Starting phenix.real_space_refine
on Thu May  1 00:16:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8syo_40886/05_2025/8syo_40886.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8syo_40886/05_2025/8syo_40886.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8syo_40886/05_2025/8syo_40886.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8syo_40886/05_2025/8syo_40886.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8syo_40886/05_2025/8syo_40886.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8syo_40886/05_2025/8syo_40886.cif"
  }
  resolution = 2.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    6487      2.51       5
     N    1695      2.21       5
     O    1825      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10069
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 802, 6474
          Classifications: {'peptide': 802}
          Link IDs: {'PTRANS': 31, 'TRANS': 770}
          Chain breaks: 3
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 1463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1463
          Classifications: {'peptide': 184}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 175}
    Chain: "C"
      Number of atoms: 2132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2132
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 15, 'TRANS': 257}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 5.76, per 1000 atoms: 0.57
  Number of scatterers: 10069
  At special positions: 0
  Unit cell: (78.6176, 108.365, 172.109, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    1825      8.00
     N    1695      7.00
     C    6487      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2410

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 10 sheets defined
      53.5% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
    Processing helix  chain 'A' and resid 116 through 128
      removed outlier: 3.805A  pdb=" N   LYS A 120 " --> pdb=" O   PRO A 116 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLY A 122 " --> pdb=" O   THR A 118 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 201
    Processing helix  chain 'A' and resid 203 through 218
      removed outlier: 3.731A  pdb=" N   LEU A 218 " --> pdb=" O   CYS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 225
      No H-bonds generated for 'chain 'A' and resid 223 through 225'
    Processing helix  chain 'A' and resid 226 through 254
      removed outlier: 3.628A  pdb=" N   ASP A 236 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 286
    Processing helix  chain 'A' and resid 289 through 300
      removed outlier: 3.647A  pdb=" N   ILE A 300 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 307
    Processing helix  chain 'A' and resid 310 through 323
      Proline residue:  A 317  - end of helix
    Processing helix  chain 'A' and resid 324 through 326
      No H-bonds generated for 'chain 'A' and resid 324 through 326'
    Processing helix  chain 'A' and resid 328 through 347
    Processing helix  chain 'A' and resid 350 through 365
      removed outlier: 4.224A  pdb=" N   LYS A 356 " --> pdb=" O   GLU A 352 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ASN A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   PHE A 358 " --> pdb=" O   LEU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 368
      No H-bonds generated for 'chain 'A' and resid 366 through 368'
    Processing helix  chain 'A' and resid 370 through 381
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 391 through 403
      removed outlier: 4.004A  pdb=" N   TRP A 397 " --> pdb=" O   PRO A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 420
    Processing helix  chain 'A' and resid 424 through 435
      removed outlier: 3.666A  pdb=" N   ASN A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   SER A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 443
    Processing helix  chain 'A' and resid 443 through 453
      removed outlier: 3.666A  pdb=" N   GLU A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.885A  pdb=" N   LEU A 464 " --> pdb=" O   PRO A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 480
      No H-bonds generated for 'chain 'A' and resid 478 through 480'
    Processing helix  chain 'A' and resid 481 through 494
      removed outlier: 3.569A  pdb=" N   VAL A 492 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 517
      removed outlier: 3.879A  pdb=" N   VAL A 508 " --> pdb=" O   ASN A 504 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLU A 511 " --> pdb=" O   GLU A 507 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   TYR A 512 " --> pdb=" O   VAL A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 534
    Processing helix  chain 'A' and resid 537 through 541
      removed outlier: 3.805A  pdb=" N   GLU A 540 " --> pdb=" O   ARG A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 556
    Processing helix  chain 'A' and resid 559 through 564
      removed outlier: 3.689A  pdb=" N   PHE A 564 " --> pdb=" O   PHE A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 576
      removed outlier: 4.008A  pdb=" N   PHE A 576 " --> pdb=" O   PHE A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 3.607A  pdb=" N   GLU A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 619
    Processing helix  chain 'A' and resid 626 through 643
      removed outlier: 3.773A  pdb=" N   MET A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 664
    Processing helix  chain 'A' and resid 667 through 689
    Processing helix  chain 'A' and resid 694 through 712
      removed outlier: 3.736A  pdb=" N   ALA A 699 " --> pdb=" O   ARG A 695 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE A 700 " --> pdb=" O   LYS A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 715
      No H-bonds generated for 'chain 'A' and resid 713 through 715'
    Processing helix  chain 'A' and resid 717 through 734
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 753 through 755
      No H-bonds generated for 'chain 'A' and resid 753 through 755'
    Processing helix  chain 'A' and resid 768 through 784
    Processing helix  chain 'A' and resid 795 through 808
    Processing helix  chain 'A' and resid 815 through 832
      removed outlier: 3.587A  pdb=" N   ARG A 819 " --> pdb=" O   ASP A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 850
    Processing helix  chain 'A' and resid 853 through 881
    Processing helix  chain 'A' and resid 883 through 901
    Processing helix  chain 'A' and resid 906 through 923
      removed outlier: 3.633A  pdb=" N   HIS A 923 " --> pdb=" O   LEU A 919 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 30
      removed outlier: 3.602A  pdb=" N   LYS B  27 " --> pdb=" O   PRO B  23 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LYS B  28 " --> pdb=" O   ALA B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 55
      removed outlier: 3.784A  pdb=" N   TYR B  50 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 111
    Processing helix  chain 'C' and resid 166 through 171
      removed outlier: 3.862A  pdb=" N   ALA C 171 " --> pdb=" O   VAL C 167 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26
      removed outlier: 3.589A  pdb=" N   ARG B 180 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 758 through 761
    Processing sheet with id=AA3, first strand: chain 'B' and resid 76 through 81
      removed outlier: 6.530A  pdb=" N   LYS B  85 " --> pdb=" O   ILE B 114 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   ILE B 116 " --> pdb=" O   LYS B  85 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   GLY B  87 " --> pdb=" O   ILE B 116 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE B 134 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER B 117 " --> pdb=" O   ILE B 134 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 9
    Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 16
    Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 79
      removed outlier: 5.878A  pdb=" N   GLN C  70 " --> pdb=" O   VAL C  47 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL C  47 " --> pdb=" O   GLN C  70 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE C  72 " --> pdb=" O   GLY C  45 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL C  39 " --> pdb=" O   MET C  78 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 79
      removed outlier: 5.878A  pdb=" N   GLN C  70 " --> pdb=" O   VAL C  47 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   VAL C  47 " --> pdb=" O   GLN C  70 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ILE C  72 " --> pdb=" O   GLY C  45 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL C  39 " --> pdb=" O   MET C  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 159
      removed outlier: 6.726A  pdb=" N   LEU C 177 " --> pdb=" O   GLU C 200 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 226 through 239
      removed outlier: 6.962A  pdb=" N   LEU C 213 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASN C 234 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU C 211 " --> pdb=" O   ASN C 234 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   GLN C 236 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   VAL C 209 " --> pdb=" O   GLN C 236 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ALA C 238 " --> pdb=" O   ARG C 207 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ARG C 207 " --> pdb=" O   ALA C 238 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 226 through 239
      removed outlier: 6.962A  pdb=" N   LEU C 213 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.435A  pdb=" N   ASN C 234 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU C 211 " --> pdb=" O   ASN C 234 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   GLN C 236 " --> pdb=" O   VAL C 209 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   VAL C 209 " --> pdb=" O   GLN C 236 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ALA C 238 " --> pdb=" O   ARG C 207 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   ARG C 207 " --> pdb=" O   ALA C 238 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE C 272 " --> pdb=" O   LEU C 292 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   HIS C 284 " --> pdb=" O   LEU C 280 " (cutoff:3.500A)

    610 hydrogen bonds defined for protein.
