Starting phenix.real_space_refine
on Sat Aug 23 12:03:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r23_18834/08_2025/8r23_18834.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r23_18834/08_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_18834/08_2025/8r23_18834.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r23_18834/08_2025/8r23_18834.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r23_18834/08_2025/8r23_18834.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r23_18834/08_2025/8r23_18834.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU: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: 3.35, per 1000 atoms: 0.28
  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: 1.00
  Conformation dependent library (CDL) restraints added in 592.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  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: 0.35
  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: 1.62

  Time building geometry restraints manager: 1.35 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:             0.860
  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:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.850
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.360
-------------------------------------------------------------------------------
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 : 6.92
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.004   0.000   ARG A  20 
 TYR   0.013   0.001   TYR C 278 
 PHE   0.017   0.001   PHE C 312 
 TRP   0.014   0.001   TRP A 114 
 HIS   0.005   0.001   HIS A 294 

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

*********************** 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  : 0.506 
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: 0.1472
  time to fit residues: 37.6283
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  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0970
   chunk 149 optimal weight:    0.7980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.130274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.095018 restraints weight = 18837.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.52
r_work: 0.2999 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3003
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3003 r_free = 0.3003    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 = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12241  Z= 0.125
  Angle     :  0.579   6.461  16621  Z= 0.290
  Chirality :  0.041   0.150   1931
  Planarity :  0.005   0.087   2118
  Dihedral  :  4.512  42.946   1633
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  9.57 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.20), residues: 1508
  helix: -1.45 (0.17), residues: 785
  sheet: -2.53 (0.40), residues: 155
  loop : -2.75 (0.23), residues: 568

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (12235)
  covalent geometry    : angle       0.57948 (16621)
  hydrogen bonds       : bond        0.05072 (  348)
  hydrogen bonds       : angle       4.43914 ( 1044)
  metal coordination   : bond        0.00605 (    6)

*********************** 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  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.7221 (mtp) cc_final: 0.6946 (mtp)
REVERT: A  261 ASP cc_start: 0.8549 (m-30) cc_final: 0.8121 (m-30)
REVERT: A  396 THR cc_start: 0.9501 (t) cc_final: 0.9264 (m)
REVERT: A  458 GLU cc_start: 0.8465 (pp20) cc_final: 0.7902 (pp20)
REVERT: A  529 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7741 (ttm-80)
REVERT: A  692 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8672 (tp)
REVERT: A  718 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8288 (mmtp)
REVERT: B  489 MET cc_start: 0.8395 (ttp) cc_final: 0.7864 (ttp)
REVERT: C  143 GLN cc_start: 0.8330 (tp40) cc_final: 0.8127 (mm-40)
REVERT: C  149 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7085 (mt-10)
REVERT: C  259 MET cc_start: 0.8319 (mmm) cc_final: 0.7787 (mmp)
REVERT: C  430 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7395 (tm-30)
  outliers start: 18
  outliers final: 9
  residues processed: 161
  average time/residue: 0.1222
  time to fit residues: 27.9605
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  : 0.387 
-------------------------------------------------------------------------------
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 53 optimal weight:    0.8980
   chunk 74 optimal weight:    8.9990
   chunk 149 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 147 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0170
   chunk 82 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.6820

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

Flipped N/Q/H residues before XYZ refinement:
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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.130874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.095574 restraints weight = 19018.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.55
r_work: 0.3008 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3008
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    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 = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.1774

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= 0.119
  Angle     :  0.547   8.851  16621  Z= 0.271
  Chirality :  0.041   0.150   1931
  Planarity :  0.005   0.080   2118
  Dihedral  :  4.193  39.351   1633
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.07 (0.21), residues: 1508
  helix: -0.43 (0.19), residues: 788
  sheet: -2.34 (0.41), residues: 148
  loop : -2.35 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 180 
 TYR   0.018   0.001   TYR C 107 
 PHE   0.024   0.001   PHE C 282 
 TRP   0.006   0.001   TRP A 232 
 HIS   0.005   0.001   HIS B 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (12235)
  covalent geometry    : angle       0.54681 (16621)
  hydrogen bonds       : bond        0.03888 (  348)
  hydrogen bonds       : angle       3.73981 ( 1044)
  metal coordination   : bond        0.00473 (    6)

