 (m-10) cc_final: 0.6652 (m-90) REVERT: C 103 LYS cc_start: 0.7155 (tttt) cc_final: 0.6836 (ptmm) REVERT: D 41 TYR cc_start: 0.7452 (p90) cc_final: 0.6584 (p90) REVERT: D 42 ARG cc_start: 0.8464 (ptp-110) cc_final: 0.8109 (ptm160) REVERT: B 168 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8555 (p) REVERT: B 195 GLU cc_start: 0.6520 (tm-30) cc_final: 0.6209 (tm-30) REVERT: B 519 MET cc_start: 0.8601 (mmt) cc_final: 0.8233 (mmt) REVERT: B 538 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7255 (tmt170) REVERT: B 615 LEU cc_start: 0.8515 (tt) cc_final: 0.7346 (mp) outliers start: 26 outliers final: 18 residues processed: 164 average time/residue: 0.2000 time to fit residues: 44.3985 Evaluate side-chains 163 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.150573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.100991 restraints weight = 12579.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.104196 restraints weight = 6619.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.106314 restraints weight = 4449.491| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7922 Z= 0.171 Angle : 0.598 10.009 10772 Z= 0.285 Chirality : 0.042 0.159 1246 Planarity : 0.004 0.031 1320 Dihedral : 4.429 27.792 1084 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.26 % Allowed : 15.22 % Favored : 81.52 % 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: -0.95 (0.28), residues: 976 helix: 0.01 (0.24), residues: 496 sheet: 0.10 (0.47), residues: 140 loop : -1.81 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.001 0.000 HIS B 203 PHE 0.012 0.001 PHE A 128 TYR 0.021 0.001 TYR A 617 ARG 0.001 0.000 ARG D 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 196 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8803 (mp) REVERT: A 538 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7266 (tmt170) REVERT: A 615 LEU cc_start: 0.8528 (tt) cc_final: 0.7342 (mp) REVERT: C 51 TRP cc_start: 0.6867 (m-10) cc_final: 0.6569 (m-90) REVERT: C 103 LYS cc_start: 0.7195 (tttt) cc_final: 0.6944 (ptmm) REVERT: D 41 TYR cc_start: 0.7493 (p90) cc_final: 0.6414 (p90) REVERT: D 42 ARG cc_start: 0.8479 (ptp-110) cc_final: 0.8095 (ptm160) REVERT: B 168 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8507 (p) REVERT: B 195 GLU cc_start: 0.6562 (tm-30) cc_final: 0.6286 (tm-30) REVERT: B 519 MET cc_start: 0.8645 (mmt) cc_final: 0.8130 (mmt) REVERT: B 538 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7245 (tmt170) REVERT: B 615 LEU cc_start: 0.8534 (tt) cc_final: 0.7363 (mp) outliers start: 27 outliers final: 22 residues processed: 159 average time/residue: 0.2116 time to fit residues: 44.8513 Evaluate side-chains 166 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 0.9980 chunk 85 optimal weight: 0.0980 chunk 94 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 39 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.152472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103215 restraints weight = 12371.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.106332 restraints weight = 6447.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.108510 restraints weight = 4339.676| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7922 Z= 0.144 Angle : 0.592 9.987 10772 Z= 0.281 Chirality : 0.041 0.146 1246 Planarity : 0.004 0.031 1320 Dihedral : 4.317 28.148 1084 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.90 % Allowed : 15.94 % Favored : 81.16 % 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: -0.61 (0.28), residues: 976 helix: 0.28 (0.25), residues: 490 sheet: 0.18 (0.47), residues: 140 loop : -1.55 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 37 HIS 0.001 0.000 HIS B 203 PHE 0.011 0.001 PHE A 128 TYR 0.021 0.001 TYR A 617 ARG 0.011 0.000 ARG D 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8445 (p) REVERT: A 196 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8794 (mp) REVERT: A 538 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7270 (tmt170) REVERT: A 555 MET cc_start: 0.8086 (tpp) cc_final: 0.7046 (tpp) REVERT: A 615 LEU cc_start: 0.8494 (tt) cc_final: 0.7307 (mp) REVERT: C 71 ARG cc_start: 0.5801 (ttp-170) cc_final: 0.5262 (ptt-90) REVERT: D 41 TYR cc_start: 0.7488 (p90) cc_final: 0.6645 (p90) REVERT: D 42 ARG cc_start: 0.8479 (ptp-110) cc_final: 0.8135 (ptm160) REVERT: D 78 ASN cc_start: 0.7614 (m-40) cc_final: 0.7321 (p0) REVERT: B 168 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8448 (p) REVERT: B 195 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6199 (tm-30) REVERT: B 538 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7259 (tmt170) REVERT: B 615 LEU cc_start: 0.8501 (tt) cc_final: 0.7319 (mp) outliers start: 24 outliers final: 18 residues processed: 167 average time/residue: 0.2226 time to fit residues: 48.9662 Evaluate side-chains 161 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 182 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 10 optimal weight: 0.0070 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN D 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.152116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.103033 restraints weight = 12392.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106237 restraints weight = 6460.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108376 restraints weight = 4323.268| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7922 Z= 0.148 Angle : 0.615 12.841 10772 Z= 0.291 Chirality : 0.042 0.144 1246 Planarity : 0.004 0.039 1320 Dihedral : 4.256 27.460 1084 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.14 % Allowed : 16.30 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.28), residues: 976 helix: 0.37 (0.25), residues: 494 sheet: 0.02 (0.45), residues: 162 loop : -1.47 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 37 HIS 0.001 0.000 HIS B 203 PHE 0.011 0.001 PHE A 128 TYR 0.024 0.001 TYR C 56 ARG 0.011 0.000 ARG D 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.98 seconds wall clock time: 47 minutes 59.62 seconds (2879.62 seconds total)