    1761 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: 3.01

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3228
        1.34 -     1.46: 1988
        1.46 -     1.58: 4977
        1.58 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 10283
  Sorted by residual:
  bond pdb=" CG1 ILE A 712 "
       pdb=" CD1 ILE A 712 "
    ideal  model  delta    sigma   weight residual
    1.513  1.444  0.069 3.90e-02 6.57e+02 3.11e+00
  bond pdb=" CA  ILE A 712 "
       pdb=" CB  ILE A 712 "
    ideal  model  delta    sigma   weight residual
    1.539  1.547 -0.008 5.40e-03 3.43e+04 2.09e+00
  bond pdb=" N   ILE A 712 "
       pdb=" CA  ILE A 712 "
    ideal  model  delta    sigma   weight residual
    1.463  1.478 -0.015 1.20e-02 6.94e+03 1.55e+00
  bond pdb=" C   THR A 534 "
       pdb=" N   PRO A 535 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.36e+00
  bond pdb=" SD  MET A 395 "
       pdb=" CE  MET A 395 "
    ideal  model  delta    sigma   weight residual
    1.791  1.762  0.029 2.50e-02 1.60e+03 1.34e+00
  ... (remaining 10278 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.95: 13658
        1.95 -     3.90: 222
        3.90 -     5.85: 34
        5.85 -     7.80: 4
        7.80 -     9.75: 2
  Bond angle restraints: 13920
  Sorted by residual:
  angle pdb=" N   ILE A 712 "
        pdb=" CA  ILE A 712 "
        pdb=" CB  ILE A 712 "
      ideal   model   delta    sigma   weight residual
     110.45  115.92   -5.47 7.80e-01 1.64e+00 4.91e+01
  angle pdb=" C   ILE A 712 "
        pdb=" CA  ILE A 712 "
        pdb=" CB  ILE A 712 "
      ideal   model   delta    sigma   weight residual
     114.00  106.87    7.13 1.31e+00 5.83e-01 2.96e+01
  angle pdb=" C   LEU B  44 "
        pdb=" N   CYS B  45 "
        pdb=" CA  CYS B  45 "
      ideal   model   delta    sigma   weight residual
     121.54  129.09   -7.55 1.91e+00 2.74e-01 1.56e+01
  angle pdb=" CB  LYS A 602 "
        pdb=" CG  LYS A 602 "
        pdb=" CD  LYS A 602 "
      ideal   model   delta    sigma   weight residual
     111.30  103.21    8.09 2.30e+00 1.89e-01 1.24e+01
  angle pdb=" CB  MET A 533 "
        pdb=" CG  MET A 533 "
        pdb=" SD  MET A 533 "
      ideal   model   delta    sigma   weight residual
     112.70  102.95    9.75 3.00e+00 1.11e-01 1.06e+01
  ... (remaining 13915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 5653
       17.65 -    35.31: 473
       35.31 -    52.96: 67
       52.96 -    70.61: 8
       70.61 -    88.27: 9
  Dihedral angle restraints: 6210
    sinusoidal: 2513
      harmonic: 3697
  Sorted by residual:
  dihedral pdb=" CA  CYS A 737 "
           pdb=" C   CYS A 737 "
           pdb=" N   LEU A 738 "
           pdb=" CA  LEU A 738 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.24  -18.76     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  GLY C 148 "
           pdb=" C   GLY C 148 "
           pdb=" N   LYS C 149 "
           pdb=" CA  LYS C 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  PRO A 535 "
           pdb=" C   PRO A 535 "
           pdb=" N   ASP A 536 "
           pdb=" CA  ASP A 536 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.34  -17.66     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 6207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1131
       0.040 -    0.080: 318
       0.080 -    0.120: 130
       0.120 -    0.160: 23
       0.160 -    0.199: 1
  Chirality restraints: 1603
  Sorted by residual:
  chirality pdb=" CB  ILE A 718 "
            pdb=" CA  ILE A 718 "
            pdb=" CG1 ILE A 718 "
            pdb=" CG2 ILE A 718 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.95e-01
  chirality pdb=" CA  MET A 533 "
            pdb=" N   MET A 533 "
            pdb=" C   MET A 533 "
            pdb=" CB  MET A 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.82e-01
  chirality pdb=" CA  PRO A 535 "
            pdb=" N   PRO A 535 "
            pdb=" C   PRO A 535 "
            pdb=" CB  PRO A 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.75e-01
  ... (remaining 1600 not shown)

  Planarity restraints: 1761
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 384 "   -0.055 5.00e-02 4.00e+02   8.35e-02 1.11e+01
        pdb=" N   PRO A 385 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 385 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 385 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 821 "   -0.019 2.00e-02 2.50e+03   1.65e-02 5.45e+00
        pdb=" CG  TYR A 821 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 821 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 821 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 821 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 821 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 821 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 821 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 534 "   -0.032 5.00e-02 4.00e+02   4.83e-02 3.74e+00
        pdb=" N   PRO A 535 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 535 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 535 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1758 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 453
        2.73 -     3.27: 10483
        3.27 -     3.81: 16677
        3.81 -     4.36: 19664
        4.36 -     4.90: 33992
  Nonbonded interactions: 81269
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B  25 "
            pdb=" O   ASP B 174 "
     model   vdw
     2.182 3.120
  nonbonded pdb=" OH  TYR A 387 "
            pdb=" OH  TYR A 391 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OE2 GLU A 297 "
            pdb=" NH2 ARG A 318 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   PRO A  34 "
            pdb=" NZ  LYS B  34 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   PHE A 656 "
            pdb=" OG  SER A 660 "
     model   vdw
     2.232 3.040
  ... (remaining 81264 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.110
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.210