*********************** 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
  153 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7203 (mtp) cc_final: 0.6963 (mtp)
REVERT: A  261 ASP cc_start: 0.8392 (m-30) cc_final: 0.7984 (m-30)
REVERT: A  396 THR cc_start: 0.9492 (t) cc_final: 0.9241 (m)
REVERT: A  458 GLU cc_start: 0.8498 (pp20) cc_final: 0.7895 (pp20)
REVERT: A  644 ARG cc_start: 0.8237 (mmp80) cc_final: 0.7932 (mmm160)
REVERT: A  708 LEU cc_start: 0.8567 (tp) cc_final: 0.8325 (tp)
REVERT: A  718 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8331 (mmtp)
REVERT: B  250 MET cc_start: 0.6692 (tpt) cc_final: 0.6436 (tpt)
REVERT: B  489 MET cc_start: 0.8259 (ttp) cc_final: 0.7749 (ttp)
REVERT: C  143 GLN cc_start: 0.8230 (tp40) cc_final: 0.7967 (mm-40)
REVERT: C  149 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7364 (mt-10)
REVERT: C  259 MET cc_start: 0.8177 (mmm) cc_final: 0.7790 (mmt)
REVERT: C  430 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7556 (tm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 149
  average time/residue: 0.1110
  time to fit residues: 24.2328
Evaluate side-chains
  131 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
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  223 SER
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  200 LEU
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 55 optimal weight:    0.4980
   chunk 117 optimal weight:    2.9990
   chunk 151 optimal weight:    0.7980
   chunk 120 optimal weight:    0.3980
   chunk 124 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0670
   chunk 142 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   overall best weight:    0.4318

-------------------------------------------------------------------------------
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 472 GLN
A 800 GLN
A 804 GLN
C 260 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.132579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.097422 restraints weight = 19002.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 2.53
r_work: 0.3040 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    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 = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12241  Z= 0.098
  Angle     :  0.513   7.065  16621  Z= 0.254
  Chirality :  0.040   0.143   1931
  Planarity :  0.004   0.073   2118
  Dihedral  :  3.939  34.645   1633
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.66 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.22), residues: 1508
  helix:  0.15 (0.19), residues: 791
  sheet: -1.68 (0.44), residues: 143
  loop : -2.14 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 215 
 TYR   0.018   0.001   TYR C 107 
 PHE   0.023   0.001   PHE C 282 
 TRP   0.006   0.001   TRP A 514 
 HIS   0.004   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (12235)
  covalent geometry    : angle       0.51337 (16621)
  hydrogen bonds       : bond        0.03042 (  348)
  hydrogen bonds       : angle       3.40514 ( 1044)
  metal coordination   : bond        0.00213 (    6)

