Starting phenix.real_space_refine
on Wed Jul 30 03:16:51 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8r23_18834/07_2025/8r23_18834.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r23_18834/07_2025/8r23_18834.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/8r23_18834/07_2025/8r23_18834.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r23_18834/07_2025/8r23_18834.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r23_18834/07_2025/8r23_18834.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r23_18834/07_2025/8r23_18834.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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      94      5.16       5
     C    7660      2.51       5
     N    2015      2.21       5
     O    2208      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11979
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5468
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 718, 5468
          Classifications: {'peptide': 718}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 674}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 3128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 401, 3128
          Classifications: {'peptide': 401}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 370}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 3381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3381
          Classifications: {'peptide': 429}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 18, 'TRANS': 410}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5455  SG  CYS A 820      59.662  42.201  71.145  1.00 42.52           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   PRO A 492 " occ=0.25
      ... (5 atoms not shown)
      pdb=" CD  PRO A 492 " occ=0.25
  Time building chain proxies: 7.14, per 1000 atoms: 0.60
  Number of scatterers: 11979
  At special positions: 0
  Unit cell: (130.68, 109.56, 116.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      94     16.00
     O    2208      8.00
     N    2015      7.00
     C    7660      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 800 "
        pdb="ZN    ZN C 800 " - pdb=" ND1 HIS C  70 "
        pdb="ZN    ZN C 800 " - pdb=" NE2 HIS C  68 "
        pdb="ZN    ZN C 800 " - pdb=" NE2 HIS C 157 "
      pdb="  ZN C 801 "
        pdb="ZN    ZN C 801 " - pdb=" NE2 HIS C  73 "
        pdb="ZN    ZN C 801 " - pdb=" NE2 HIS C 414 "
        pdb="ZN    ZN C 801 " - pdb=" SG  CYS A 820 "


  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2908

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 0 sheets defined
      43.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 6
      No H-bonds generated for 'chain 'A' and resid 3 through 6'
    Processing helix  chain 'A' and resid 9 through 17
      removed outlier: 3.756A  pdb=" N   VAL A  17 " --> pdb=" O   CYS A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 26 through 42
      removed outlier: 3.750A  pdb=" N   TRP A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LYS A  37 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR A  38 " --> pdb=" O   ASP A  34 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY A  42 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 51
      removed outlier: 3.505A  pdb=" N   GLN A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 62
    Processing helix  chain 'A' and resid 73 through 83
    Processing helix  chain 'A' and resid 87 through 92
    Processing helix  chain 'A' and resid 99 through 102
      No H-bonds generated for 'chain 'A' and resid 99 through 102'
    Processing helix  chain 'A' and resid 117 through 130
      removed outlier: 3.802A  pdb=" N   SER A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 142
    Processing helix  chain 'A' and resid 146 through 152
      removed outlier: 3.849A  pdb=" N   SER A 151 " --> pdb=" O   ASP A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 175
      removed outlier: 3.696A  pdb=" N   ALA A 163 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 169 " --> pdb=" O   SER A 165 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   HIS A 170 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 206
      removed outlier: 3.777A  pdb=" N   LYS A 197 " --> pdb=" O   ALA A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 227
      removed outlier: 3.540A  pdb=" N   VAL A 220 " --> pdb=" O   GLN A 216 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   THR A 223 " --> pdb=" O   ASN A 219 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   GLY A 226 " --> pdb=" O   THR A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 245
      removed outlier: 3.558A  pdb=" N   ALA A 235 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   VAL A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ARG A 239 " --> pdb=" O   ALA A 235 " (cutoff:3.500A)
      Proline residue:  A 242  - end of helix
    Processing helix  chain 'A' and resid 256 through 267
    Processing helix  chain 'A' and resid 270 through 273
      No H-bonds generated for 'chain 'A' and resid 270 through 273'
    Processing helix  chain 'A' and resid 278 through 289
      removed outlier: 3.542A  pdb=" N   THR A 282 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   SER A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 303
      removed outlier: 3.617A  pdb=" N   LEU A 303 " --> pdb=" O   ALA A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 320
      removed outlier: 3.693A  pdb=" N   GLN A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 329
      removed outlier: 3.671A  pdb=" N   VAL A 327 " --> pdb=" O   PRO A 323 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS A 329 " --> pdb=" O   ALA A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 356
      removed outlier: 3.789A  pdb=" N   THR A 353 " --> pdb=" O   THR A 349 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LEU A 355 " --> pdb=" O   VAL A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 374
    Processing helix  chain 'A' and resid 387 through 402