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:11.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
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      :  0.004   0.069  10283  Z= 0.167
  Angle     :  0.625   9.753  13920  Z= 0.341
  Chirality :  0.044   0.199   1603
  Planarity :  0.005   0.083   1761
  Dihedral  : 13.189  88.268   3800
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.25), residues: 1237
  helix:  1.23 (0.21), residues: 597
  sheet:  0.19 (0.38), residues: 197
  loop :  0.04 (0.32), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 490 
 HIS   0.014   0.001   HIS A 596 
 PHE   0.024   0.002   PHE C  93 
 TYR   0.041   0.002   TYR A 821 
 ARG   0.003   0.000   ARG A 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13598 (  575)
  hydrogen bonds       : angle       6.51715 ( 1761)
  covalent geometry    : bond        0.00387 (10283)
  covalent geometry    : angle       0.62483 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 352
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ASP cc_start: 0.6920 (m-30) cc_final: 0.6653 (m-30)
REVERT: A  123 GLU cc_start: 0.7404 (mp0) cc_final: 0.6884 (mp0)
REVERT: A  344 MET cc_start: 0.8537 (mmt) cc_final: 0.8164 (mpp)
REVERT: A  345 GLU cc_start: 0.7234 (pp20) cc_final: 0.6761 (pp20)
REVERT: A  376 GLN cc_start: 0.6893 (tt0) cc_final: 0.6669 (mt0)
REVERT: A  408 GLU cc_start: 0.7506 (tt0) cc_final: 0.6837 (tm-30)
REVERT: A  416 GLU cc_start: 0.7041 (mp0) cc_final: 0.6501 (mp0)
REVERT: A  420 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7784 (mtpm)
REVERT: A  488 GLU cc_start: 0.7844 (tp30) cc_final: 0.7200 (tm-30)
REVERT: A  567 GLU cc_start: 0.7564 (mp0) cc_final: 0.6937 (mp0)
REVERT: A  590 MET cc_start: 0.8216 (mmm) cc_final: 0.8012 (mmm)
REVERT: A  591 ASP cc_start: 0.7362 (m-30) cc_final: 0.7150 (m-30)
REVERT: A  599 GLU cc_start: 0.7649 (pm20) cc_final: 0.7393 (pp20)
REVERT: A  615 LYS cc_start: 0.8094 (tppt) cc_final: 0.7671 (tptp)
REVERT: A  626 LEU cc_start: 0.8081 (tp) cc_final: 0.7878 (tt)
REVERT: A  652 GLN cc_start: 0.7667 (tp-100) cc_final: 0.7017 (tp-100)
REVERT: A  655 SER cc_start: 0.8290 (m) cc_final: 0.7758 (p)
REVERT: A  724 LEU cc_start: 0.8033 (mt) cc_final: 0.7798 (mt)
REVERT: A  761 ILE cc_start: 0.8516 (mt) cc_final: 0.8112 (mt)
REVERT: A  860 ASN cc_start: 0.7812 (t0) cc_final: 0.7554 (t0)
REVERT: A  864 CYS cc_start: 0.7524 (m) cc_final: 0.7292 (m)
REVERT: A  903 ASP cc_start: 0.7230 (t0) cc_final: 0.7021 (t0)
REVERT: B  124 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6598 (tt0)
REVERT: B  165 VAL cc_start: 0.8022 (m) cc_final: 0.7549 (p)
REVERT: C   20 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8285 (mt-10)
REVERT: C   21 VAL cc_start: 0.8634 (t) cc_final: 0.8317 (p)
REVERT: C   43 MET cc_start: 0.8870 (tmm) cc_final: 0.8319 (ttp)
REVERT: C   50 GLN cc_start: 0.8293 (mm-40) cc_final: 0.7966 (mm-40)
REVERT: C  112 VAL cc_start: 0.8775 (p) cc_final: 0.8536 (t)
REVERT: C  113 PHE cc_start: 0.8487 (m-10) cc_final: 0.8191 (m-10)
REVERT: C  175 LYS cc_start: 0.8177 (mppt) cc_final: 0.7931 (mppt)
REVERT: C  200 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7166 (mt-10)
REVERT: C  201 SER cc_start: 0.8473 (p) cc_final: 0.8247 (m)
REVERT: C  231 GLU cc_start: 0.7537 (pt0) cc_final: 0.7240 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 352
  average time/residue: 1.2049
  time to fit residues: 456.3707
Evaluate side-chains
  283 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    0.0060
   chunk 94 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 63 optimal weight:    0.4980
   chunk 50 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 113 optimal weight:    0.5980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
A  12 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
A 673 GLN
** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   4 HIS
B  72 ASN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 128 HIS
C 115 ASN
C 117 GLN
C 183 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.135293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.123590 restraints weight = 17508.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.42
r_work: 0.3619 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10283  Z= 0.159
  Angle     :  0.624  10.373  13920  Z= 0.319
  Chirality :  0.045   0.198   1603
  Planarity :  0.005   0.061   1761
  Dihedral  :  4.249  19.268   1338
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.81 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.25), residues: 1237
  helix:  1.47 (0.21), residues: 623
  sheet:  0.57 (0.39), residues: 195
  loop :  0.02 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 490 
 HIS   0.013   0.001   HIS A 789 
 PHE   0.025   0.002   PHE A 796 
 TYR   0.031   0.002   TYR B  73 
 ARG   0.007   0.001   ARG A 766 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04378 (  575)
  hydrogen bonds       : angle       4.75689 ( 1761)
  covalent geometry    : bond        0.00371 (10283)
  covalent geometry    : angle       0.62436 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 290
  time to evaluate  : 1.095 
Fit side-chains
REVERT: A   12 ASN cc_start: 0.8047 (t0) cc_final: 0.7801 (t0)
REVERT: A   14 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7744 (tmmt)
REVERT: A   31 ASP cc_start: 0.7225 (m-30) cc_final: 0.6889 (m-30)
REVERT: A  123 GLU cc_start: 0.7362 (mp0) cc_final: 0.6803 (mp0)
REVERT: A  344 MET cc_start: 0.8642 (mmt) cc_final: 0.8249 (mpp)
REVERT: A  345 GLU cc_start: 0.7253 (pp20) cc_final: 0.6759 (pp20)
REVERT: A  366 LYS cc_start: 0.8348 (ptpp) cc_final: 0.7911 (tppt)
REVERT: A  376 GLN cc_start: 0.7065 (tt0) cc_final: 0.6833 (mt0)
REVERT: A  395 MET cc_start: 0.7809 (mtt) cc_final: 0.7545 (mtp)
REVERT: A  416 GLU cc_start: 0.7024 (mp0) cc_final: 0.6547 (mp0)
REVERT: A  420 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7633 (mtpm)
REVERT: A  567 GLU cc_start: 0.7811 (mp0) cc_final: 0.7251 (mp0)
