Starting phenix.real_space_refine on Sat Dec 28 04:57:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y9v_33693/12_2024/7y9v_33693_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y9v_33693/12_2024/7y9v_33693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y9v_33693/12_2024/7y9v_33693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y9v_33693/12_2024/7y9v_33693.map" model { file = "/net/cci-nas-00/data/ceres_data/7y9v_33693/12_2024/7y9v_33693_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y9v_33693/12_2024/7y9v_33693_neut.cif" } resolution = 3.2 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= 0.087 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 5062 2.51 5 N 1272 2.21 5 O 1344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7734 Number of models: 1 Model: "" Number of chains: 5 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: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: B, D Time building chain proxies: 5.79, per 1000 atoms: 0.75 Number of scatterers: 7734 At special positions: 0 Unit cell: (111.28, 119.6, 95.68, 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 1344 8.00 N 1272 7.00 C 5062 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: 1.83 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 6 sheets defined 55.3% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 5 through 30 removed outlier: 3.645A pdb=" N VAL A 10 " --> pdb=" O ASP A 6 " (cutoff:3.500A) Proline residue: A 16 - end of helix removed outlier: 3.620A pdb=" N ALA A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 49 removed outlier: 3.713A pdb=" N ILE A 42 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN A 43 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 44 " --> pdb=" O SER A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 91 removed outlier: 3.605A pdb=" N ALA A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 110 removed outlier: 3.685A pdb=" N THR A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 removed outlier: 3.609A pdb=" N LEU A 120 " --> pdb=" O MET A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 removed outlier: 4.109A pdb=" N VAL A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.517A pdb=" N LEU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 457 through 474 removed outlier: 3.988A pdb=" N ARG A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 removed outlier: 4.086A pdb=" N TYR A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 507 through 512 Processing helix chain 'A' and resid 513 through 529 removed outlier: 3.776A pdb=" N MET A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 547 removed outlier: 4.021A pdb=" N PHE A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 558 through 563 removed outlier: 3.876A pdb=" N GLY A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.543A pdb=" N HIS A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 592 Processing helix chain 'A' and resid 596 through 608 removed outlier: 4.052A pdb=" N VAL A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 608 " --> pdb=" O PHE A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 620 removed outlier: 3.504A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 30 removed outlier: 3.645A pdb=" N VAL B 10 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Proline residue: B 16 - end of helix removed outlier: 3.620A pdb=" N ALA B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 49 removed outlier: 3.713A pdb=" N ILE B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 43 " --> pdb=" O CYS B 39 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.604A pdb=" N ALA B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 110 removed outlier: 3.684A pdb=" N THR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 126 removed outlier: 3.608A pdb=" N LEU B 120 " --> pdb=" O MET B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 removed outlier: 4.109A pdb=" N VAL B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.518A pdb=" N LEU B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 457 through 474 removed outlier: 3.988A pdb=" N ARG B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 492 removed outlier: 4.087A pdb=" N TYR B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 513 through 529 removed outlier: 3.776A pdb=" N MET B 519 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 547 removed outlier: 4.020A pdb=" N PHE B 542 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 558 through 563 removed outlier: 3.876A pdb=" N GLY