      removed outlier: 3.652A  pdb=" N   VAL A 397 " --> pdb=" O   ALA A 393 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LEU A 400 " --> pdb=" O   THR A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 419
      removed outlier: 3.905A  pdb=" N   GLY A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 435
    Processing helix  chain 'A' and resid 443 through 457
      removed outlier: 3.674A  pdb=" N   VAL A 452 " --> pdb=" O   GLN A 448 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   GLU A 455 " --> pdb=" O   ALA A 451 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   CYS A 456 " --> pdb=" O   VAL A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 478
      removed outlier: 3.734A  pdb=" N   LEU A 475 " --> pdb=" O   PHE A 471 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG A 476 " --> pdb=" O   GLN A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 508
      removed outlier: 3.513A  pdb=" N   ARG A 499 " --> pdb=" O   PRO A 495 " (cutoff:3.500A)
      Proline residue:  A 503  - end of helix
      removed outlier: 3.940A  pdb=" N   LYS A 507 " --> pdb=" O   PRO A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 530
      removed outlier: 3.635A  pdb=" N   LEU A 521 " --> pdb=" O   ARG A 517 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A 525 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 542
    Processing helix  chain 'A' and resid 546 through 549
      No H-bonds generated for 'chain 'A' and resid 546 through 549'
    Processing helix  chain 'A' and resid 559 through 574
    Processing helix  chain 'A' and resid 593 through 601
      removed outlier: 3.566A  pdb=" N   HIS A 598 " --> pdb=" O   LEU A 594 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE A 599 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   SER A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 622
      removed outlier: 3.622A  pdb=" N   GLN A 614 " --> pdb=" O   ARG A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 643
      removed outlier: 3.648A  pdb=" N   GLN A 640 " --> pdb=" O   ALA A 636 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA A 641 " --> pdb=" O   THR A 637 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   SER A 643 " --> pdb=" O   LEU A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 665
      removed outlier: 3.557A  pdb=" N   GLN A 664 " --> pdb=" O   VAL A 660 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A 665 " --> pdb=" O   PHE A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 697
    Processing helix  chain 'A' and resid 700 through 708
      removed outlier: 3.534A  pdb=" N   CYS A 706 " --> pdb=" O   ASP A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 732
      removed outlier: 3.720A  pdb=" N   LYS A 718 " --> pdb=" O   PRO A 714 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS A 729 " --> pdb=" O   PHE A 725 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ALA A 731 " --> pdb=" O   ARG A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 778
    Processing helix  chain 'A' and resid 782 through 788
    Processing helix  chain 'A' and resid 799 through 807
      removed outlier: 3.721A  pdb=" N   MET A 806 " --> pdb=" O   LEU A 802 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 114
    Processing helix  chain 'B' and resid 127 through 144
      removed outlier: 3.880A  pdb=" N   LEU B 135 " --> pdb=" O   GLN B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 190
      removed outlier: 3.692A  pdb=" N   ASN B 188 " --> pdb=" O   MET B 184 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER B 189 " --> pdb=" O   GLN B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 289
    Processing helix  chain 'B' and resid 304 through 319
      removed outlier: 3.506A  pdb=" N   GLN B 314 " --> pdb=" O   GLU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 411
    Processing helix  chain 'B' and resid 454 through 464
      removed outlier: 3.549A  pdb=" N   SER B 458 " --> pdb=" O   PHE B 454 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   LYS B 459 " --> pdb=" O   ILE B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 476
      No H-bonds generated for 'chain 'B' and resid 473 through 476'
    Processing helix  chain 'C' and resid 57 through 60
      No H-bonds generated for 'chain 'C' and resid 57 through 60'
    Processing helix  chain 'C' and resid 71 through 74
      No H-bonds generated for 'chain 'C' and resid 71 through 74'
    Processing helix  chain 'C' and resid 77 through 80
      No H-bonds generated for 'chain 'C' and resid 77 through 80'
    Processing helix  chain 'C' and resid 94 through 111
      removed outlier: 3.568A  pdb=" N   ALA C  98 " --> pdb=" O   HIS C  94 " (cutoff:3.500A)
      Proline residue:  C 101  - end of helix
      removed outlier: 3.689A  pdb=" N   LYS C 109 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE C 110 " --> pdb=" O   ASP C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 130
      removed outlier: 3.670A  pdb=" N   LYS C 127 " --> pdb=" O   SER C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 216 through 229
      removed outlier: 3.655A  pdb=" N   LEU C 222 " --> pdb=" O   GLU C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 246 through 257
      removed outlier: 3.948A  pdb=" N   LEU C 251 " --> pdb=" O   GLU C 247 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   THR C 254 " --> pdb=" O   ILE C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 282
    Processing helix  chain 'C' and resid 332 through 339
    Processing helix  chain 'C' and resid 359 through 364
      removed outlier: 3.714A  pdb=" N   LEU C 364 " --> pdb=" O   GLY C 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 395 through 405
    Processing helix  chain 'C' and resid 417 through 429
      removed outlier: 3.829A  pdb=" N   GLU C 421 " --> pdb=" O   ALA C 417 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLN C 425 " --> pdb=" O   GLU C 421 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LYS C 426 " --> pdb=" O   PHE C 422 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1044 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: 2.84

