Starting phenix.real_space_refine on Thu Nov 14 23:14:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/11_2024/8jh5_36254.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/11_2024/8jh5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/11_2024/8jh5_36254.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/11_2024/8jh5_36254.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/11_2024/8jh5_36254.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jh5_36254/11_2024/8jh5_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-5513/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: 5.49, per 1000 atoms: 0.71 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: 1.58 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: 0.77 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: 1.86 Time building geometry restraints manager: 1.88 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.770 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.280 Find NCS groups from input model: 0.220 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.580 ------------------------------------------------------------------------------- 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 : 0.985 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: 0.2548 time to fit residues: 74.3028 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 : 0.763 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.771 Fit side-chains revert: symmetry clash REVERT: A 196 ILE cc_start: 0.8524 (mt) cc_final: 0.8142 (mt) REVERT: A 468 MET cc_start: 0.8781 (mmm) cc_final: 0.8420 (mmm) REVERT: A 517 MET cc_start: 0.7908 (mmm) cc_final: 0.7511 (ttm) REVERT: A 538 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7230 (tmt170) REVERT: C 51 TRP cc_start: 0.7448 (m-10) cc_final: 0.7129 (m100) REVERT: C 76 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6507 (ttm110) REVERT: D 42 ARG cc_start: 0.8693 (ptp-110) cc_final: 0.8396 (ptp-110) REVERT: D 76 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.5842 (ttp-110) REVERT: B 195 GLU cc_start: 0.7409 (tp30) cc_final: 0.7194 (tm-30) REVERT: B 196 ILE cc_start: 0.8503 (mt) cc_final: 0.7992 (mt) REVERT: B 468 MET cc_start: 0.8758 (mmm) cc_final: 0.8385 (mmm) REVERT: B 517 MET cc_start: 0.8025 (mmm) cc_final: 0.7683 (ttm) REVERT: B 519 MET cc_start: 0.8524 (mmt) cc_final: 0.8113 (mmt) REVERT: B 538 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7224 (tmt170) outliers start: 30 outliers final: 20 residues processed: 200 average time/residue: 0.1994 time to fit residues: 53.5983 Evaluate side-chains 167 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 48 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.0060 chunk 70 optimal weight: 0.9980 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7922 Z= 0.138 Angle : 0.567 7.578 10772 Z= 0.284 Chirality : 0.041 0.147 1246 Planarity : 0.005 0.037 1320 Dihedral : 4.981 31.335 1084 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.05 % Allowed : 14.01 % Favored : 83.94 % 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: -3.17 (0.24), residues: 976 helix: -2.16 (0.19), residues: 498 sheet: 0.87 (0.52), residues: 100 loop : -2.73 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.002 0.000 HIS B 203 PHE 0.019 0.001 PHE A 128 TYR 0.023 0.001 TYR A 617 ARG 0.005 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 175 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 461 MET cc_start: 0.8056 (tpp) cc_final: 0.7770 (mtt) REVERT: A 468 MET cc_start: 0.8754 (mmm) cc_final: 0.8328 (mmm) REVERT: A 538 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7320 (tmt170) REVERT: C 51 TRP cc_start: 0.7259 (m-10) cc_final: 0.6829 (m-90) REVERT: C 76 ARG cc_start: 0.6866 (ttp-170) cc_final: 0.6482 (ttm170) REVERT: C 87 MET cc_start: 0.8706 (mmm) cc_final: 0.8358 (mmp) REVERT: D 41 TYR cc_start: 0.7840 (p90) cc_final: 0.6845 (p90) REVERT: D 42 ARG cc_start: 0.8677 (ptp-110) cc_final: 0.8397 (ptm160) REVERT: D 71 ARG cc_start: 0.4605 (ttp-110) cc_final: 0.4387 (ttp-170) REVERT: D 76 ARG cc_start: 0.7275 (ttp-170) cc_final: 0.5842 (ttp-110) REVERT: B 168 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8645 (p) REVERT: B 196 ILE cc_start: 0.8567 (mt) cc_final: 0.8057 (mt) REVERT: B 461 MET cc_start: 0.8052 (tpp) cc_final: 0.7764 (mtt) REVERT: B 468 MET cc_start: 0.8743 (mmm) cc_final: 0.8315 (mmm) REVERT: B 538 ARG cc_start: 0.7670 (mtt180) cc_final: 0.7253 (tmt170) outliers start: 17 outliers final: 9 residues processed: 169 average time/residue: 0.2241 time to fit residues: 50.3537 Evaluate side-chains 154 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 45 optimal weight: 20.0000 chunk 9 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.0020 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.6748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7922 Z= 0.161 Angle : 0.561 7.858 10772 Z= 0.278 Chirality : 0.042 0.148 1246 Planarity : 0.004 0.032 1320 Dihedral : 4.740 30.268 1084 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.66 % Allowed : 13.89 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.35 (0.25), residues: 976 helix: -1.37 (0.21), residues: 498 sheet: 1.04 (0.52), residues: 100 