B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 577 removed outlier: 3.543A pdb=" N HIS B 570 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 592 Processing helix chain 'B' and resid 596 through 608 removed outlier: 4.052A pdb=" N VAL B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 608 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 620 removed outlier: 3.504A pdb=" N ILE B 612 " --> pdb=" O ILE B 608 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 removed outlier: 7.244A pdb=" N VAL A 204 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE A 175 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 206 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL A 177 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR C 107 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 99 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C 41 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU C 39 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP C 40 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU C 50 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.920A pdb=" N SER C 29 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C 11 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 25 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS C 26 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 83 " --> pdb=" O CYS C 26 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 77 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 14 through 17 removed outlier: 5.744A pdb=" N GLY C 14 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER C 118 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 16 " --> pdb=" O SER C 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 7 through 11 removed outlier: 3.921A pdb=" N SER D 29 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D 11 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 25 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS D 26 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 83 " --> pdb=" O CYS D 26 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP D 77 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 14 through 17 removed outlier: 5.744A pdb=" N GLY D 14 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N SER D 118 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 16 " --> pdb=" O SER D 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 50 through 54 removed outlier: 4.144A pdb=" N GLU D 50 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP D 40 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 39 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 41 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR D 99 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TYR D 107 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE B 196 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG D 109 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B 204 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE B 175 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 206 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL B 177 " --> pdb=" O VAL B 206 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 996 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: 2.09 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1180 1.27 - 1.41: 2058 1.41 - 1.54: 4482 1.54 - 1.67: 96 1.67 - 1.80: 100 Bond restraints: 7916 Sorted by residual: bond pdb=" CA LEU B 147 " pdb=" C LEU B 147 " ideal model delta sigma weight residual 1.519 1.361 0.158 1.01e-02 9.80e+03 2.46e+02 bond pdb=" CA LEU A 147 " pdb=" C LEU A 147 " ideal model delta sigma weight residual 1.519 1.361 0.158 1.01e-02 9.80e+03 2.46e+02 bond pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 1.526 1.405 0.121 1.11e-02 8.12e+03 1.19e+02 bond pdb=" CA ASN A 112 " pdb=" C ASN A 112 " ideal model delta sigma weight residual 1.526 1.406 0.121 1.11e-02 8.12e+03 1.18e+02 bond pdb=" CA ALA B 561 " pdb=" C ALA B 561 " ideal model delta sigma weight residual 1.522 1.421 0.101 1.39e-02 5.18e+03 5.31e+01 ... (remaining 7911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 10466 3.17 - 6.34: 252 6.34 - 9.51: 32 9.51 - 12.69: 8 12.69 - 15.86: 4 Bond angle restraints: 10762 Sorted by residual: angle pdb=" N SER A 479 " pdb=" CA SER A 479 " pdb=" C SER A 479 " ideal model delta sigma weight residual 114.04 98.18 15.86 1.24e+00 6.50e-01 1.64e+02 angle pdb=" N SER B 479 " pdb=" CA SER B 479 " pdb=" C SER B 479 " ideal model delta sigma weight