  Time building geometry restraints manager: 2.89 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 3870
        1.34 -     1.46: 1747
        1.46 -     1.57: 6482
        1.57 -     1.69: 0
        1.69 -     1.81: 136
  Bond restraints: 12235
  Sorted by residual:
  bond pdb=" N   ASP A 251 "
       pdb=" CA  ASP A 251 "
    ideal  model  delta    sigma   weight residual
    1.463  1.456  0.007 6.90e-03 2.10e+04 1.07e+00
  bond pdb=" C   VAL A 795 "
       pdb=" O   VAL A 795 "
    ideal  model  delta    sigma   weight residual
    1.231  1.242 -0.010 1.02e-02 9.61e+03 1.02e+00
  bond pdb=" CA  CYS A 246 "
       pdb=" C   CYS A 246 "
    ideal  model  delta    sigma   weight residual
    1.523  1.505  0.018 1.80e-02 3.09e+03 9.78e-01
  bond pdb=" CG  LEU A 300 "
       pdb=" CD1 LEU A 300 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 9.01e-01
  bond pdb=" CG  PRO A 384 "
       pdb=" CD  PRO A 384 "
    ideal  model  delta    sigma   weight residual
    1.512  1.487  0.025 2.70e-02 1.37e+03 8.84e-01
  ... (remaining 12230 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 16032
        1.54 -     3.08: 495
        3.08 -     4.62: 72
        4.62 -     6.15: 19
        6.15 -     7.69: 3
  Bond angle restraints: 16621
  Sorted by residual:
  angle pdb=" N   THR C 324 "
        pdb=" CA  THR C 324 "
        pdb=" C   THR C 324 "
      ideal   model   delta    sigma   weight residual
     109.81  117.50   -7.69 2.21e+00 2.05e-01 1.21e+01
  angle pdb=" N   ALA A 115 "
        pdb=" CA  ALA A 115 "
        pdb=" C   ALA A 115 "
      ideal   model   delta    sigma   weight residual
     114.75  110.68    4.07 1.26e+00 6.30e-01 1.04e+01
  angle pdb=" N   VAL A 397 "
        pdb=" CA  VAL A 397 "
        pdb=" C   VAL A 397 "
      ideal   model   delta    sigma   weight residual
     113.43  109.92    3.51 1.09e+00 8.42e-01 1.04e+01
  angle pdb=" N   ASP A 251 "
        pdb=" CA  ASP A 251 "
        pdb=" C   ASP A 251 "
      ideal   model   delta    sigma   weight residual
     112.17  108.22    3.95 1.36e+00 5.41e-01 8.42e+00
  angle pdb=" N   GLU B 145 "
        pdb=" CA  GLU B 145 "
        pdb=" C   GLU B 145 "
      ideal   model   delta    sigma   weight residual
     110.65  107.13    3.52 1.26e+00 6.30e-01 7.78e+00
  ... (remaining 16616 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 6598
       17.81 -    35.62: 641
       35.62 -    53.44: 93
       53.44 -    71.25: 25
       71.25 -    89.06: 10
  Dihedral angle restraints: 7367
    sinusoidal: 2892
      harmonic: 4475
  Sorted by residual:
  dihedral pdb=" CA  THR C 324 "
           pdb=" C   THR C 324 "
           pdb=" N   PRO C 325 "
           pdb=" CA  PRO C 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.02   23.98     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  ILE C  24 "
           pdb=" C   ILE C  24 "
           pdb=" N   ALA C  25 "
           pdb=" CA  ALA C  25 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.12  -19.88     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  GLY C 366 "
           pdb=" C   GLY C 366 "
           pdb=" N   GLN C 367 "
           pdb=" CA  GLN C 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.27  -18.73     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 7364 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1416
       0.041 -    0.082: 382
       0.082 -    0.122: 121
       0.122 -    0.163: 11
       0.163 -    0.204: 1
  Chirality restraints: 1931
  Sorted by residual:
  chirality pdb=" CB  ILE B 490 "
            pdb=" CA  ILE B 490 "
            pdb=" CG1 ILE B 490 "
            pdb=" CG2 ILE B 490 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  THR C 324 "
            pdb=" N   THR C 324 "
            pdb=" C   THR C 324 "
            pdb=" CB  THR C 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CB  ILE C  24 "
            pdb=" CA  ILE C  24 "
            pdb=" CG1 ILE C  24 "
            pdb=" CG2 ILE C  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 5.13e-01
  ... (remaining 1928 not shown)

  Planarity restraints: 2118
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 324 "   -0.060 5.00e-02 4.00e+02   9.00e-02 1.30e+01
        pdb=" N   PRO C 325 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO C 325 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO C 325 "   -0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 105 "    0.033 5.00e-02 4.00e+02   4.94e-02 3.90e+00
        pdb=" N   PRO A 106 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 106 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 106 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 556 "   -0.033 5.00e-02 4.00e+02   4.91e-02 3.86e+00
        pdb=" N   PRO A 557 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 557 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 557 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 2115 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 80
        2.56 -     3.15: 9748
        3.15 -     3.73: 17243
        3.73 -     4.32: 24987
        4.32 -     4.90: 41178
  Nonbonded interactions: 93236
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 178 "
            pdb="ZN    ZN C 800 "
     model   vdw
     1.978 2.230
  nonbonded pdb=" OD2 ASP C  72 "
            pdb="ZN    ZN C 801 "
     model   vdw
     2.047 2.230
  nonbonded pdb=" OH  TYR B 112 "
            pdb=" O   ARG B 180 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" O   ASP A 556 "
            pdb=" NH1 ARG A 562 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" O   TRP A 237 "
            pdb=" OG  SER A 241 "
     model   vdw
     2.219 3.040
  ... (remaining 93231 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 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:             0.750
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.640