REVERT: A  599 GLU cc_start: 0.7776 (pm20) cc_final: 0.7511 (pp20)
REVERT: A  615 LYS cc_start: 0.8007 (tppt) cc_final: 0.7704 (tptp)
REVERT: A  652 GLN cc_start: 0.7714 (tp-100) cc_final: 0.6625 (tp-100)
REVERT: A  655 SER cc_start: 0.8185 (m) cc_final: 0.7795 (p)
REVERT: A  722 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8461 (tp)
REVERT: A  811 GLU cc_start: 0.6354 (tm-30) cc_final: 0.6125 (tm-30)
REVERT: A  870 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7523 (mm-40)
REVERT: A  903 ASP cc_start: 0.7375 (t0) cc_final: 0.7148 (t0)
REVERT: B  108 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7256 (mtm-85)
REVERT: B  124 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7268 (tt0)
REVERT: B  143 TYR cc_start: 0.8512 (p90) cc_final: 0.8240 (p90)
REVERT: C   21 VAL cc_start: 0.8532 (t) cc_final: 0.8224 (p)
REVERT: C   50 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8046 (mm-40)
REVERT: C   80 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7969 (mmmt)
REVERT: C  112 VAL cc_start: 0.8648 (p) cc_final: 0.8351 (t)
REVERT: C  231 GLU cc_start: 0.7466 (pt0) cc_final: 0.7217 (pt0)
  outliers start: 41
  outliers final: 11
  residues processed: 308
  average time/residue: 1.6368
  time to fit residues: 542.9813
Evaluate side-chains
  258 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 246
  time to evaluate  : 1.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain B residue    4 HIS
Chi-restraints excluded: chain B residue   43 ASN
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain C residue   78 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 100 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   chunk 54 optimal weight:    0.2980
   chunk 110 optimal weight:    0.0040
   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 380 GLN
** A 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 806 GLN
A 826 HIS
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  70 GLN
C 115 ASN
C 183 ASN
C 233 GLN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.133919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.122159 restraints weight = 17706.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.45
r_work: 0.3599 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10283  Z= 0.167
  Angle     :  0.636  12.571  13920  Z= 0.322
  Chirality :  0.044   0.270   1603
  Planarity :  0.004   0.051   1761
  Dihedral  :  4.296  19.560   1338
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 17.70 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.25), residues: 1237
  helix:  1.60 (0.21), residues: 624
  sheet:  0.59 (0.39), residues: 192
  loop :  0.02 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A   6 
 HIS   0.009   0.001   HIS B   4 
 PHE   0.031   0.002   PHE A 358 
 TYR   0.029   0.002   TYR B  73 
 ARG   0.008   0.001   ARG C 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  575)
  hydrogen bonds       : angle       4.56929 ( 1761)
  covalent geometry    : bond        0.00394 (10283)
  covalent geometry    : angle       0.63599 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 259
  time to evaluate  : 1.421 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8059 (t0) cc_final: 0.7811 (t0)
REVERT: A   14 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7723 (tmmt)
REVERT: A   22 LEU cc_start: 0.6264 (pp) cc_final: 0.5975 (mt)
REVERT: A   31 ASP cc_start: 0.7308 (m-30) cc_final: 0.6967 (m-30)
REVERT: A  366 LYS cc_start: 0.8392 (ptpp) cc_final: 0.7917 (tppt)
REVERT: A  376 GLN cc_start: 0.7008 (tt0) cc_final: 0.6770 (mt0)
REVERT: A  416 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6629 (mp0)
REVERT: A  561 SER cc_start: 0.8533 (m) cc_final: 0.8106 (t)
REVERT: A  567 GLU cc_start: 0.7817 (mp0) cc_final: 0.7600 (mm-30)
REVERT: A  590 MET cc_start: 0.8384 (mmm) cc_final: 0.7918 (tpp)
REVERT: A  595 LYS cc_start: 0.8374 (tmmt) cc_final: 0.8089 (tmmt)
REVERT: A  599 GLU cc_start: 0.7761 (pm20) cc_final: 0.7540 (pp20)
REVERT: A  615 LYS cc_start: 0.8043 (tppt) cc_final: 0.7713 (tptp)
REVERT: A  643 MET cc_start: 0.8423 (mmm) cc_final: 0.8184 (mmm)
REVERT: A  652 GLN cc_start: 0.7694 (tp-100) cc_final: 0.6634 (tp-100)
REVERT: A  655 SER cc_start: 0.8177 (m) cc_final: 0.7783 (p)
REVERT: A  689 MET cc_start: 0.7971 (mtp) cc_final: 0.7710 (ttm)
REVERT: A  766 ARG cc_start: 0.7690 (tpp80) cc_final: 0.7077 (mtt180)
REVERT: A  796 PHE cc_start: 0.7455 (t80) cc_final: 0.7242 (t80)
REVERT: A  806 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8255 (mm110)
REVERT: A  811 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.6214 (tm-30)
REVERT: A  836 TYR cc_start: 0.7778 (m-10) cc_final: 0.7513 (m-10)
REVERT: A  847 ASP cc_start: 0.7511 (p0) cc_final: 0.7254 (p0)
REVERT: A  870 GLN cc_start: 0.7627 (mm-40) cc_final: 0.6852 (tm-30)
REVERT: A  873 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6819 (pp20)
REVERT: A  896 ASN cc_start: 0.7880 (m-40) cc_final: 0.7328 (m-40)
REVERT: A  903 ASP cc_start: 0.7434 (t0) cc_final: 0.7226 (t0)
REVERT: B  108 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7200 (mtm-85)
REVERT: B  165 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7658 (m)
REVERT: C   43 MET cc_start: 0.8552 (tmm) cc_final: 0.8290 (ttp)
REVERT: C   50 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8049 (mm-40)
REVERT: C   80 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8096 (mmmt)
REVERT: C  175 LYS cc_start: 0.8243 (mppt) cc_final: 0.7959 (mppt)
REVERT: C  231 GLU cc_start: 0.7555 (pt0) cc_final: 0.7294 (pt0)
  outliers start: 48
  outliers final: 12
  residues processed: 280
  average time/residue: 1.1795
  time to fit residues: 356.1303
Evaluate side-chains
  263 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 247
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  416 GLU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  806 GLN
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  172 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 68 optimal weight:    0.1980