*********************** 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
  150 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 133
  time to evaluate  : 0.543 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7123 (mtp) cc_final: 0.6903 (mtp)
REVERT: A  191 TRP cc_start: 0.7770 (m100) cc_final: 0.7452 (m100)
REVERT: A  261 ASP cc_start: 0.8431 (m-30) cc_final: 0.8008 (m-30)
REVERT: A  302 ILE cc_start: 0.8925 (mm) cc_final: 0.8671 (mt)
REVERT: A  396 THR cc_start: 0.9529 (t) cc_final: 0.9277 (m)
REVERT: A  458 GLU cc_start: 0.8447 (pp20) cc_final: 0.7894 (pp20)
REVERT: A  692 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8705 (tp)
REVERT: A  708 LEU cc_start: 0.8530 (tp) cc_final: 0.8278 (tp)
REVERT: B   35 THR cc_start: 0.8588 (t) cc_final: 0.8336 (p)
REVERT: B  250 MET cc_start: 0.6543 (tpt) cc_final: 0.6202 (tpt)
REVERT: B  489 MET cc_start: 0.8200 (ttp) cc_final: 0.7767 (ttp)
REVERT: C  143 GLN cc_start: 0.8208 (tp40) cc_final: 0.7922 (mm-40)
REVERT: C  149 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7374 (mt-10)
REVERT: C  259 MET cc_start: 0.8176 (mmm) cc_final: 0.7785 (mmt)
REVERT: C  430 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7643 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 145
  average time/residue: 0.1100
  time to fit residues: 23.7373
Evaluate side-chains
  132 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
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  692 LEU
Chi-restraints excluded: chain B residue  275 ASP
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  202 THR
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 38 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 152 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 129 optimal weight:    2.9990
   chunk 87 optimal weight:    9.9990
   chunk 17 optimal weight:    0.0370
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7060

-------------------------------------------------------------------------------
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 800 GLN
A 804 GLN
B 493 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.131968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.096778 restraints weight = 18985.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 2.51
r_work: 0.3029 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3033
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    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 = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.2183

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= 0.114
  Angle     :  0.521   7.466  16621  Z= 0.258
  Chirality :  0.040   0.160   1931
  Planarity :  0.004   0.071   2118
  Dihedral  :  3.886  32.199   1633
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.96 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.22), residues: 1508
  helix:  0.46 (0.19), residues: 788
  sheet: -1.49 (0.45), residues: 143
  loop : -1.98 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.018   0.001   TYR C 107 
 PHE   0.019   0.001   PHE C 282 
 TRP   0.006   0.001   TRP C 285 
 HIS   0.004   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (12235)
  covalent geometry    : angle       0.52130 (16621)
  hydrogen bonds       : bond        0.03154 (  348)
  hydrogen bonds       : angle       3.31989 ( 1044)
  metal coordination   : bond        0.00352 (    6)

*********************** 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  : 0.492 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7143 (mtp) cc_final: 0.6923 (mtp)
REVERT: A  191 TRP cc_start: 0.7801 (m100) cc_final: 0.7461 (m100)
REVERT: A  261 ASP cc_start: 0.8441 (m-30) cc_final: 0.7982 (m-30)
REVERT: A  302 ILE cc_start: 0.8941 (mm) cc_final: 0.8676 (mt)
REVERT: A  396 THR cc_start: 0.9530 (t) cc_final: 0.9260 (m)
REVERT: A  458 GLU cc_start: 0.8447 (pp20) cc_final: 0.7905 (pp20)
REVERT: A  692 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8676 (tp)
REVERT: B  486 MET cc_start: 0.8444 (mmp) cc_final: 0.8243 (mmp)
REVERT: B  489 MET cc_start: 0.8193 (ttp) cc_final: 0.7740 (ttp)
REVERT: C  143 GLN cc_start: 0.8245 (tp40) cc_final: 0.7997 (mm-40)
REVERT: C  149 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7097 (mt-10)
REVERT: C  219 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7081 (mmm160)
REVERT: C  259 MET cc_start: 0.8230 (mmm) cc_final: 0.7844 (mmt)
REVERT: C  430 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7629 (tm-30)
  outliers start: 23
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1079
  time to fit residues: 23.4546
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  : 0.470 
-------------------------------------------------------------------------------
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  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  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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 66 optimal weight:    4.9990
   chunk 58 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0970
   chunk 85 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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
B 493 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.132169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.096894 restraints weight = 18949.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 2.54
r_work: 0.3031 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    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 = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2289