residual 114.04 98.19 15.85 1.24e+00 6.50e-01 1.63e+02 angle pdb=" N LEU A 147 " pdb=" CA LEU A 147 " pdb=" C LEU A 147 " ideal model delta sigma weight residual 112.72 98.40 14.32 1.28e+00 6.10e-01 1.25e+02 angle pdb=" N LEU B 147 " pdb=" CA LEU B 147 " pdb=" C LEU B 147 " ideal model delta sigma weight residual 112.72 98.45 14.27 1.28e+00 6.10e-01 1.24e+02 angle pdb=" C ASN A 112 " pdb=" CA ASN A 112 " pdb=" CB ASN A 112 " ideal model delta sigma weight residual 112.05 102.06 9.99 1.52e+00 4.33e-01 4.32e+01 ... (remaining 10757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 4406 16.93 - 33.85: 197 33.85 - 50.78: 44 50.78 - 67.71: 2 67.71 - 84.63: 4 Dihedral angle restraints: 4653 sinusoidal: 1791 harmonic: 2862 Sorted by residual: dihedral pdb=" CA GLN C 56 " pdb=" C GLN C 56 " pdb=" N SER C 57 " pdb=" CA SER C 57 " ideal model delta harmonic sigma weight residual -180.00 -138.53 -41.47 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA GLN D 56 " pdb=" C GLN D 56 " pdb=" N SER D 57 " pdb=" CA SER D 57 " ideal model delta harmonic sigma weight residual -180.00 -138.55 -41.45 0 5.00e+00 4.00e-02 6.87e+01 dihedral pdb=" C LEU A 147 " pdb=" N LEU A 147 " pdb=" CA LEU A 147 " pdb=" CB LEU A 147 " ideal model delta harmonic sigma weight residual -122.60 -107.71 -14.89 0 2.50e+00 1.60e-01 3.55e+01 ... (remaining 4650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 939 0.065 - 0.130: 253 0.130 - 0.196: 44 0.196 - 0.261: 7 0.261 - 0.326: 3 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CB ILE C 55 " pdb=" CA ILE C 55 " pdb=" CG1 ILE C 55 " pdb=" CG2 ILE C 55 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE D 55 " pdb=" CA ILE D 55 " pdb=" CG1 ILE D 55 " pdb=" CG2 ILE D 55 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE D 35 " pdb=" CA ILE D 35 " pdb=" CG1 ILE D 35 " pdb=" CG2 ILE D 35 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1243 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 551 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO A 552 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 551 " -0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO B 552 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 552 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 552 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 140 " -0.013 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C GLN A 140 " 0.043 2.00e-02 2.50e+03 pdb=" O GLN A 140 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS A 141 " -0.015 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 66 2.60 - 3.18: 6227 3.18 - 3.75: 11267 3.75 - 4.33: 16526 4.33 - 4.90: 27084 Nonbonded interactions: 61170 Sorted by model distance: nonbonded pdb=" SG CYS D 26 " pdb=" SG CYS D 100 " model vdw 2.030 3.760 nonbonded pdb=" NH2 ARG D 71 " pdb=" O SER D 89 " model vdw 2.057 3.120 nonbonded pdb=" NH2 ARG C 71 " pdb=" O SER C 89 " model vdw 2.057 3.120 nonbonded pdb=" NE1 TRP D 37 " pdb=" OE2 GLU D 39 " model vdw 2.227 3.120 nonbonded pdb=" NE1 TRP C 37 " pdb=" OE2 GLU C 39 " model vdw 2.228 3.120 ... (remaining 61165 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.450 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.013 0.158 7916 Z= 0.860 Angle : 1.209 15.856 10762 Z= 0.690 Chirality : 0.063 0.326 1246 Planarity : 0.009 0.066 1322 Dihedral : 10.859 84.631 2810 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.48 % Allowed : 3.13 % Favored : 96.39 % Cbeta Deviations : 0.65 % 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: -5.91 (0.18), residues: 976 helix: -4.55 (0.09), residues: 540 sheet: -2.50 (0.46), residues: 116 loop : -2.74 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 31 HIS 0.006 0.002 HIS B 594 PHE 0.021 0.003 PHE B 58 TYR 0.034 0.003 TYR A 617 ARG 0.013 0.001 ARG D 109 *********************** 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 190 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 0.812 Fit side-chains REVERT: A 32 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8376 (mmtt) REVERT: A 122 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8307 (mtpp) REVERT: A 147 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8377 (tp) REVERT: A 181 ILE cc_start: 0.8457 (mt) cc_final: 0.8224 (mt) REVERT: A 201 LYS cc_start: 0.7289 (mttt) cc_final: 0.6916 (mmtt) REVERT: A 459 SER cc_start: 0.8610 (t) cc_final: 0.8205 (p) REVERT: A 505 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8356 (mmmt) REVERT: A 512 ASP cc_start: 0.8374 (m-30) cc_final: 0.7925 (m-30) REVERT: C 55 ILE