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
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   0.286  12241  Z= 0.230
  Angle     :  0.661   7.693  16621  Z= 0.372
  Chirality :  0.041   0.204   1931
  Planarity :  0.005   0.090   2118
  Dihedral  : 14.388  89.059   4459
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -5.33 (0.16), residues: 1508
  helix: -3.39 (0.13), residues: 768
  sheet: -3.29 (0.34), residues: 179
  loop : -3.55 (0.21), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 114 
 HIS   0.005   0.001   HIS A 294 
 PHE   0.017   0.001   PHE C 312 
 TYR   0.013   0.001   TYR C 278 
 ARG   0.004   0.000   ARG A  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30613 (  348)
  hydrogen bonds       : angle       9.28693 ( 1044)
  metal coordination   : bond        0.18343 (    6)
  covalent geometry    : bond        0.00431 (12235)
  covalent geometry    : angle       0.66108 (16621)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7198 (mtp) cc_final: 0.6967 (mtp)
REVERT: A  199 MET cc_start: 0.7790 (mtt) cc_final: 0.7165 (mtt)
REVERT: A  458 GLU cc_start: 0.7817 (pp20) cc_final: 0.7194 (pp20)
REVERT: A  718 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8376 (mmtp)
REVERT: B   32 MET cc_start: 0.6886 (mmp) cc_final: 0.6148 (tpp)
REVERT: B  464 VAL cc_start: 0.8334 (t) cc_final: 0.8102 (m)
REVERT: C  143 GLN cc_start: 0.7985 (tp-100) cc_final: 0.6987 (mm110)
REVERT: C  149 GLU cc_start: 0.6840 (mt-10) cc_final: 0.5884 (mm-30)
REVERT: C  259 MET cc_start: 0.8041 (mmm) cc_final: 0.7653 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.2932
  time to fit residues: 75.3018
Evaluate side-chains
  123 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 129 optimal weight:    0.0170
   chunk 115 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 78 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 119 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 138 optimal weight:    2.9990
   overall best weight:    0.6418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
A 472 GLN
A 506 GLN
A 767 GLN
A 800 GLN
A 804 GLN
B 224 ASN
B 456 GLN
B 493 GLN
C 124 GLN
C 143 GLN
C 277 HIS
C 332 GLN
C 343 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.130450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.095165 restraints weight = 18763.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.52
r_work: 0.3004 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12241  Z= 0.125
  Angle     :  0.579   6.383  16621  Z= 0.289
  Chirality :  0.041   0.153   1931
  Planarity :  0.005   0.087   2118
  Dihedral  :  4.508  42.729   1633
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.50 %
    Favored  : 89.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -3.16 (0.20), residues: 1508
  helix: -1.46 (0.17), residues: 786
  sheet: -2.53 (0.40), residues: 155
  loop : -2.74 (0.23), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 385 
 HIS   0.006   0.001   HIS B 484 
 PHE   0.014   0.001   PHE C 312 
 TYR   0.017   0.001   TYR C 278 
 ARG   0.005   0.000   ARG C 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04795 (  348)
  hydrogen bonds       : angle       4.40565 ( 1044)
  metal coordination   : bond        0.00610 (    6)
  covalent geometry    : bond        0.00289 (12235)
  covalent geometry    : angle       0.57854 (16621)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 1.473 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7227 (mtp) cc_final: 0.6956 (mtp)
REVERT: A  261 ASP cc_start: 0.8544 (m-30) cc_final: 0.8114 (m-30)
REVERT: A  396 THR cc_start: 0.9493 (t) cc_final: 0.9262 (m)
REVERT: A  458 GLU cc_start: 0.8463 (pp20) cc_final: 0.7902 (pp20)
REVERT: A  692 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8674 (tp)
REVERT: A  718 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8298 (mmtp)
REVERT: B  489 MET cc_start: 0.8388 (ttp) cc_final: 0.7862 (ttp)
REVERT: C  143 GLN cc_start: 0.8329 (tp40) cc_final: 0.8123 (mm-40)
REVERT: C  149 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7084 (mt-10)
REVERT: C  259 MET cc_start: 0.8307 (mmm) cc_final: 0.7789 (mmp)
REVERT: C  430 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7392 (tm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 160
  average time/residue: 0.2592
  time to fit residues: 59.0612
Evaluate side-chains
  132 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain C residue  347 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0470
   chunk 56 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0010
   chunk 121 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.4684

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 472 GLN
A 800 GLN
A 804 GLN
B 407 HIS
** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.132003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.100751 restraints weight = 19042.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.77
r_work: 0.3015 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3018 r_free = 0.3018    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3018
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12241  Z= 0.105
  Angle     :  0.537   8.749  16621  Z= 0.265
  Chirality :  0.040   0.153   1931
  Planarity :  0.005   0.078   2118
  Dihedral  :  4.103  37.843   1633
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.83 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.98 (0.21), residues: 1508
  helix: -0.38 (0.19), residues: 788
  sheet: -2.29 (0.41), residues: 148
  loop : -2.28 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 385 
 HIS   0.006   0.001   HIS B 484 
 PHE   0.025   0.001   PHE C 282 
 TYR   0.020   0.001   TYR C 107 
 ARG   0.004   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03618 (  348)
  hydrogen bonds       : angle       3.65926 ( 1044)
  metal coordination   : bond        0.00298 (    6)
  covalent geometry    : bond        0.00243 (12235)
  covalent geometry    : angle       0.53691 (16621)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.357 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7182 (mtp) cc_final: 0.6953 (mtp)