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= 0.106
  Angle     :  0.519   7.587  16621  Z= 0.255
  Chirality :  0.040   0.170   1931
  Planarity :  0.004   0.067   2118
  Dihedral  :  3.812  30.062   1633
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 13.87 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.22), residues: 1508
  helix:  0.67 (0.19), residues: 789
  sheet: -1.28 (0.46), residues: 143
  loop : -1.87 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 215 
 TYR   0.017   0.001   TYR C 107 
 PHE   0.016   0.001   PHE C 422 
 TRP   0.005   0.001   TRP C 285 
 HIS   0.003   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (12235)
  covalent geometry    : angle       0.51877 (16621)
  hydrogen bonds       : bond        0.03019 (  348)
  hydrogen bonds       : angle       3.22865 ( 1044)
  metal coordination   : bond        0.00279 (    6)

*********************** 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
  148 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.530 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7169 (mtp) cc_final: 0.6958 (mtp)
REVERT: A  191 TRP cc_start: 0.7733 (m100) cc_final: 0.7428 (m100)
REVERT: A  261 ASP cc_start: 0.8437 (m-30) cc_final: 0.7997 (m-30)
REVERT: A  302 ILE cc_start: 0.8941 (mm) cc_final: 0.8680 (mt)
REVERT: A  396 THR cc_start: 0.9526 (t) cc_final: 0.9258 (m)
REVERT: A  458 GLU cc_start: 0.8455 (pp20) cc_final: 0.7928 (pp20)
REVERT: A  644 ARG cc_start: 0.8217 (mmp80) cc_final: 0.7910 (tpp80)
REVERT: A  692 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8689 (tp)
REVERT: A  708 LEU cc_start: 0.8546 (tp) cc_final: 0.8260 (tp)
REVERT: B   32 MET cc_start: 0.6119 (mmp) cc_final: 0.5028 (mmm)
REVERT: B  250 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5862 (tpt)
REVERT: B  489 MET cc_start: 0.8211 (ttp) cc_final: 0.7758 (ttp)
REVERT: C  143 GLN cc_start: 0.8244 (tp40) cc_final: 0.7834 (mm-40)
REVERT: C  149 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7339 (mt-10)
REVERT: C  219 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7070 (mmm160)
REVERT: C  259 MET cc_start: 0.8344 (mmm) cc_final: 0.7836 (mmt)
REVERT: C  430 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7681 (tm-30)
  outliers start: 23
  outliers final: 19
  residues processed: 141
  average time/residue: 0.1068
  time to fit residues: 22.4834
Evaluate side-chains
  135 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
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  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  317 ASP
Chi-restraints excluded: chain B residue  324 VAL
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  112 VAL
Chi-restraints excluded: chain C residue  158 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 152 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 118 optimal weight:    0.0870
   chunk 116 optimal weight:    0.7980
   chunk 133 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 143 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.1162

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.130771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.095319 restraints weight = 18846.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.51
r_work: 0.3007 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    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 = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12241  Z= 0.148
  Angle     :  0.548   7.881  16621  Z= 0.269
  Chirality :  0.041   0.192   1931
  Planarity :  0.005   0.069   2118
  Dihedral  :  3.913  30.502   1633
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.39 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.68 (0.22), residues: 1508
  helix:  0.70 (0.19), residues: 788
  sheet: -1.25 (0.46), residues: 143
  loop : -1.85 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  17 
 TYR   0.017   0.001   TYR C 107 
 PHE   0.018   0.001   PHE C 422 
 TRP   0.008   0.001   TRP C 285 
 HIS   0.005   0.001   HIS C 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (12235)
  covalent geometry    : angle       0.54786 (16621)
  hydrogen bonds       : bond        0.03391 (  348)
  hydrogen bonds       : angle       3.31811 ( 1044)
  metal coordination   : bond        0.00451 (    6)