cc_start: 0.7367 (tp) cc_final: 0.7102 (tt) REVERT: B 9 HIS cc_start: 0.8203 (m-70) cc_final: 0.7902 (m170) REVERT: B 29 LYS cc_start: 0.7516 (tppt) cc_final: 0.7224 (tppt) REVERT: B 32 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8204 (mmtm) REVERT: B 122 LYS cc_start: 0.8627 (ttmt) cc_final: 0.8303 (mtpp) REVERT: B 181 ILE cc_start: 0.8458 (mt) cc_final: 0.8236 (mt) REVERT: B 201 LYS cc_start: 0.7210 (mttt) cc_final: 0.6783 (mmtt) REVERT: B 459 SER cc_start: 0.8487 (t) cc_final: 0.8204 (p) REVERT: B 467 ILE cc_start: 0.8984 (mm) cc_final: 0.8641 (mt) REVERT: B 505 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8313 (mmmt) REVERT: B 512 ASP cc_start: 0.8358 (m-30) cc_final: 0.7759 (m-30) outliers start: 4 outliers final: 0 residues processed: 188 average time/residue: 0.2602 time to fit residues: 62.0285 Evaluate side-chains 129 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 75 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 164 GLN B 43 ASN B 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7916 Z= 0.202 Angle : 0.639 6.971 10762 Z= 0.335 Chirality : 0.043 0.149 1246 Planarity : 0.006 0.045 1322 Dihedral : 6.855 83.544 1074 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.45 % Allowed : 9.88 % Favored : 88.67 % 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: -3.71 (0.23), residues: 976 helix: -2.45 (0.18), residues: 544 sheet: -2.36 (0.44), residues: 124 loop : -2.02 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 40 HIS 0.002 0.001 HIS A 203 PHE 0.015 0.002 PHE D 72 TYR 0.014 0.001 TYR C 41 ARG 0.006 0.001 ARG B 207 *********************** 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 159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.869 Fit side-chains REVERT: A 1 MET cc_start: 0.5593 (ppp) cc_final: 0.5301 (ppp) REVERT: A 21 MET cc_start: 0.8590 (ttp) cc_final: 0.8241 (ttt) REVERT: A 29 LYS cc_start: 0.7814 (tppt) cc_final: 0.7362 (tppt) REVERT: A 32 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8373 (mmtt) REVERT: A 201 LYS cc_start: 0.7286 (mttt) cc_final: 0.6799 (mmtt) REVERT: A 208 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7319 (mmm-85) REVERT: A 459 SER cc_start: 0.8482 (t) cc_final: 0.8242 (p) REVERT: A 505 LYS cc_start: 0.8457 (mmtp) cc_final: 0.8167 (mmmt) REVERT: A 512 ASP cc_start: 0.8206 (m-30) cc_final: 0.7828 (m-30) REVERT: A 517 MET cc_start: 0.8327 (mmm) cc_final: 0.8102 (mmm) REVERT: A 554 VAL cc_start: 0.8510 (p) cc_final: 0.8280 (p) REVERT: C 56 GLN cc_start: 0.6788 (pp30) cc_final: 0.6327 (pt0) REVERT: D 56 GLN cc_start: 0.7423 (pp30) cc_final: 0.7219 (pt0) REVERT: B 1 MET cc_start: 0.5430 (ppp) cc_final: 0.5081 (ppp) REVERT: B 21 MET cc_start: 0.8538 (ttp) cc_final: 0.8271 (ttt) REVERT: B 32 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8296 (mmtt) REVERT: B 173 VAL cc_start: 0.9021 (t) cc_final: 0.8678 (m) REVERT: B 201 LYS cc_start: 0.7035 (mttt) cc_final: 0.6543 (mmtt) REVERT: B 208 ARG cc_start: 0.7927 (mmm-85) cc_final: 0.7325 (mmm-85) REVERT: B 467 ILE cc_start: 0.8888 (mm) cc_final: 0.8516 (mt) REVERT: B 505 LYS cc_start: 0.8506 (mmtp) cc_final: 0.8204 (mmmt) REVERT: B 512 ASP cc_start: 0.8180 (m-30) cc_final: 0.7839 (m-30) REVERT: B 517 MET cc_start: 0.8284 (mmm) cc_final: 0.8000 (mmm) outliers start: 12 outliers final: 7 residues processed: 155 average time/residue: 0.2184 time to fit residues: 45.2047 Evaluate side-chains 135 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 479 SER 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: 0.5980 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7916 Z= 0.205 Angle : 0.558 5.702 10762 Z= 0.292 Chirality : 0.042 0.146 1246 Planarity : 0.005 0.043 1322 Dihedral : 6.174 77.767 1072 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.05 % Allowed : 10.84 % Favored : 87.11 % 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: -2.64 (0.25), residues: 976 helix: -1.26 (0.21), residues: 540 sheet: -2.40 (0.39), residues: 164 loop : -1.83 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 40 HIS 0.006 0.001 HIS A 57 PHE 0.011 0.001 PHE B 585 TYR 0.013 0.001 TYR C 41 ARG 0.003 0.000 ARG B 207 *********************** 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 154 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.787 Fit side-chains REVERT: A 21 MET cc_start: 0.8598 (ttp) cc_final: 0.8317 (ttt) REVERT: A 29 LYS cc_start: 0.7795 (tppt) cc_final: 0.7526 (ttmt) REVERT: A 32 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8395 (mmtt) REVERT: A 461 MET cc_start: 