REVERT: A  261 ASP cc_start: 0.8410 (m-30) cc_final: 0.8004 (m-30)
REVERT: A  396 THR cc_start: 0.9494 (t) cc_final: 0.9246 (m)
REVERT: A  458 GLU cc_start: 0.8488 (pp20) cc_final: 0.7891 (pp20)
REVERT: A  644 ARG cc_start: 0.8251 (mmp80) cc_final: 0.7940 (mmm160)
REVERT: A  708 LEU cc_start: 0.8533 (tp) cc_final: 0.8301 (tp)
REVERT: B  250 MET cc_start: 0.6717 (tpt) cc_final: 0.6432 (tpt)
REVERT: B  489 MET cc_start: 0.8206 (ttp) cc_final: 0.7693 (ttp)
REVERT: C  143 GLN cc_start: 0.8228 (tp40) cc_final: 0.7959 (mm-40)
REVERT: C  149 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7406 (mt-10)
REVERT: C  219 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7147 (mmm160)
REVERT: C  259 MET cc_start: 0.8195 (mmm) cc_final: 0.7785 (mmt)
REVERT: C  430 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7641 (tm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 143
  average time/residue: 0.2200
  time to fit residues: 47.4245
Evaluate side-chains
  127 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 1.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain C residue  347 MET
Chi-restraints excluded: chain C residue  446 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0030
   chunk 61 optimal weight:    2.9990
   chunk 150 optimal weight:    0.4980
   chunk 71 optimal weight:    6.9990
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 151 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   overall best weight:    0.8192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 260 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.131413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.096036 restraints weight = 18865.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.51
r_work: 0.3018 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12241  Z= 0.125
  Angle     :  0.531   7.280  16621  Z= 0.263
  Chirality :  0.041   0.151   1931
  Planarity :  0.005   0.074   2118
  Dihedral  :  4.042  35.764   1633
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.43 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -1.45 (0.22), residues: 1508
  helix:  0.07 (0.19), residues: 791
  sheet: -1.74 (0.44), residues: 143
  loop : -2.18 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 285 
 HIS   0.004   0.001   HIS A 294 
 PHE   0.024   0.001   PHE C 282 
 TYR   0.019   0.001   TYR C 107 
 ARG   0.003   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03447 (  348)
  hydrogen bonds       : angle       3.49151 ( 1044)
  metal coordination   : bond        0.00374 (    6)
  covalent geometry    : bond        0.00301 (12235)
  covalent geometry    : angle       0.53120 (16621)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 1.152 
Fit side-chains
REVERT: A  191 TRP cc_start: 0.7749 (m100) cc_final: 0.7405 (m100)
REVERT: A  261 ASP cc_start: 0.8466 (m-30) cc_final: 0.8017 (m-30)
REVERT: A  396 THR cc_start: 0.9545 (t) cc_final: 0.9282 (m)
REVERT: A  458 GLU cc_start: 0.8419 (pp20) cc_final: 0.7878 (pp20)
REVERT: A  522 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7773 (mm-30)
REVERT: A  692 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8696 (tp)
REVERT: B   35 THR cc_start: 0.8616 (t) cc_final: 0.8361 (p)
REVERT: B  250 MET cc_start: 0.6653 (tpt) cc_final: 0.6401 (tpt)
REVERT: B  489 MET cc_start: 0.8215 (ttp) cc_final: 0.7771 (ttp)
REVERT: C  143 GLN cc_start: 0.8250 (tp40) cc_final: 0.7913 (mm-40)
REVERT: C  149 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7337 (mt-10)
REVERT: C  219 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7121 (mmm160)
REVERT: C  259 MET cc_start: 0.8233 (mmm) cc_final: 0.7848 (mmt)
REVERT: C  430 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7654 (tm-30)
  outliers start: 22
  outliers final: 15
  residues processed: 138
  average time/residue: 0.2337
  time to fit residues: 48.4151
Evaluate side-chains
  131 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  219 ARG
Chi-restraints excluded: chain C residue  347 MET
Chi-restraints excluded: chain C residue  446 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 87 optimal weight:    9.9990
   chunk 95 optimal weight:    0.0020
   chunk 94 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0270
   chunk 119 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 93 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.4446

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 438 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.133020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.101546 restraints weight = 18911.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.75
r_work: 0.3028 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12241  Z= 0.095
  Angle     :  0.504   7.350  16621  Z= 0.250
  Chirality :  0.040   0.159   1931
  Planarity :  0.004   0.069   2118
  Dihedral  :  3.819  31.255   1633
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.26 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.22), residues: 1508
  helix:  0.51 (0.19), residues: 795
  sheet: -1.45 (0.45), residues: 143
  loop : -2.04 (0.25), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 514 
 HIS   0.004   0.001   HIS A 294 
 PHE   0.020   0.001   PHE C 282 
 TYR   0.018   0.001   TYR C 107 
 ARG   0.003   0.000   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02855 (  348)
  hydrogen bonds       : angle       3.24672 ( 1044)
  metal coordination   : bond        0.00244 (    6)
  covalent geometry    : bond        0.00224 (12235)
  covalent geometry    : angle       0.50406 (16621)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 1.264 
Fit side-chains
REVERT: A  191 TRP cc_start: 0.7723 (m100) cc_final: 0.7435 (m100)
REVERT: A  261 ASP cc_start: 0.8464 (m-30) cc_final: 0.8034 (m-30)
REVERT: A  302 ILE cc_start: 0.8940 (mm) cc_final: 0.8680 (mt)
REVERT: A  396 THR cc_start: 0.9526 (t) cc_final: 0.9262 (m)
REVERT: A  458 GLU cc_start: 0.8447 (pp20) cc_final: 0.7913 (pp20)