loop : -2.47 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 C 56 ARG 0.003 0.000 ARG B 463 *********************** 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 170 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.9075 (m-10) cc_final: 0.8852 (m-10) REVERT: A 168 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8628 (p) REVERT: A 468 MET cc_start: 0.8803 (mmm) cc_final: 0.8572 (mmm) REVERT: A 538 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7315 (tmt170) REVERT: A 616 TYR cc_start: 0.8352 (m-80) cc_final: 0.8115 (m-80) REVERT: C 51 TRP cc_start: 0.7369 (m-10) cc_final: 0.6875 (m-90) REVERT: D 41 TYR cc_start: 0.7731 (p90) cc_final: 0.6803 (p90) REVERT: D 42 ARG cc_start: 0.8546 (ptp-110) cc_final: 0.8194 (ptm160) REVERT: B 145 TYR cc_start: 0.9114 (m-10) cc_final: 0.8845 (m-10) REVERT: B 168 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8636 (p) REVERT: B 195 GLU cc_start: 0.6854 (tm-30) cc_final: 0.6556 (tm-30) REVERT: B 196 ILE cc_start: 0.8224 (mt) cc_final: 0.7964 (mt) REVERT: B 468 MET cc_start: 0.8798 (mmm) cc_final: 0.8571 (mmm) REVERT: B 517 MET cc_start: 0.7937 (mmm) cc_final: 0.7554 (ttm) REVERT: B 538 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7253 (tmt170) outliers start: 22 outliers final: 18 residues processed: 164 average time/residue: 0.2066 time to fit residues: 45.7153 Evaluate side-chains 159 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 557 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 72 PHE 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 555 MET Chi-restraints excluded: chain B residue 557 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 52 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7922 Z= 0.208 Angle : 0.574 8.652 10772 Z= 0.284 Chirality : 0.043 0.149 1246 Planarity : 0.004 0.032 1320 Dihedral : 4.691 29.002 1084 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.74 % Allowed : 13.65 % 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: -1.92 (0.26), residues: 976 helix: -1.01 (0.22), residues: 490 sheet: 1.07 (0.53), residues: 100 loop : -2.20 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 37 HIS 0.001 0.001 HIS A 570 PHE 0.015 0.001 PHE A 128 TYR 0.025 0.001 TYR C 56 ARG 0.002 0.000 ARG B 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 171 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.746 Fit side-chains REVERT: A 168 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8637 (p) REVERT: A 195 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6848 (tm-30) REVERT: A 468 MET cc_start: 0.8829 (mmm) cc_final: 0.8627 (mmm) REVERT: A 517 MET cc_start: 0.7782 (mmm) cc_final: 0.7493 (ttm) REVERT: A 538 ARG cc_start: 0.7790 (mtt180) cc_final: 0.7351 (tmt170) REVERT: C 51 TRP cc_start: 0.7214 (m-10) cc_final: 0.6803 (m-90) REVERT: D 41 TYR cc_start: 0.7681 (p90) cc_final: 0.6691 (p90) REVERT: D 42 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.8132 (ptm160) REVERT: B 145 TYR cc_start: 0.9109 (m-10) cc_final: 0.8893 (m-10) REVERT: B 168 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 195 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6417 (tm-30) REVERT: B 196 ILE cc_start: 0.8259 (mt) cc_final: 0.7968 (mt) REVERT: B 517 MET cc_start: 0.7961 (mmm) cc_final: 0.7391 (ttm) REVERT: B 538 ARG cc_start: 0.7694 (mtt180) cc_final: 0.7251 (tmt170) outliers start: 31 outliers final: 24 residues processed: 165 average time/residue: 0.1899 time to fit residues: 42.7713 Evaluate side-chains 165 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 142 ILE 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 557 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 72 PHE 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 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 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 83 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.0060 chunk 48 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7922 Z= 0.133 Angle : 0.544 7.829 10772 Z= 0.266 Chirality : 0.041 0.136 1246 Planarity : 0.004 0.030 1320 Dihedral : 4.410 28.696 1084 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.14 % Allowed : 14.49 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.27), residues: 976 helix: -0.49 (0.23), residues: 490 sheet: -0.16 (0.45), residues: 140 loop : -1.83 (0.34), residues: 346 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 0.024 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 172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8492 (p) REVERT: A 517 MET cc_start: 0.7719 (mmm) cc_final: 0.7371 (ttm) REVERT: A 538 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7299 (tmt170) REVERT: A 555 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7148 (tpp) REVERT: C 51 TRP cc_start: 0.7126 (m-10) cc_final: 0.6795 (m-90) REVERT: D 41 TYR cc_start: 0.7594 (p90) cc_final: 0.6939 (p90) REVERT: D 42 ARG cc_start: 0.8506 (ptp-110) cc_final: 0.8190 (ptm160) REVERT: B 168 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 195 GLU cc_start: 0.6741 (tm-30) cc_final: 0.6176 (tm-30) REVERT: B 196 ILE cc_start: 0.8261 (mt) cc_final: 0.7995 (mp) REVERT: B 517 MET cc_start: 0.7922 (mmm) cc_final: 0.7291 (ttm) REVERT: B 538 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7226 (tmt170) outliers start: 26 outliers final: 16 residues processed: 167 average time/residue: 0.1999 time to fit residues: 45.1457 Evaluate side-chains 156 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 142 ILE Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 555 MET 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 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 142 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 36 optimal weight: 0.0050 chunk 55 optimal weight: 8.