   chunk 7 optimal weight:    0.8980
   chunk 96 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 81 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 596 HIS
A 666 ASN
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 HIS
B   4 HIS
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 ASN
C 115 ASN
C 183 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.133324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.121686 restraints weight = 17632.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.48
r_work: 0.3602 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10283  Z= 0.154
  Angle     :  0.610  11.535  13920  Z= 0.308
  Chirality :  0.044   0.155   1603
  Planarity :  0.004   0.047   1761
  Dihedral  :  4.268  18.661   1338
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 19.73 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.25), residues: 1237
  helix:  1.69 (0.21), residues: 626
  sheet:  0.63 (0.39), residues: 192
  loop :  0.02 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A   6 
 HIS   0.005   0.001   HIS B 128 
 PHE   0.015   0.001   PHE A 796 
 TYR   0.027   0.001   TYR B  73 
 ARG   0.008   0.000   ARG A 819 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03819 (  575)
  hydrogen bonds       : angle       4.45820 ( 1761)
  covalent geometry    : bond        0.00364 (10283)
  covalent geometry    : angle       0.60981 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 257
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8102 (t0) cc_final: 0.7862 (t0)
REVERT: A   14 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7727 (tmmt)
REVERT: A   31 ASP cc_start: 0.7273 (m-30) cc_final: 0.6906 (m-30)
REVERT: A  288 ARG cc_start: 0.8145 (ttt180) cc_final: 0.7819 (ttt-90)
REVERT: A  376 GLN cc_start: 0.7089 (tt0) cc_final: 0.6852 (mt0)
REVERT: A  474 LEU cc_start: 0.8633 (mt) cc_final: 0.8432 (mt)
REVERT: A  561 SER cc_start: 0.8564 (m) cc_final: 0.8122 (t)
REVERT: A  567 GLU cc_start: 0.7808 (mp0) cc_final: 0.7571 (mm-30)
REVERT: A  595 LYS cc_start: 0.8396 (tmmt) cc_final: 0.8116 (tttm)
REVERT: A  599 GLU cc_start: 0.7725 (pm20) cc_final: 0.7520 (pp20)
REVERT: A  615 LYS cc_start: 0.8087 (tppt) cc_final: 0.7751 (tptp)
REVERT: A  643 MET cc_start: 0.8421 (mmm) cc_final: 0.8138 (mmm)
REVERT: A  652 GLN cc_start: 0.7810 (tp-100) cc_final: 0.6731 (tp-100)
REVERT: A  655 SER cc_start: 0.8136 (m) cc_final: 0.7729 (p)
REVERT: A  766 ARG cc_start: 0.7766 (tpp80) cc_final: 0.7204 (mtt180)
REVERT: A  769 GLU cc_start: 0.7909 (tp30) cc_final: 0.7679 (tp30)
REVERT: A  803 ASN cc_start: 0.7991 (m-40) cc_final: 0.7777 (m110)
REVERT: A  811 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6221 (tm-30)
REVERT: A  819 ARG cc_start: 0.7830 (mpp80) cc_final: 0.7462 (mpp80)
REVERT: A  836 TYR cc_start: 0.7781 (m-10) cc_final: 0.7504 (m-10)
REVERT: A  847 ASP cc_start: 0.7522 (p0) cc_final: 0.7231 (p0)
REVERT: B  143 TYR cc_start: 0.8515 (p90) cc_final: 0.7796 (p90)
REVERT: B  158 ASP cc_start: 0.6567 (t70) cc_final: 0.6259 (t70)
REVERT: B  165 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7600 (m)
REVERT: C   43 MET cc_start: 0.8590 (tmm) cc_final: 0.8350 (ttp)
REVERT: C   50 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8066 (mm-40)
REVERT: C   66 VAL cc_start: 0.8212 (m) cc_final: 0.7922 (p)
REVERT: C   80 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8197 (mmmt)
REVERT: C  112 VAL cc_start: 0.8733 (p) cc_final: 0.8422 (t)
REVERT: C  175 LYS cc_start: 0.8269 (mppt) cc_final: 0.7978 (mppt)
REVERT: C  231 GLU cc_start: 0.7609 (pt0) cc_final: 0.7341 (pt0)
  outliers start: 44
  outliers final: 18
  residues processed: 280
  average time/residue: 1.2017
  time to fit residues: 361.1507
Evaluate side-chains
  277 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 257
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain B residue    4 HIS
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain C residue   10 LYS
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue   78 MET
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  151 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 101 optimal weight:    0.6980
   chunk 86 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 HIS
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 ASN
C 115 ASN
C 183 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.132411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.120743 restraints weight = 17490.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 2.46
r_work: 0.3588 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10283  Z= 0.174
  Angle     :  0.628  11.892  13920  Z= 0.314
  Chirality :  0.044   0.186   1603
  Planarity :  0.004   0.045   1761
  Dihedral  :  4.326  18.973   1338
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 21.24 %
    Favored  : 75.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.25), residues: 1237
  helix:  1.62 (0.21), residues: 629
  sheet:  0.61 (0.38), residues: 197
  loop : -0.01 (0.33), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A   6 
 HIS   0.011   0.001   HIS B   4 
 PHE   0.033   0.002   PHE A 358 
 TYR   0.027   0.002   TYR B  73 
 ARG   0.005   0.000   ARG A 819 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03867 (  575)
  hydrogen bonds       : angle       4.49018 ( 1761)
  covalent geometry    : bond        0.00411 (10283)
  covalent geometry    : angle       0.62808 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 263
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 ASN cc_start: 0.8139 (t0) cc_final: 0.7863 (t0)
REVERT: A   14 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7706 (tmmt)
REVERT: A   31 ASP cc_start: 0.7261 (m-30) cc_final: 0.6921 (m-30)
REVERT: A  123 GLU cc_start: 0.7427 (mp0) cc_final: 0.6996 (mt-10)
REVERT: A  376 GLN cc_start: 0.7116 (tt0) cc_final: 0.6878 (mt0)
REVERT: A  395 MET cc_start: 0.7617 (mtt) cc_final: 0.7399 (mtp)
REVERT: A  416 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6703 (mp0)