REVERT: B   32 MET cc_start: 0.6423 (mmp) cc_final: 0.5388 (mmm)
REVERT: B  250 MET cc_start: 0.6450 (tpt) cc_final: 0.6230 (tpt)
REVERT: B  489 MET cc_start: 0.8197 (ttp) cc_final: 0.7744 (ttp)
REVERT: C  143 GLN cc_start: 0.8220 (tp40) cc_final: 0.7804 (mm-40)
REVERT: C  149 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7386 (mt-10)
REVERT: C  259 MET cc_start: 0.8241 (mmm) cc_final: 0.7850 (mmt)
REVERT: C  430 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7684 (tm-30)
  outliers start: 23
  outliers final: 15
  residues processed: 145
  average time/residue: 0.2191
  time to fit residues: 48.8619
Evaluate side-chains
  133 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  347 MET
Chi-restraints excluded: chain C residue  446 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 115 optimal weight:    0.0970
   chunk 125 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9990
   chunk 128 optimal weight:    2.9990
   chunk 134 optimal weight:    0.0170
   chunk 15 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 94 optimal weight:    0.3980
   chunk 117 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   overall best weight:    0.5018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.132636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.097911 restraints weight = 18811.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 2.49
r_work: 0.3045 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12241  Z= 0.098
  Angle     :  0.509   7.415  16621  Z= 0.250
  Chirality :  0.040   0.176   1931
  Planarity :  0.004   0.067   2118
  Dihedral  :  3.717  28.219   1633
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.39 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -0.65 (0.22), residues: 1508
  helix:  0.74 (0.19), residues: 796
  sheet: -1.19 (0.46), residues: 143
  loop : -1.90 (0.25), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 514 
 HIS   0.004   0.001   HIS B 484 
 PHE   0.016   0.001   PHE C 422 
 TYR   0.025   0.001   TYR C 107 
 ARG   0.003   0.000   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02874 (  348)
  hydrogen bonds       : angle       3.18856 ( 1044)
  metal coordination   : bond        0.00246 (    6)
  covalent geometry    : bond        0.00234 (12235)
  covalent geometry    : angle       0.50864 (16621)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 1.282 
Fit side-chains
REVERT: A  191 TRP cc_start: 0.7708 (m100) cc_final: 0.7414 (m100)
REVERT: A  261 ASP cc_start: 0.8408 (m-30) cc_final: 0.7983 (m-30)
REVERT: A  302 ILE cc_start: 0.8942 (mm) cc_final: 0.8661 (mt)
REVERT: A  396 THR cc_start: 0.9502 (t) cc_final: 0.9257 (m)
REVERT: A  458 GLU cc_start: 0.8456 (pp20) cc_final: 0.7954 (pp20)
REVERT: A  522 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7908 (mm-30)
REVERT: A  644 ARG cc_start: 0.8199 (mmp80) cc_final: 0.7904 (tpp80)
REVERT: A  708 LEU cc_start: 0.8423 (tp) cc_final: 0.8185 (mt)
REVERT: B   32 MET cc_start: 0.6084 (mmp) cc_final: 0.4934 (mmm)
REVERT: B  137 MET cc_start: 0.9129 (mtt) cc_final: 0.8830 (mtt)
REVERT: B  486 MET cc_start: 0.8331 (mmp) cc_final: 0.7997 (mmp)
REVERT: B  489 MET cc_start: 0.8172 (ttp) cc_final: 0.7728 (ttp)
REVERT: B  503 GLU cc_start: 0.7804 (tp30) cc_final: 0.7315 (tp30)
REVERT: C  143 GLN cc_start: 0.8218 (tp40) cc_final: 0.7771 (mm-40)
REVERT: C  149 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7357 (mt-10)
REVERT: C  259 MET cc_start: 0.8222 (mmm) cc_final: 0.7854 (mmt)
REVERT: C  430 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7692 (tm-30)
  outliers start: 20
  outliers final: 17
  residues processed: 138
  average time/residue: 0.2038
  time to fit residues: 43.0797
Evaluate side-chains
  133 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  347 MET
Chi-restraints excluded: chain C residue  446 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 6 optimal weight:    5.9990
   chunk 115 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9990
   chunk 139 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 47 optimal weight:    0.0000
   chunk 137 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.9390

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 GLN
B 493 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.131345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.095959 restraints weight = 19000.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 2.51
r_work: 0.3018 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3021
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3021 r_free = 0.3021    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3021
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12241  Z= 0.133
  Angle     :  0.531   8.015  16621  Z= 0.261
  Chirality :  0.041   0.189   1931
  Planarity :  0.004   0.067   2118
  Dihedral  :  3.845  27.925   1633
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.17 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -0.57 (0.22), residues: 1508
  helix:  0.79 (0.19), residues: 795
  sheet: -1.13 (0.46), residues: 143
  loop : -1.85 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 285 
 HIS   0.004   0.001   HIS C 157 
 PHE   0.018   0.001   PHE C 422 
 TYR   0.020   0.001   TYR C 107 
 ARG   0.003   0.000   ARG A 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03246 (  348)
  hydrogen bonds       : angle       3.26310 ( 1044)
  metal coordination   : bond        0.00355 (    6)
  covalent geometry    : bond        0.00324 (12235)
  covalent geometry    : angle       0.53147 (16621)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 1.367 
Fit side-chains
REVERT: A  191 TRP cc_start: 0.7719 (m100) cc_final: 0.7445 (m100)
REVERT: A  302 ILE cc_start: 0.8976 (mm) cc_final: 0.8727 (mt)
REVERT: A  396 THR cc_start: 0.9548 (t) cc_final: 0.9282 (m)
REVERT: A  458 GLU cc_start: 0.8571 (pp20) cc_final: 0.8091 (pp20)
REVERT: A  644 ARG cc_start: 0.8274 (mmp80) cc_final: 0.7963 (tpp80)
REVERT: B   32 MET cc_start: 0.6425 (mmp) cc_final: 0.5271 (mmm)