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7922 Z= 0.205 Angle : 0.586 8.997 10772 Z= 0.285 Chirality : 0.043 0.141 1246 Planarity : 0.004 0.031 1320 Dihedral : 4.514 27.874 1084 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.62 % Allowed : 14.49 % Favored : 81.88 % 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: -1.33 (0.27), residues: 976 helix: -0.32 (0.24), residues: 492 sheet: -0.05 (0.45), residues: 140 loop : -1.96 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 37 HIS 0.001 0.000 HIS B 203 PHE 0.013 0.001 PHE A 128 TYR 0.025 0.001 TYR C 56 ARG 0.002 0.000 ARG A 471 *********************** 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 168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.860 Fit side-chains REVERT: A 168 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8566 (p) REVERT: A 517 MET cc_start: 0.7739 (mmm) cc_final: 0.7463 (ttm) REVERT: A 538 ARG cc_start: 0.7743 (mtt180) cc_final: 0.7296 (tmt170) REVERT: A 555 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7300 (tpp) REVERT: C 51 TRP cc_start: 0.7101 (m-10) cc_final: 0.6811 (m-90) REVERT: D 41 TYR cc_start: 0.7555 (p90) cc_final: 0.6513 (p90) REVERT: D 42 ARG cc_start: 0.8471 (ptp-110) cc_final: 0.8112 (ptm160) REVERT: D 87 MET cc_start: 0.7961 (mmm) cc_final: 0.7368 (mmm) REVERT: B 168 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8570 (p) REVERT: B 195 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6284 (tm-30) REVERT: B 196 ILE cc_start: 0.8279 (mt) cc_final: 0.8004 (mp) REVERT: B 517 MET cc_start: 0.7955 (mmm) cc_final: 0.7380 (ttm) REVERT: B 538 ARG cc_start: 0.7710 (mtt180) cc_final: 0.7240 (tmt170) outliers start: 30 outliers final: 23 residues processed: 160 average time/residue: 0.1921 time to fit residues: 42.0482 Evaluate side-chains 161 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 92 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 142 ILE 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 550 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 49 ARG 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 14 MET 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 619 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7922 Z= 0.186 Angle : 0.585 8.540 10772 Z= 0.283 Chirality : 0.042 0.140 1246 Planarity : 0.004 0.032 1320 Dihedral : 4.478 28.841 1084 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.50 % Allowed : 14.98 % 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: -1.13 (0.27), residues: 976 helix: -0.12 (0.24), residues: 492 sheet: 0.04 (0.46), residues: 140 loop : -1.92 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 37 HIS 0.001 0.000 HIS B 203 PHE 0.013 0.001 PHE A 128 TYR 0.025 0.001 TYR C 56 ARG 0.002 0.000 ARG A 471 *********************** 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: 29 poor density : 141 time to evaluate : 0.788 Fit side-chains REVERT: A 168 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8495 (p) REVERT: A 196 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8929 (mp) REVERT: A 517 MET cc_start: 0.7774 (mmm) cc_final: 0.7497 (ttm) REVERT: A 538 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7290 (tmt170) REVERT: A 555 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7204 (tpp) REVERT: C 51 TRP cc_start: 0.7029 (m-10) cc_final: 0.6804 (m-90) REVERT: D 41 TYR cc_start: 0.7696 (p90) cc_final: 0.6919 (p90) REVERT: D 42 ARG cc_start: 0.8472 (ptp-110) cc_final: 0.8152 (ptm160) REVERT: D 87 MET cc_start: 0.8171 (mmm) cc_final: 0.7919 (mmm) REVERT: B 168 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 195 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6297 (tm-30) REVERT: B 196 ILE cc_start: 0.8271 (mt) cc_final: 0.7999 (mp) REVERT: B 517 MET cc_start: 0.7977 (mmm) cc_final: 0.7378 (ttm) REVERT: B 538 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7283 (tmt170) outliers start: 29 outliers final: 23 residues processed: 161 average time/residue: 0.1991 time to fit residues: 42.7597 Evaluate side-chains 164 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 142 ILE 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 555 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 49 ARG 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 14 MET 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 Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4308 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= 0.204 Angle : 0.595 8.912 10772 Z= 0.287 Chirality : 0.043 0.164 1246 Planarity : 0.004 0.032 1320 Dihedral : 4.512 28.717 1084 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.99 % Allowed : 14.73 % Favored : 81.28 % 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: -1.01 (0.27), residues: 976 helix: -0.04 (0.24), residues: 494 sheet: 0.08 (0.46), residues: 140 loop : -1.83 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 37 HIS 0.001 0.001 HIS B 203 PHE 0.013 0.001 PHE A 128 TYR 0.028 0.001 TYR C 56 ARG 0.002 0.000 ARG A 471 *********************** 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 172 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.941 Fit side-chains REVERT: A 168 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8515 (p) REVERT: A 196 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8906 (mp) REVERT: A 517 MET cc_start: 0.7768 (mmm) cc_final: 0.7496 (ttm) REVERT: A 538 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7302 (tmt170) REVERT: A 555 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7200 (tpp) REVERT: C 51 TRP cc_start: 0.7005 (m-10) cc_final: 0.6673 (m-90) REVERT: D 41 TYR cc_start: 0.7690 (p90) cc_final: 0.6920 (p90) REVERT: D 42 ARG cc_start: 0.8462 (ptp-110) cc_final: 0.8144 (ptm160) REVERT: D 87 MET cc_start: 0.8298 (mmm) cc_final: 0.8021 (mmm) REVERT: B 168 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8527 (p) REVERT: B 195 GLU cc_start: 0.6765 (tm-30) cc_final: 0.6507 (tm-30) REVERT: B 517 MET cc_start: 0.8027 (mmm) cc_final: 0.7553 (ttm) REVERT: B 538 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7280 (tmt170) outliers start: 33 outliers final: 28 residues processed: 162 average time/residue: 0.1988 time to fit residues: 43.4390 Evaluate side-chains 168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 142 ILE 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 528 LEU Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 49 ARG 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 49 ARG Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain B residue 14 MET 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 Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.0030 chunk 88 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 overall best weight: 0.4768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4523 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 : 0.593 12.574 10772 Z= 0.285 Chirality : 0.041 0.157 1246 Planarity : 0.004 0.031 1320 Dihedral : 4.300 27.562 1084 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.26 % Allowed : 15.70 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.28), residues: 976 helix: 0.34 (0.25), residues: 488 sheet: 0.31 (0.47), residues: 140 loop : -1.54 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 37 HIS 0.001 0.000 HIS A 203 PHE 0.011 0.001 PHE A 128 TYR 0.024 0.001 TYR C 56 ARG 0.002 0.000 ARG A 531 ********************** 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: 27 poor density : 147 time to evaluate : 0.887 Fit side-chains REVERT: A 168 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8406 (p) REVERT: A 196 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8929 (mp) REVERT: A 517 MET cc_start: 0.7759 (mmm) cc_final: 0.7546 (ttm) REVERT: A 538 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7319 (tmt170) REVERT: C 51 TRP cc_start: 0.6855 (m-10) cc_final: 0.6644 (m-90) REVERT: D 41 TYR cc_start: 0.7550 (p90) cc_final: 0.6731 (p90) REVERT: D 42 ARG cc_start: 0.8436 (ptp-110) cc_final: 0.8105 (ptm160) REVERT: D 78 ASN cc_start: 0.7494 (m-40) cc_final: 0.7273 (p0) REVERT: B 168 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8407 (p) REVERT: B 538 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7272 (tmt170) REVERT: B 619 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8440 (mm) outliers start: 27 outliers final: 21 residues processed: 165 average time/residue: 0.2015 time to fit residues: 44.7409 Evaluate side-chains 168 residues out of total 828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 142 ILE 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 550 VAL Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 49 ARG 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 619 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.0470 chunk 9 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.152675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103733 restraints weight = 12241.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106887 restraints weight = 6423.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109053 restraints weight = 4334.044| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7922 Z= 0.140 Angle : 0.597 11.568 10772 Z= 0.285 Chirality : 0.041 0.146 1246 Planarity : 0.004 0.032 1320 Dihedral : 4.145 27.212 1084 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.78 % Allowed : 17.27 % Favored : 79.95 % 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: -0.33 (0.28), residues: 976 helix: 0.52 (0.25), residues: 488 sheet: 0.36 (0.47), residues: 140 loop : -1.46 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 37 HIS 0.001 0.000 HIS B 176 PHE 0.011 0.001 PHE A 128 TYR 0.025 0.001 TYR C 56 ARG 0.002 0.000 ARG C 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.61 seconds wall clock time: 33 minutes 47.06 seconds (2027.06 seconds total)