REVERT: A  445 MET cc_start: 0.7796 (mmm) cc_final: 0.7591 (mmm)
REVERT: A  561 SER cc_start: 0.8590 (m) cc_final: 0.8133 (t)
REVERT: A  567 GLU cc_start: 0.7835 (mp0) cc_final: 0.7583 (mm-30)
REVERT: A  595 LYS cc_start: 0.8412 (tmmt) cc_final: 0.8124 (tttm)
REVERT: A  615 LYS cc_start: 0.8111 (tppt) cc_final: 0.7729 (tptp)
REVERT: A  643 MET cc_start: 0.8446 (mmm) cc_final: 0.8117 (mmm)
REVERT: A  655 SER cc_start: 0.8102 (m) cc_final: 0.7822 (p)
REVERT: A  663 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7463 (tmm)
REVERT: A  766 ARG cc_start: 0.7756 (tpp80) cc_final: 0.7223 (mtt180)
REVERT: A  769 GLU cc_start: 0.7967 (tp30) cc_final: 0.7750 (tp30)
REVERT: A  803 ASN cc_start: 0.7937 (m-40) cc_final: 0.7652 (m110)
REVERT: A  811 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6238 (tm-30)
REVERT: A  836 TYR cc_start: 0.7771 (m-10) cc_final: 0.7474 (m-10)
REVERT: A  847 ASP cc_start: 0.7553 (p0) cc_final: 0.7076 (p0)
REVERT: A  870 GLN cc_start: 0.7619 (mm-40) cc_final: 0.6884 (mm-40)
REVERT: A  873 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6751 (pp20)
REVERT: B  143 TYR cc_start: 0.8556 (p90) cc_final: 0.8014 (p90)
REVERT: B  158 ASP cc_start: 0.6687 (t70) cc_final: 0.6331 (t70)
REVERT: B  165 VAL cc_start: 0.8011 (OUTLIER) cc_final: 0.7529 (m)
REVERT: B  168 VAL cc_start: 0.8533 (p) cc_final: 0.8308 (m)
REVERT: C   13 ASN cc_start: 0.8529 (p0) cc_final: 0.8237 (p0)
REVERT: C   43 MET cc_start: 0.8562 (tmm) cc_final: 0.8296 (ttp)
REVERT: C   50 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8050 (mm-40)
REVERT: C   66 VAL cc_start: 0.8209 (m) cc_final: 0.7897 (p)
REVERT: C   80 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8202 (mmmt)
REVERT: C  112 VAL cc_start: 0.8770 (p) cc_final: 0.8494 (t)
REVERT: C  175 LYS cc_start: 0.8279 (mppt) cc_final: 0.7977 (mppt)
REVERT: C  231 GLU cc_start: 0.7625 (pt0) cc_final: 0.7358 (pt0)
  outliers start: 41
  outliers final: 15
  residues processed: 285
  average time/residue: 1.1600
  time to fit residues: 354.9686
Evaluate side-chains
  281 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 263
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  547 GLN
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  663 MET
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain C residue   76 ILE
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  151 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 62 optimal weight:    0.1980
   chunk 57 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    0.4980
   chunk 122 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 26 optimal weight:    0.1980
   chunk 80 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 471 ASN
** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
A 673 GLN
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 HIS
B   4 HIS
B  92 HIS
** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 115 ASN
C 183 ASN
C 234 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.133152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.121468 restraints weight = 17564.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.47
r_work: 0.3599 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.3485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10283  Z= 0.148
  Angle     :  0.626  10.317  13920  Z= 0.313
  Chirality :  0.044   0.180   1603
  Planarity :  0.004   0.044   1761
  Dihedral  :  4.260  19.029   1338
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.45 %
    Favored  : 73.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.25), residues: 1237
  helix:  1.68 (0.21), residues: 629
  sheet:  0.61 (0.38), residues: 197
  loop : -0.01 (0.33), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A   6 
 HIS   0.007   0.001   HIS B  90 
 PHE   0.026   0.001   PHE A 358 
 TYR   0.014   0.001   TYR A 128 
 ARG   0.008   0.000   ARG A 819 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03713 (  575)
  hydrogen bonds       : angle       4.40374 ( 1761)
  covalent geometry    : bond        0.00351 (10283)
  covalent geometry    : angle       0.62568 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 258
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 HIS cc_start: 0.7535 (m90) cc_final: 0.7309 (m90)
REVERT: A   14 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7700 (tmmt)
REVERT: A   31 ASP cc_start: 0.7183 (m-30) cc_final: 0.6877 (m-30)
REVERT: A  123 GLU cc_start: 0.7392 (mp0) cc_final: 0.6970 (mt-10)
REVERT: A  206 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7381 (tttm)
REVERT: A  366 LYS cc_start: 0.8461 (ptpp) cc_final: 0.7918 (tppt)
REVERT: A  376 GLN cc_start: 0.7116 (tt0) cc_final: 0.6885 (mt0)
REVERT: A  416 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6756 (mp0)
REVERT: A  561 SER cc_start: 0.8579 (m) cc_final: 0.8108 (t)
REVERT: A  567 GLU cc_start: 0.7817 (mp0) cc_final: 0.7567 (mm-30)
REVERT: A  595 LYS cc_start: 0.8419 (tmmt) cc_final: 0.8193 (tmmt)
REVERT: A  615 LYS cc_start: 0.8096 (tppt) cc_final: 0.7772 (tptp)
REVERT: A  643 MET cc_start: 0.8410 (mmm) cc_final: 0.8077 (mmm)
REVERT: A  655 SER cc_start: 0.8045 (m) cc_final: 0.7780 (p)
REVERT: A  663 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7463 (tmm)
REVERT: A  751 LEU cc_start: 0.8468 (tm) cc_final: 0.8264 (tt)
REVERT: A  754 GLU cc_start: 0.8144 (tp30) cc_final: 0.7837 (tm-30)
REVERT: A  796 PHE cc_start: 0.7600 (t80) cc_final: 0.7371 (t80)
REVERT: A  803 ASN cc_start: 0.7870 (m-40) cc_final: 0.7593 (m110)
REVERT: A  811 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6270 (tm-30)
REVERT: A  819 ARG cc_start: 0.7712 (mpp80) cc_final: 0.7416 (mtm-85)
REVERT: A  836 TYR cc_start: 0.7748 (m-10) cc_final: 0.7448 (m-10)
REVERT: A  847 ASP cc_start: 0.7485 (p0) cc_final: 0.6994 (p0)
REVERT: A  870 GLN cc_start: 0.7564 (mm-40) cc_final: 0.6918 (mm-40)
REVERT: A  873 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6773 (pp20)
REVERT: B  143 TYR cc_start: 0.8539 (p90) cc_final: 0.8087 (p90)