REVERT: B  137 MET cc_start: 0.9120 (mtt) cc_final: 0.8868 (mtt)
REVERT: B  250 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5612 (tpt)
REVERT: B  489 MET cc_start: 0.8195 (ttp) cc_final: 0.7841 (ttp)
REVERT: C  143 GLN cc_start: 0.8278 (tp40) cc_final: 0.8029 (mm-40)
REVERT: C  149 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7129 (mt-10)
REVERT: C  259 MET cc_start: 0.8352 (mmm) cc_final: 0.7858 (mmt)
REVERT: C  420 MET cc_start: 0.8503 (mtp) cc_final: 0.8161 (mtm)
REVERT: C  430 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7633 (tm-30)
  outliers start: 30
  outliers final: 24
  residues processed: 139
  average time/residue: 0.2106
  time to fit residues: 44.9167
Evaluate side-chains
  136 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 1.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  515 GLU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  250 MET
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  347 MET
Chi-restraints excluded: chain C residue  446 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 108 optimal weight:    0.3980
   chunk 3 optimal weight:    0.6980
   chunk 125 optimal weight:    0.7980
   chunk 94 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 135 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.132100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.096838 restraints weight = 18967.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3182 rms_B_bonded: 2.51
r_work: 0.3031 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12241  Z= 0.110
  Angle     :  0.521   7.878  16621  Z= 0.256
  Chirality :  0.040   0.207   1931
  Planarity :  0.004   0.066   2118
  Dihedral  :  3.788  26.868   1633
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.54 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -0.42 (0.23), residues: 1508
  helix:  0.90 (0.19), residues: 798
  sheet: -1.00 (0.47), residues: 143
  loop : -1.79 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 285 
 HIS   0.003   0.001   HIS A 294 
 PHE   0.018   0.001   PHE C 422 
 TYR   0.027   0.001   TYR C 107 
 ARG   0.008   0.000   ARG B 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02992 (  348)
  hydrogen bonds       : angle       3.19500 ( 1044)
  metal coordination   : bond        0.00246 (    6)
  covalent geometry    : bond        0.00266 (12235)
  covalent geometry    : angle       0.52057 (16621)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 1.286 
Fit side-chains
REVERT: A  191 TRP cc_start: 0.7697 (m100) cc_final: 0.7434 (m100)
REVERT: A  261 ASP cc_start: 0.8423 (m-30) cc_final: 0.7999 (m-30)
REVERT: A  302 ILE cc_start: 0.8969 (mm) cc_final: 0.8726 (mt)
REVERT: A  396 THR cc_start: 0.9539 (t) cc_final: 0.9275 (m)
REVERT: A  458 GLU cc_start: 0.8557 (pp20) cc_final: 0.8087 (pp20)
REVERT: A  569 MET cc_start: 0.8479 (mmm) cc_final: 0.8247 (mmm)
REVERT: A  644 ARG cc_start: 0.8263 (mmp80) cc_final: 0.7954 (tpp80)
REVERT: B   32 MET cc_start: 0.6337 (mmp) cc_final: 0.5184 (mmm)
REVERT: B  137 MET cc_start: 0.9130 (mtt) cc_final: 0.8903 (mtt)
REVERT: B  250 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5671 (tpt)
REVERT: B  489 MET cc_start: 0.8183 (ttp) cc_final: 0.7832 (ttp)
REVERT: C  143 GLN cc_start: 0.8255 (tp40) cc_final: 0.8008 (mm-40)
REVERT: C  149 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7114 (mt-10)
REVERT: C  259 MET cc_start: 0.8221 (mmm) cc_final: 0.7874 (mmt)
REVERT: C  420 MET cc_start: 0.8482 (mtp) cc_final: 0.8143 (mtm)
REVERT: C  430 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7616 (tm-30)
  outliers start: 25
  outliers final: 22
  residues processed: 134
  average time/residue: 0.2057
  time to fit residues: 42.6531
Evaluate side-chains
  137 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  515 GLU
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  250 MET
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  347 MET
Chi-restraints excluded: chain C residue  394 ASP
Chi-restraints excluded: chain C residue  446 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 82 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   chunk 109 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 126 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:
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.095659 restraints weight = 18897.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 2.49
r_work: 0.3014 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12241  Z= 0.139
  Angle     :  0.535   8.120  16621  Z= 0.263
  Chirality :  0.041   0.213   1931
  Planarity :  0.005   0.068   2118
  Dihedral  :  3.881  27.195   1633
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.69 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -0.42 (0.23), residues: 1508
  helix:  0.91 (0.19), residues: 793
  sheet: -1.00 (0.46), residues: 143
  loop : -1.79 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 285 
 HIS   0.004   0.001   HIS C 157 
 PHE   0.020   0.001   PHE C 422 
 TYR   0.028   0.001   TYR C 107 
 ARG   0.007   0.000   ARG B 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03327 (  348)
  hydrogen bonds       : angle       3.27198 ( 1044)
  metal coordination   : bond        0.00355 (    6)
  covalent geometry    : bond        0.00341 (12235)
  covalent geometry    : angle       0.53450 (16621)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 1.295 
Fit side-chains
REVERT: A  191 TRP cc_start: 0.7731 (m100) cc_final: 0.7468 (m100)
REVERT: A  302 ILE cc_start: 0.8978 (mm) cc_final: 0.8730 (mt)
REVERT: A  458 GLU cc_start: 0.8586 (pp20) cc_final: 0.8124 (pp20)
REVERT: A  644 ARG cc_start: 0.8296 (mmp80) cc_final: 0.7981 (tpp80)
REVERT: A  718 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8336 (mmtp)
REVERT: B   32 MET cc_start: 0.6435 (mmp) cc_final: 0.5312 (mmm)
REVERT: B  489 MET cc_start: 0.8177 (ttp) cc_final: 0.7819 (ttp)
REVERT: C  143 GLN cc_start: 0.8321 (tp40) cc_final: 0.7858 (mm-40)
REVERT: C  149 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7268 (mt-10)