*********************** 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
  140 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.458 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7186 (mtp) cc_final: 0.6981 (mtp)
REVERT: A  191 TRP cc_start: 0.7747 (m100) cc_final: 0.7465 (m100)
REVERT: A  458 GLU cc_start: 0.8575 (pp20) cc_final: 0.8085 (pp20)
REVERT: A  692 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8670 (tp)
REVERT: A  708 LEU cc_start: 0.8574 (tp) cc_final: 0.8346 (tp)
REVERT: B   32 MET cc_start: 0.6518 (mmp) cc_final: 0.5381 (mmm)
REVERT: B  489 MET cc_start: 0.8206 (ttp) cc_final: 0.7845 (ttp)
REVERT: C  143 GLN cc_start: 0.8289 (tp40) cc_final: 0.7844 (mm-40)
REVERT: C  149 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7300 (mt-10)
REVERT: C  219 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7097 (mmm160)
REVERT: C  259 MET cc_start: 0.8255 (mmm) cc_final: 0.7872 (mmt)
REVERT: C  372 MET cc_start: 0.7153 (mtp) cc_final: 0.6948 (mtp)
REVERT: C  420 MET cc_start: 0.8496 (mtp) cc_final: 0.8147 (mtm)
REVERT: C  430 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7620 (tm-30)
  outliers start: 26
  outliers final: 21
  residues processed: 134
  average time/residue: 0.1049
  time to fit residues: 21.0481
Evaluate side-chains
  133 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
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  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  112 VAL
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  394 ASP
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 38 optimal weight:    0.6980
   chunk 124 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0010
   chunk 95 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 93 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.6788

-------------------------------------------------------------------------------
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 = 0.3678 r_free = 0.3678 target = 0.131893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.096651 restraints weight = 18846.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.50
r_work: 0.3030 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2350

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     :  0.519   7.951  16621  Z= 0.256
  Chirality :  0.040   0.209   1931
  Planarity :  0.004   0.064   2118
  Dihedral  :  3.799  28.780   1633
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.07 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.23), residues: 1508
  helix:  0.85 (0.19), residues: 791
  sheet: -1.06 (0.47), residues: 143
  loop : -1.77 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 215 
 TYR   0.018   0.001   TYR C 107 
 PHE   0.018   0.001   PHE C 422 
 TRP   0.006   0.001   TRP C 285 
 HIS   0.003   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (12235)
  covalent geometry    : angle       0.51938 (16621)
  hydrogen bonds       : bond        0.03024 (  348)
  hydrogen bonds       : angle       3.19620 ( 1044)
  metal coordination   : bond        0.00236 (    6)

*********************** 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
  140 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.482 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7186 (mtp) cc_final: 0.6958 (mtp)
REVERT: A  191 TRP cc_start: 0.7696 (m100) cc_final: 0.7428 (m100)
REVERT: A  261 ASP cc_start: 0.8438 (m-30) cc_final: 0.7987 (m-30)
REVERT: A  302 ILE cc_start: 0.8942 (mm) cc_final: 0.8676 (mt)
REVERT: A  458 GLU cc_start: 0.8533 (pp20) cc_final: 0.8050 (pp20)
REVERT: A  522 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7945 (mm-30)
REVERT: A  644 ARG cc_start: 0.8248 (mmp80) cc_final: 0.7951 (tpp80)
REVERT: A  708 LEU cc_start: 0.8541 (tp) cc_final: 0.8310 (tp)
REVERT: B   32 MET cc_start: 0.6424 (mmp) cc_final: 0.5253 (mmm)
REVERT: B  137 MET cc_start: 0.9079 (mtt) cc_final: 0.8814 (mtt)
REVERT: B  489 MET cc_start: 0.8198 (ttp) cc_final: 0.7843 (ttp)
REVERT: C  143 GLN cc_start: 0.8259 (tp40) cc_final: 0.8018 (mm-40)
REVERT: C  149 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7128 (mt-10)
REVERT: C  219 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7132 (mmm160)
REVERT: C  259 MET cc_start: 0.8244 (mmm) cc_final: 0.7878 (mmt)
REVERT: C  430 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7606 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 134
  average time/residue: 0.1074
  time to fit residues: 21.6210
Evaluate side-chains
  134 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
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  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  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  112 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 140 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 146 optimal weight:    0.8980
   chunk 114 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 111 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 133 optimal weight:    0.0970
   overall best weight:    0.7778