0.8415 (mmm) cc_final: 0.8170 (tpp) REVERT: A 467 ILE cc_start: 0.8858 (mm) cc_final: 0.8457 (mt) REVERT: A 505 LYS cc_start: 0.8410 (mmtp) cc_final: 0.8149 (mmmt) REVERT: A 512 ASP cc_start: 0.8166 (m-30) cc_final: 0.7894 (m-30) REVERT: A 517 MET cc_start: 0.8303 (mmm) cc_final: 0.8051 (mmm) REVERT: A 521 SER cc_start: 0.8283 (t) cc_final: 0.8074 (t) REVERT: C 56 GLN cc_start: 0.6759 (pp30) cc_final: 0.6414 (pt0) REVERT: D 56 GLN cc_start: 0.7394 (pp30) cc_final: 0.6994 (pt0) REVERT: B 1 MET cc_start: 0.5567 (ppp) cc_final: 0.5262 (ppp) REVERT: B 21 MET cc_start: 0.8544 (ttp) cc_final: 0.8257 (ttt) REVERT: B 32 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8277 (mmtt) REVERT: B 173 VAL cc_start: 0.9098 (t) cc_final: 0.8736 (m) REVERT: B 201 LYS cc_start: 0.7147 (mttt) cc_final: 0.6700 (mmtt) REVERT: B 467 ILE cc_start: 0.8867 (mm) cc_final: 0.8464 (mt) REVERT: B 505 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8191 (mmmt) REVERT: B 512 ASP cc_start: 0.8179 (m-30) cc_final: 0.7911 (m-30) REVERT: B 517 MET cc_start: 0.8304 (mmm) cc_final: 0.7999 (mmm) outliers start: 17 outliers final: 8 residues processed: 151 average time/residue: 0.2180 time to fit residues: 43.6813 Evaluate side-chains 134 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 479 SER 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: 0.9990 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 25 optimal weight: 0.0170 chunk 77 optimal weight: 2.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7916 Z= 0.185 Angle : 0.543 9.257 10762 Z= 0.281 Chirality : 0.042 0.144 1246 Planarity : 0.004 0.043 1322 Dihedral : 5.897 77.111 1072 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.77 % Allowed : 10.84 % Favored : 86.39 % 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: -1.97 (0.26), residues: 976 helix: -0.70 (0.22), residues: 540 sheet: -2.14 (0.40), residues: 164 loop : -1.56 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 488 HIS 0.004 0.001 HIS A 57 PHE 0.011 0.001 PHE A 585 TYR 0.012 0.001 TYR B 617 ARG 0.003 0.000 ARG A 208 *********************** 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 159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 1.294 Fit side-chains REVERT: A 21 MET cc_start: 0.8588 (ttp) cc_final: 0.8307 (ttt) REVERT: A 29 LYS cc_start: 0.7775 (tppt) cc_final: 0.7486 (ttmt) REVERT: A 459 SER cc_start: 0.8538 (t) cc_final: 0.8246 (p) REVERT: A 467 ILE cc_start: 0.8834 (mm) cc_final: 0.8434 (mt) REVERT: A 505 LYS cc_start: 0.8412 (mmtp) cc_final: 0.8123 (mmmt) REVERT: A 512 ASP cc_start: 0.8160 (m-30) cc_final: 0.7904 (m-30) REVERT: A 517 MET cc_start: 0.8273 (mmm) cc_final: 0.7945 (mmm) REVERT: A 521 SER cc_start: 0.8294 (t) cc_final: 0.8079 (t) REVERT: D 56 GLN cc_start: 0.7293 (pp30) cc_final: 0.7085 (pt0) REVERT: B 1 MET cc_start: 0.5588 (ppp) cc_final: 0.5357 (ppp) REVERT: B 32 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8290 (mmtt) REVERT: B 173 VAL cc_start: 0.9148 (t) cc_final: 0.8758 (m) REVERT: B 180 ASP cc_start: 0.8149 (t0) cc_final: 0.7768 (t0) REVERT: B 201 LYS cc_start: 0.7200 (mttt) cc_final: 0.6751 (mmtt) REVERT: B 208 ARG cc_start: 0.7811 (mmm-85) cc_final: 0.7414 (mmm-85) REVERT: B 467 ILE cc_start: 0.8842 (mm) cc_final: 0.8441 (mt) REVERT: B 505 LYS cc_start: 0.8476 (mmtp) cc_final: 0.8174 (mmmt) REVERT: B 512 ASP cc_start: 0.8130 (m-30) cc_final: 0.7881 (m-30) REVERT: B 517 MET cc_start: 0.8248 (mmm) cc_final: 0.7953 (mmm) outliers start: 23 outliers final: 14 residues processed: 153 average time/residue: 0.2273 time to fit residues: 46.5929 Evaluate side-chains 152 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 589 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.0670 chunk 1 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 30.0000 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN C 56 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7916 Z= 0.210 Angle : 0.548 8.281 10762 Z= 0.280 Chirality : 0.043 0.145 1246 Planarity : 0.004 0.043 1322 Dihedral : 5.743 76.783 1072 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.49 % Allowed : 10.36 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.27), residues: 976 helix: -0.33 (0.22), residues: 542 sheet: -1.80 (0.42), residues: 156 loop : -1.37 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 488 HIS 0.005 0.001 HIS B 57 PHE 0.010 0.001 PHE A 585 TYR 0.013 0.001 TYR B 617 ARG 0.004 0.000 ARG B 207 *********************** 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 165 