REVERT: C  259 MET cc_start: 0.8253 (mmm) cc_final: 0.7940 (mmt)
REVERT: C  420 MET cc_start: 0.8481 (mtp) cc_final: 0.8122 (mtm)
REVERT: C  430 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7605 (tm-30)
  outliers start: 25
  outliers final: 25
  residues processed: 135
  average time/residue: 0.2119
  time to fit residues: 44.0900
Evaluate side-chains
  138 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 1.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  515 GLU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  347 MET
Chi-restraints excluded: chain C residue  394 ASP
Chi-restraints excluded: chain C residue  446 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 0 optimal weight:    0.6980
   chunk 130 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 111 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 118 optimal weight:    0.5980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.131487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.100020 restraints weight = 18870.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.74
r_work: 0.3004 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3010
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3010 r_free = 0.3010    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3010
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12241  Z= 0.122
  Angle     :  0.543   8.022  16621  Z= 0.269
  Chirality :  0.041   0.223   1931
  Planarity :  0.005   0.066   2118
  Dihedral  :  3.866  26.936   1633
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.22 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -0.36 (0.23), residues: 1508
  helix:  0.95 (0.19), residues: 794
  sheet: -0.93 (0.47), residues: 143
  loop : -1.75 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 285 
 HIS   0.004   0.001   HIS C 157 
 PHE   0.020   0.001   PHE C 422 
 TYR   0.028   0.001   TYR C 107 
 ARG   0.006   0.000   ARG B 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03196 (  348)
  hydrogen bonds       : angle       3.25081 ( 1044)
  metal coordination   : bond        0.00289 (    6)
  covalent geometry    : bond        0.00295 (12235)
  covalent geometry    : angle       0.54256 (16621)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 1.233 
Fit side-chains
REVERT: A  191 TRP cc_start: 0.7738 (m100) cc_final: 0.7487 (m100)
REVERT: A  261 ASP cc_start: 0.8415 (m-30) cc_final: 0.8122 (m-30)
REVERT: A  302 ILE cc_start: 0.8974 (mm) cc_final: 0.8731 (mt)
REVERT: A  458 GLU cc_start: 0.8604 (pp20) cc_final: 0.8133 (pp20)
REVERT: A  644 ARG cc_start: 0.8315 (mmp80) cc_final: 0.7998 (tpp80)
REVERT: A  718 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8338 (mmtp)
REVERT: B   32 MET cc_start: 0.6428 (mmp) cc_final: 0.5302 (mmm)
REVERT: B  489 MET cc_start: 0.8177 (ttp) cc_final: 0.7812 (ttp)
REVERT: C  143 GLN cc_start: 0.8323 (tp40) cc_final: 0.7874 (mm-40)
REVERT: C  149 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7320 (mt-10)
REVERT: C  259 MET cc_start: 0.8270 (mmm) cc_final: 0.7941 (mmt)
REVERT: C  420 MET cc_start: 0.8480 (mtp) cc_final: 0.8115 (mtm)
REVERT: C  430 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7655 (tm-30)
  outliers start: 24
  outliers final: 24
  residues processed: 130
  average time/residue: 0.2007
  time to fit residues: 40.3008
Evaluate side-chains
  136 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 1.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   88 ASN
Chi-restraints excluded: chain A residue  113 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  515 GLU
Chi-restraints excluded: chain A residue  692 LEU
Chi-restraints excluded: chain A residue  812 PHE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  223 SER
Chi-restraints excluded: chain B residue  255 LEU
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  419 THR
Chi-restraints excluded: chain B residue  504 VAL
Chi-restraints excluded: chain C residue   21 LEU
Chi-restraints excluded: chain C residue   30 MET
Chi-restraints excluded: chain C residue  106 ASP
Chi-restraints excluded: chain C residue  112 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  202 THR
Chi-restraints excluded: chain C residue  347 MET
Chi-restraints excluded: chain C residue  394 ASP
Chi-restraints excluded: chain C residue  446 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 56 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.2980
   chunk 80 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.5182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.132951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.097804 restraints weight = 18706.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 2.49
r_work: 0.3048 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3053
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3053 r_free = 0.3053    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3053
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12241  Z= 0.098
  Angle     :  0.504   7.835  16621  Z= 0.248
  Chirality :  0.040   0.217   1931
  Planarity :  0.004   0.064   2118
  Dihedral  :  3.669  23.761   1633
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.45 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    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: -0.17 (0.23), residues: 1508
  helix:  1.10 (0.19), residues: 797
  sheet: -0.81 (0.47), residues: 143
  loop : -1.69 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 385 
 HIS   0.003   0.001   HIS C  68 
 PHE   0.019   0.001   PHE C 422 
 TYR   0.026   0.001   TYR C 107 
 ARG   0.006   0.000   ARG B 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02731 (  348)
  hydrogen bonds       : angle       3.11419 ( 1044)
  metal coordination   : bond        0.00193 (    6)
  covalent geometry    : bond        0.00234 (12235)
  covalent geometry    : angle       0.50408 (16621)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5869.36 seconds
wall clock time: 101 minutes 24.10 seconds (6084.10 seconds total)