-------------------------------------------------------------------------------
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 = 0.3676 r_free = 0.3676 target = 0.131768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.096453 restraints weight = 18881.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.50
r_work: 0.3027 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2395

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= 0.119
  Angle     :  0.526   9.270  16621  Z= 0.258
  Chirality :  0.041   0.219   1931
  Planarity :  0.005   0.067   2118
  Dihedral  :  3.792  27.606   1633
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 15.15 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.23), residues: 1508
  helix:  0.93 (0.19), residues: 791
  sheet: -0.99 (0.47), residues: 143
  loop : -1.76 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 500 
 TYR   0.019   0.001   TYR C 107 
 PHE   0.019   0.001   PHE C 422 
 TRP   0.006   0.001   TRP C 285 
 HIS   0.003   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (12235)
  covalent geometry    : angle       0.52585 (16621)
  hydrogen bonds       : bond        0.03058 (  348)
  hydrogen bonds       : angle       3.18172 ( 1044)
  metal coordination   : bond        0.00305 (    6)

*********************** 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
  138 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.590 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7202 (mtp) cc_final: 0.6987 (mtp)
REVERT: A  191 TRP cc_start: 0.7684 (m100) cc_final: 0.7431 (m100)
REVERT: A  261 ASP cc_start: 0.8462 (m-30) cc_final: 0.8011 (m-30)
REVERT: A  302 ILE cc_start: 0.8940 (mm) cc_final: 0.8673 (mt)
REVERT: A  458 GLU cc_start: 0.8550 (pp20) cc_final: 0.8085 (pp20)
REVERT: A  708 LEU cc_start: 0.8548 (tp) cc_final: 0.8314 (tp)
REVERT: B   32 MET cc_start: 0.6407 (mmp) cc_final: 0.5257 (mmm)
REVERT: B  137 MET cc_start: 0.9132 (mtt) cc_final: 0.8901 (mtt)
REVERT: B  203 ILE cc_start: 0.9102 (mm) cc_final: 0.8867 (mm)
REVERT: B  489 MET cc_start: 0.8158 (ttp) cc_final: 0.7694 (ttp)
REVERT: C  143 GLN cc_start: 0.8273 (tp40) cc_final: 0.7831 (mm-40)
REVERT: C  149 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7295 (mt-10)
REVERT: C  219 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7100 (mmm160)
REVERT: C  259 MET cc_start: 0.8266 (mmm) cc_final: 0.7935 (mmt)
REVERT: C  420 MET cc_start: 0.8413 (mtp) cc_final: 0.8026 (mtm)
REVERT: C  430 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7603 (tm-30)
  outliers start: 23
  outliers final: 20
  residues processed: 133
  average time/residue: 0.1025
  time to fit residues: 20.9292
Evaluate side-chains
  132 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
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  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  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  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 27 optimal weight:    0.5980
   chunk 114 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0040
   chunk 115 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 131 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 121 optimal weight:    1.9990
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.132817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.097561 restraints weight = 18849.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.52
r_work: 0.3044 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3043
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3043 r_free = 0.3043    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3043
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2523

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= 0.100
  Angle     :  0.512   8.361  16621  Z= 0.250
  Chirality :  0.040   0.206   1931
  Planarity :  0.004   0.062   2118
  Dihedral  :  3.659  24.347   1633
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 15.75 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.23), residues: 1508
  helix:  1.06 (0.19), residues: 798
  sheet: -0.84 (0.47), residues: 143
  loop : -1.69 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 500 
 TYR   0.017   0.001   TYR C 107 
 PHE   0.019   0.001   PHE C 422 
 TRP   0.006   0.001   TRP A 514 
 HIS   0.003   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (12235)
  covalent geometry    : angle       0.51193 (16621)
  hydrogen bonds       : bond        0.02738 (  348)
  hydrogen bonds       : angle       3.07845 ( 1044)
  metal coordination   : bond        0.00227 (    6)