REVERT: B  158 ASP cc_start: 0.6565 (t70) cc_final: 0.6294 (t70)
REVERT: B  165 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7519 (m)
REVERT: B  168 VAL cc_start: 0.8461 (p) cc_final: 0.8237 (m)
REVERT: C   13 ASN cc_start: 0.8508 (p0) cc_final: 0.8183 (p0)
REVERT: C   43 MET cc_start: 0.8595 (tmm) cc_final: 0.8385 (ttp)
REVERT: C   50 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8082 (mm-40)
REVERT: C   66 VAL cc_start: 0.8203 (m) cc_final: 0.7904 (p)
REVERT: C   80 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8255 (mmmt)
REVERT: C  112 VAL cc_start: 0.8766 (p) cc_final: 0.8495 (t)
REVERT: C  175 LYS cc_start: 0.8290 (mppt) cc_final: 0.7973 (mppt)
REVERT: C  231 GLU cc_start: 0.7613 (pt0) cc_final: 0.7364 (pt0)
  outliers start: 39
  outliers final: 17
  residues processed: 280
  average time/residue: 1.2521
  time to fit residues: 376.0950
Evaluate side-chains
  274 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 253
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  547 GLN
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  663 MET
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain B residue    4 HIS
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 104 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 HIS
B   4 HIS
B  36 GLN
** B  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.132321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.120619 restraints weight = 17685.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.48
r_work: 0.3586 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10283  Z= 0.171
  Angle     :  0.645  10.846  13920  Z= 0.322
  Chirality :  0.045   0.169   1603
  Planarity :  0.004   0.044   1761
  Dihedral  :  4.288  19.343   1338
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 24.42 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.25), residues: 1237
  helix:  1.65 (0.21), residues: 630
  sheet:  0.62 (0.38), residues: 197
  loop : -0.03 (0.33), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A   6 
 HIS   0.016   0.001   HIS B   4 
 PHE   0.018   0.001   PHE A 796 
 TYR   0.014   0.001   TYR A 128 
 ARG   0.005   0.000   ARG A 819 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03815 (  575)
  hydrogen bonds       : angle       4.45540 ( 1761)
  covalent geometry    : bond        0.00403 (10283)
  covalent geometry    : angle       0.64537 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 257
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 HIS cc_start: 0.7634 (m90) cc_final: 0.7392 (m90)
REVERT: A   14 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7706 (tmmt)
REVERT: A   31 ASP cc_start: 0.7099 (m-30) cc_final: 0.6829 (m-30)
REVERT: A  123 GLU cc_start: 0.7422 (mp0) cc_final: 0.7011 (mt-10)
REVERT: A  202 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7665 (t70)
REVERT: A  288 ARG cc_start: 0.8165 (ttt180) cc_final: 0.7798 (ttt-90)
REVERT: A  376 GLN cc_start: 0.7141 (tt0) cc_final: 0.6904 (mt0)
REVERT: A  395 MET cc_start: 0.7639 (mtt) cc_final: 0.7423 (mtp)
REVERT: A  416 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6739 (mp0)
REVERT: A  561 SER cc_start: 0.8596 (m) cc_final: 0.8126 (t)
REVERT: A  567 GLU cc_start: 0.7882 (mp0) cc_final: 0.7610 (mm-30)
REVERT: A  595 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8120 (tmmt)
REVERT: A  615 LYS cc_start: 0.8098 (tppt) cc_final: 0.7775 (tptp)
REVERT: A  643 MET cc_start: 0.8452 (mmm) cc_final: 0.8119 (mmm)
REVERT: A  655 SER cc_start: 0.8048 (m) cc_final: 0.7789 (p)
REVERT: A  663 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7539 (tmm)
REVERT: A  754 GLU cc_start: 0.8169 (tp30) cc_final: 0.7891 (tm-30)
REVERT: A  803 ASN cc_start: 0.7919 (m-40) cc_final: 0.7645 (m110)
REVERT: A  811 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6315 (tm-30)
REVERT: A  819 ARG cc_start: 0.7708 (mpp80) cc_final: 0.7400 (mtm-85)
REVERT: A  836 TYR cc_start: 0.7773 (m-10) cc_final: 0.7399 (m-10)
REVERT: A  847 ASP cc_start: 0.7528 (p0) cc_final: 0.7068 (p0)
REVERT: A  870 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7029 (mm-40)
REVERT: A  873 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6786 (pp20)
REVERT: B  143 TYR cc_start: 0.8550 (p90) cc_final: 0.8092 (p90)
REVERT: B  157 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6930 (mtm)
REVERT: B  158 ASP cc_start: 0.6876 (t70) cc_final: 0.6556 (t70)
REVERT: B  165 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7823 (m)
REVERT: B  168 VAL cc_start: 0.8506 (p) cc_final: 0.8289 (m)
REVERT: C   13 ASN cc_start: 0.8517 (p0) cc_final: 0.8174 (p0)
REVERT: C   14 LYS cc_start: 0.8540 (mtpm) cc_final: 0.8339 (mtmt)
REVERT: C   43 MET cc_start: 0.8566 (tmm) cc_final: 0.8355 (ttp)
REVERT: C   50 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8076 (mm-40)
REVERT: C   52 SER cc_start: 0.7538 (t) cc_final: 0.7317 (m)
REVERT: C   66 VAL cc_start: 0.8238 (m) cc_final: 0.7954 (p)
REVERT: C   79 VAL cc_start: 0.8901 (t) cc_final: 0.8505 (m)
REVERT: C   80 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8301 (mmmt)
REVERT: C  112 VAL cc_start: 0.8772 (p) cc_final: 0.8541 (t)
  outliers start: 40
  outliers final: 15
  residues processed: 277
  average time/residue: 1.2246
  time to fit residues: 363.8082
Evaluate side-chains
  277 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 257
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain A residue  599 GLU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  663 MET
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain A residue  794 VAL
Chi-restraints excluded: chain B residue    4 HIS
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  147 LYS
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  173 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0670
   chunk 63 optimal weight:    0.0980
   chunk 68 optimal weight:    0.9990
   chunk 78 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
A 516 HIS
A 666 ASN
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 HIS