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.882 Fit side-chains REVERT: A 208 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7580 (mmm-85) REVERT: A 459 SER cc_start: 0.8572 (t) cc_final: 0.8228 (p) REVERT: A 467 ILE cc_start: 0.8828 (mm) cc_final: 0.8426 (mt) REVERT: A 505 LYS cc_start: 0.8456 (mmtp) cc_final: 0.8162 (mmmt) REVERT: A 512 ASP cc_start: 0.8148 (m-30) cc_final: 0.7869 (m-30) REVERT: A 517 MET cc_start: 0.8260 (mmm) cc_final: 0.7943 (mmm) REVERT: A 521 SER cc_start: 0.8279 (t) cc_final: 0.8055 (t) REVERT: A 547 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8027 (tpt90) REVERT: B 1 MET cc_start: 0.5654 (ppp) cc_final: 0.5442 (ppp) REVERT: B 32 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8296 (mmtt) REVERT: B 180 ASP cc_start: 0.8138 (t0) cc_final: 0.7866 (t0) REVERT: B 201 LYS cc_start: 0.7182 (mttt) cc_final: 0.6767 (mmtt) REVERT: B 208 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7388 (mmm-85) REVERT: B 467 ILE cc_start: 0.8834 (mm) cc_final: 0.8435 (mt) REVERT: B 505 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8123 (mmmt) REVERT: B 512 ASP cc_start: 0.8157 (m-30) cc_final: 0.7895 (m-30) REVERT: B 547 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8588 (tpm170) outliers start: 29 outliers final: 18 residues processed: 159 average time/residue: 0.2416 time to fit residues: 49.9924 Evaluate side-chains 154 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 589 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7916 Z= 0.184 Angle : 0.528 8.452 10762 Z= 0.271 Chirality : 0.042 0.140 1246 Planarity : 0.004 0.043 1322 Dihedral : 5.576 75.535 1072 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.89 % Allowed : 11.08 % Favored : 86.02 % 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: -1.08 (0.27), residues: 976 helix: -0.01 (0.22), residues: 542 sheet: -1.63 (0.43), residues: 156 loop : -1.27 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 37 HIS 0.005 0.001 HIS A 57 PHE 0.010 0.001 PHE A 585 TYR 0.013 0.001 TYR A 617 ARG 0.005 0.000 ARG B 207 *********************** 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 163 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.828 Fit side-chains REVERT: A 131 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6583 (m-30) REVERT: A 459 SER cc_start: 0.8513 (t) cc_final: 0.8217 (p) REVERT: A 467 ILE cc_start: 0.8830 (mm) cc_final: 0.8427 (mt) REVERT: A 505 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8156 (mmmt) REVERT: A 512 ASP cc_start: 0.8120 (m-30) cc_final: 0.7872 (m-30) REVERT: A 517 MET cc_start: 0.8244 (mmm) cc_final: 0.7902 (mmm) REVERT: A 521 SER cc_start: 0.8260 (t) cc_final: 0.8025 (t) REVERT: A 547 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8002 (tpt90) REVERT: B 32 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8303 (mmtt) REVERT: B 180 ASP cc_start: 0.7985 (t0) cc_final: 0.7736 (t0) REVERT: B 208 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.7374 (mmm-85) REVERT: B 461 MET cc_start: 0.8368 (mmm) cc_final: 0.8071 (tpp) REVERT: B 467 ILE cc_start: 0.8833 (mm) cc_final: 0.8434 (mt) REVERT: B 505 LYS cc_start: 0.8516 (mmtp) cc_final: 0.8194 (mmmt) REVERT: B 512 ASP cc_start: 0.8132 (m-30) cc_final: 0.7901 (m-30) REVERT: B 547 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8564 (tpm170) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 0.2526 time to fit residues: 50.8925 Evaluate side-chains 153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 589 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8026 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7916 Z= 0.204 Angle : 0.549 10.036 10762 Z= 0.276 Chirality : 0.043 0.145 1246 Planarity : 0.004 0.043 1322 Dihedral : 5.503 75.223 1072 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.13 % Allowed : 11.33 % Favored : 85.54 % 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: -0.93 (0.27), residues: 976 helix: 0.14 (0.22), residues: 542 sheet: -1.59 (0.43), residues: 156 loop : -1.24 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 37 HIS 0.004 0.001 HIS A 57 PHE 0.009 0.001 PHE A 585 TYR 0.014 0.001 TYR B 617 ARG 0.003 0.000 ARG A 207 *********************** 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 156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.766 Fit side-chains REVERT: A 131 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6599 (m-30) REVERT: A 459 SER cc_start: 0.8546 (t) cc_final: 0.8255 (p) REVERT: A 461 MET cc_start: 0.8332 (mmm) cc_final: 0.8034 (tpp) REVERT: A 467 ILE