********************** 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: 19
    poor density    : 117
  time to evaluate  : 0.673 
Fit side-chains
REVERT: A    1 MET cc_start: 0.7212 (mtp) cc_final: 0.7002 (mtp)
REVERT: A  191 TRP cc_start: 0.7657 (m100) cc_final: 0.7396 (m100)
REVERT: A  261 ASP cc_start: 0.8414 (m-30) cc_final: 0.7975 (m-30)
REVERT: A  302 ILE cc_start: 0.8938 (mm) cc_final: 0.8648 (mt)
REVERT: A  458 GLU cc_start: 0.8485 (pp20) cc_final: 0.8155 (pp20)
REVERT: A  569 MET cc_start: 0.8464 (mmm) cc_final: 0.8203 (mmm)
REVERT: A  644 ARG cc_start: 0.8244 (mmp80) cc_final: 0.7953 (tpp80)
REVERT: A  708 LEU cc_start: 0.8520 (tp) cc_final: 0.8293 (tp)
REVERT: B   32 MET cc_start: 0.6281 (mmp) cc_final: 0.5112 (mmm)
REVERT: B  489 MET cc_start: 0.8174 (ttp) cc_final: 0.7715 (ttp)
REVERT: B  503 GLU cc_start: 0.7803 (tp30) cc_final: 0.7255 (tp30)
REVERT: C  143 GLN cc_start: 0.8226 (tp40) cc_final: 0.7803 (mm-40)
REVERT: C  149 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7302 (mt-10)
REVERT: C  259 MET cc_start: 0.8229 (mmm) cc_final: 0.7914 (mmt)
REVERT: C  303 LYS cc_start: 0.8368 (mmtm) cc_final: 0.8118 (mtpp)
REVERT: C  420 MET cc_start: 0.8404 (mtp) cc_final: 0.8038 (mtm)
REVERT: C  430 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7610 (tm-30)
  outliers start: 19
  outliers final: 18
  residues processed: 132
  average time/residue: 0.1014
  time to fit residues: 20.5671
Evaluate side-chains
  131 residues out of total 1333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
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 B residue   26 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  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 59 optimal weight:    0.9990
   chunk 134 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0570
   chunk 41 optimal weight:    0.0980
   chunk 61 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0770
   chunk 145 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 135 optimal weight:    2.9990
   overall best weight:    0.2656

-------------------------------------------------------------------------------
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 105 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.134625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.099543 restraints weight = 18807.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.51
r_work: 0.3070 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3078
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3078 r_free = 0.3078    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3078
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12241  Z= 0.087
  Angle     :  0.501   7.917  16621  Z= 0.245
  Chirality :  0.040   0.236   1931
  Planarity :  0.004   0.059   2118
  Dihedral  :  3.481  19.824   1633
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 16.20 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.44 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.05 (0.23), residues: 1508
  helix:  1.28 (0.20), residues: 798
  sheet: -0.37 (0.50), residues: 134
  loop : -1.69 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 500 
 TYR   0.016   0.001   TYR C 107 
 PHE   0.018   0.001   PHE C 422 
 TRP   0.008   0.001   TRP A 385 
 HIS   0.003   0.000   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 (12235)
  covalent geometry    : angle       0.50062 (16621)
  hydrogen bonds       : bond        0.02402 (  348)
  hydrogen bonds       : angle       2.95621 ( 1044)
  metal coordination   : bond        0.00189 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2888.70 seconds
wall clock time: 50 minutes 27.57 seconds (3027.57 seconds total)