cc_start: 0.8826 (mm) cc_final: 0.8419 (mt) REVERT: A 505 LYS cc_start: 0.8459 (mmtp) cc_final: 0.8177 (mmmt) REVERT: A 512 ASP cc_start: 0.8097 (m-30) cc_final: 0.7836 (m-30) REVERT: A 517 MET cc_start: 0.8244 (mmm) cc_final: 0.7921 (mmm) REVERT: A 521 SER cc_start: 0.8277 (t) cc_final: 0.8048 (t) REVERT: A 547 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.7849 (tpt90) REVERT: B 32 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8307 (mmtt) REVERT: B 180 ASP cc_start: 0.7966 (t0) cc_final: 0.7655 (t0) REVERT: B 208 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7323 (mmm-85) REVERT: B 461 MET cc_start: 0.8374 (mmm) cc_final: 0.8116 (tpp) REVERT: B 467 ILE cc_start: 0.8832 (mm) cc_final: 0.8438 (mt) REVERT: B 505 LYS cc_start: 0.8515 (mmtp) cc_final: 0.8191 (mmmt) REVERT: B 512 ASP cc_start: 0.8120 (m-30) cc_final: 0.7880 (m-30) REVERT: B 517 MET cc_start: 0.8351 (mmm) cc_final: 0.8046 (mmm) REVERT: B 547 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8574 (tpm170) outliers start: 26 outliers final: 20 residues processed: 148 average time/residue: 0.2386 time to fit residues: 46.1879 Evaluate side-chains 154 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Chi-restraints excluded: chain B residue 589 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7916 Z= 0.204 Angle : 0.541 9.404 10762 Z= 0.273 Chirality : 0.043 0.147 1246 Planarity : 0.004 0.043 1322 Dihedral : 5.426 74.100 1072 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.13 % Allowed : 11.20 % Favored : 85.66 % 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: -0.74 (0.27), residues: 976 helix: 0.31 (0.22), residues: 542 sheet: -1.53 (0.43), residues: 156 loop : -1.18 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 37 HIS 0.004 0.001 HIS A 57 PHE 0.008 0.001 PHE B 585 TYR 0.013 0.001 TYR B 617 ARG 0.003 0.000 ARG A 207 *********************** 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 157 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.977 Fit side-chains REVERT: A 131 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6601 (m-30) REVERT: A 202 LEU cc_start: 0.7942 (tp) cc_final: 0.7701 (mt) REVERT: A 459 SER cc_start: 0.8536 (t) cc_final: 0.8238 (p) REVERT: A 461 MET cc_start: 0.8356 (mmm) cc_final: 0.8084 (tpp) REVERT: A 467 ILE cc_start: 0.8825 (mm) cc_final: 0.8426 (mt) REVERT: A 505 LYS cc_start: 0.8538 (mmtp) cc_final: 0.8270 (mmmt) REVERT: A 512 ASP cc_start: 0.8103 (m-30) cc_final: 0.7857 (m-30) REVERT: A 517 MET cc_start: 0.8253 (mmm) cc_final: 0.7938 (mmm) REVERT: A 547 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8090 (tpt90) REVERT: B 1 MET cc_start: 0.5798 (ppp) cc_final: 0.5517 (ppp) REVERT: B 32 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8305 (mmtm) REVERT: B 180 ASP cc_start: 0.7910 (t0) cc_final: 0.7620 (t0) REVERT: B 208 ARG cc_start: 0.7777 (mmm-85) cc_final: 0.7338 (mmm-85) REVERT: B 461 MET cc_start: 0.8370 (mmm) cc_final: 0.8153 (tpp) REVERT: B 467 ILE cc_start: 0.8833 (mm) cc_final: 0.8438 (mt) REVERT: B 505 LYS cc_start: 0.8520 (mmtp) cc_final: 0.8198 (mmmt) REVERT: B 512 ASP cc_start: 0.8072 (m-30) cc_final: 0.7825 (m-30) REVERT: B 517 MET cc_start: 0.8354 (mmm) cc_final: 0.8149 (mmm) REVERT: B 547 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8561 (tpm170) outliers start: 26 outliers final: 22 residues processed: 149 average time/residue: 0.2308 time to fit residues: 44.9119 Evaluate side-chains 153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.0970 chunk 56 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN D 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7916 Z= 0.183 Angle : 0.538 8.510 10762 Z= 0.269 Chirality : 0.042 0.143 1246 Planarity : 0.004 0.043 1322 Dihedral : 5.308 72.469 1072 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.89 % Allowed : 11.69 % Favored : 85.42 % 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: -0.51 (0.27), residues: 976 helix: 0.51 (0.22), residues: 542 sheet: -1.45 (0.43), residues: 156 loop : -1.11 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 488 HIS 0.004 0.001 HIS B 57 PHE 0.009 0.001 PHE B 585 TYR 0.013 0.001 TYR B 617 ARG 0.004 0.000 ARG B 207 *********************** 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 156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.906 Fit side-chains REVERT: A 131 ASP cc_start: 0.7017 (OUTLIER) cc_final: 0.6444 (m-30) REVERT: A 208 ARG cc_start: 0.7701 (mmm-85) cc_final: 0.7436 (mmm-85) REVERT: A 459 SER cc_start: 0.8474 (t) cc_final: 0.8204 (p) REVERT: A 461 MET cc_start: 0.8347 (mmm) cc_final: 0.8118 (tpp) REVERT: A 467 ILE cc_start: 0.8828 (mm) cc_final: 0.8432 (mt) REVERT: A 505 LYS cc_start: 0.8530 (mmtp) cc_final: 0.8259 (mmmt) REVERT: A 512 ASP cc_start: 0.8106 (m-30) cc_final: 0.7866 (m-30) REVERT: A 517 MET cc_start: 0.8228 (mmm) cc_final: 0.7916 (mmm) REVERT: A 547 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7922 (tpt90) REVERT: B 1 MET cc_start: 0.5822 (ppp) cc_final: 0.5573 (ppp) REVERT: B 11 MET cc_start: 0.8477 (mmm) cc_final: 0.8271 (mmm) REVERT: B 32 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8308 (mmtm) REVERT: B 180 ASP cc_start: 0.7944 (t0) cc_final: 0.7656 (t0) REVERT: B 208 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.7310 (mmm-85) REVERT: B 461 MET cc_start: 0.8362 (mmm) cc_final: 0.8153 (tpp) REVERT: B 467 ILE cc_start: 0.8830 (mm) cc_final: 0.8434 (mt) REVERT: B 505 LYS cc_start: 0.8522 (mmtp) cc_final: 0.8204 (mmmt) REVERT: B 512 ASP cc_start: 0.8103 (m-30) cc_final: 0.7871 (m-30) REVERT: B 517 MET cc_start: 0.8368 (mmm) cc_final: 0.8073 (mmm) REVERT: B 547 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8555 (tpm170) outliers start: 24 outliers final: 21 residues processed: 149 average time/residue: 0.2399 time to fit residues: 46.1212 Evaluate side-chains 156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7916 Z= 0.187 Angle : 0.540 10.445 10762 Z= 0.270 Chirality : 0.042 0.143 1246 Planarity : 0.004 0.043 1322 Dihedral : 5.250 71.222 1072 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.01 % Allowed : 11.81 % Favored : 85.18 % 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: -0.35 (0.27), residues: 976 helix: 0.67 (0.22), residues: 542 sheet: -1.42 (0.43), residues: 156 loop : -1.07 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 63 HIS 0.004 0.001 HIS A 57 PHE 0.009 0.001 PHE B 585 TYR 0.013 0.001 TYR A 617 ARG 0.004 0.000 ARG A 207 ********************** 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 158 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.782 Fit side-chains REVERT: A 131 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6572 (m-30) REVERT: A 208 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7388 (mmm-85) REVERT: A 459 SER cc_start: 0.8429 (t) cc_final: 0.8179 (p) REVERT: A 461 MET cc_start: 0.8384 (mmm) cc_final: 0.8168 (tpp) REVERT: A 467 ILE cc_start: 0.8828 (mm) cc_final: 0.8435 (mt) REVERT: A 505 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8330 (mmmt) REVERT: A 512 ASP cc_start: 0.8084 (m-30) cc_final: 0.7831 (m-30) REVERT: A 547 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8024 (tpt90) REVERT: B 32 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8317 (mmtm) REVERT: B 180 ASP cc_start: 0.7972 (t0) cc_final: 0.7692 (t0) REVERT: B 208 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.7286 (mmm-85) REVERT: B 461 MET cc_start: 0.8363 (mmm) cc_final: 0.8161 (tpp) REVERT: B 467 ILE cc_start: 0.8828 (mm) cc_final: 0.8431 (mt) REVERT: B 505 LYS cc_start: 0.8571 (mmtp) cc_final: 0.8253 (mmmt) REVERT: B 512 ASP cc_start: 0.8096 (m-30) cc_final: 0.7870 (m-30) REVERT: B 517 MET cc_start: 0.8365 (mmm) cc_final: 0.8055 (mmm) REVERT: B 547 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8554 (tpm170) outliers start: 25 outliers final: 21 residues processed: 150 average time/residue: 0.2369 time to fit residues: 46.1710 Evaluate side-chains 155 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 547 ARG Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 455 MET Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 547 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.185708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127786 restraints weight = 8797.852| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.82 r_work: 0.3068 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7916 Z= 0.172 Angle : 0.549 11.741 10762 Z= 0.271 Chirality : 0.042 0.141 1246 Planarity : 0.004 0.043 1322 Dihedral : 5.142 69.046 1072 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.77 % Allowed : 12.41 % Favored : 84.82 % 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: -0.09 (0.27), residues: 976 helix: 0.90 (0.23), residues: 542 sheet: -1.35 (0.43), residues: 156 loop : -0.98 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 63 HIS 0.004 0.001 HIS A 57 PHE 0.009 0.001 PHE B 585 TYR 0.018 0.001 TYR B 617 ARG 0.005 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1983.11 seconds wall clock time: 37 minutes 25.13 seconds (2245.13 seconds total)