** B   4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.132638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.121101 restraints weight = 17707.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 2.49
r_work: 0.3579 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10283  Z= 0.157
  Angle     :  0.652  10.223  13920  Z= 0.325
  Chirality :  0.044   0.186   1603
  Planarity :  0.004   0.044   1761
  Dihedral  :  4.269  19.012   1338
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 25.13 %
    Favored  : 71.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.25), residues: 1237
  helix:  1.69 (0.21), residues: 631
  sheet:  0.59 (0.38), residues: 197
  loop : -0.07 (0.33), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A   6 
 HIS   0.006   0.001   HIS B  90 
 PHE   0.041   0.001   PHE A 358 
 TYR   0.014   0.001   TYR A 128 
 ARG   0.006   0.000   ARG A 819 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  575)
  hydrogen bonds       : angle       4.41226 ( 1761)
  covalent geometry    : bond        0.00374 (10283)
  covalent geometry    : angle       0.65164 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 266
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 HIS cc_start: 0.7703 (m90) cc_final: 0.7485 (m90)
REVERT: A   14 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7675 (tmmt)
REVERT: A   31 ASP cc_start: 0.7053 (m-30) cc_final: 0.6809 (m-30)
REVERT: A  123 GLU cc_start: 0.7440 (mp0) cc_final: 0.6946 (pt0)
REVERT: A  202 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7576 (t70)
REVERT: A  288 ARG cc_start: 0.8140 (ttt180) cc_final: 0.7772 (ttt-90)
REVERT: A  376 GLN cc_start: 0.7191 (tt0) cc_final: 0.6943 (mt0)
REVERT: A  395 MET cc_start: 0.7583 (mtt) cc_final: 0.7371 (mtp)
REVERT: A  416 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6744 (mp0)
REVERT: A  561 SER cc_start: 0.8603 (m) cc_final: 0.8112 (t)
REVERT: A  567 GLU cc_start: 0.7842 (mp0) cc_final: 0.7566 (mm-30)
REVERT: A  595 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8125 (tmmt)
REVERT: A  615 LYS cc_start: 0.8127 (tppt) cc_final: 0.7782 (tptp)
REVERT: A  619 ASP cc_start: 0.7911 (m-30) cc_final: 0.7213 (m-30)
REVERT: A  643 MET cc_start: 0.8533 (mmm) cc_final: 0.8222 (mmm)
REVERT: A  695 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7664 (mmm-85)
REVERT: A  754 GLU cc_start: 0.8158 (tp30) cc_final: 0.7730 (tm-30)
REVERT: A  766 ARG cc_start: 0.7775 (tpp80) cc_final: 0.7166 (mtt180)
REVERT: A  788 ASP cc_start: 0.5118 (m-30) cc_final: 0.4679 (m-30)
REVERT: A  803 ASN cc_start: 0.7851 (m-40) cc_final: 0.7586 (m110)
REVERT: A  811 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6276 (tm-30)
REVERT: A  819 ARG cc_start: 0.7679 (mpp80) cc_final: 0.7466 (mtm-85)
REVERT: A  836 TYR cc_start: 0.7834 (m-10) cc_final: 0.7416 (m-10)
REVERT: A  844 ASP cc_start: 0.7366 (m-30) cc_final: 0.7153 (m-30)
REVERT: A  847 ASP cc_start: 0.7423 (p0) cc_final: 0.6861 (p0)
REVERT: A  870 GLN cc_start: 0.7540 (mm-40) cc_final: 0.6954 (mm-40)
REVERT: A  873 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6779 (pp20)
REVERT: A  885 LYS cc_start: 0.8145 (pmmt) cc_final: 0.7940 (pmtt)
REVERT: A  888 SER cc_start: 0.8328 (t) cc_final: 0.8060 (p)
REVERT: B  122 LYS cc_start: 0.8224 (tmmt) cc_final: 0.7832 (tmmt)
REVERT: B  143 TYR cc_start: 0.8538 (p90) cc_final: 0.8012 (p90)
REVERT: B  157 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6927 (mtm)
REVERT: B  158 ASP cc_start: 0.6743 (t70) cc_final: 0.6431 (t70)
REVERT: B  165 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7779 (m)
REVERT: B  168 VAL cc_start: 0.8471 (p) cc_final: 0.8263 (m)
REVERT: C   13 ASN cc_start: 0.8492 (p0) cc_final: 0.8130 (p0)
REVERT: C   14 LYS cc_start: 0.8512 (mtpm) cc_final: 0.8302 (mtmt)
REVERT: C   43 MET cc_start: 0.8586 (tmm) cc_final: 0.8340 (ttp)
REVERT: C   52 SER cc_start: 0.7401 (t) cc_final: 0.7171 (m)
REVERT: C   66 VAL cc_start: 0.8223 (m) cc_final: 0.7938 (p)
REVERT: C   79 VAL cc_start: 0.8892 (t) cc_final: 0.8516 (m)
REVERT: C   80 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8368 (mmmt)
REVERT: C  112 VAL cc_start: 0.8778 (p) cc_final: 0.8563 (t)
REVERT: C  134 THR cc_start: 0.7875 (p) cc_final: 0.7641 (m)
  outliers start: 36
  outliers final: 15
  residues processed: 284
  average time/residue: 1.1972
  time to fit residues: 364.5523
Evaluate side-chains
  274 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 254
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 CYS
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain B residue    4 HIS
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  157 MET
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  147 LYS
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  172 LEU
Chi-restraints excluded: chain C residue  173 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 98 optimal weight:    0.4980
   chunk 102 optimal weight:    0.0170
   chunk 42 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 123 optimal weight:    0.7980
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
** A 789 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 826 HIS
B  36 GLN
** B  43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 ASN
C  70 GLN
C  73 ASN
** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.133220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.121767 restraints weight = 17653.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.49
r_work: 0.3585 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10283  Z= 0.152
  Angle     :  0.675  14.105  13920  Z= 0.334
  Chirality :  0.044   0.182   1603
  Planarity :  0.004   0.044   1761
  Dihedral  :  4.283  19.020   1338
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 26.19 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.25), residues: 1237
  helix:  1.67 (0.21), residues: 630
  sheet:  0.67 (0.38), residues: 195
  loop : -0.07 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 490 
 HIS   0.006   0.001   HIS B  90 
 PHE   0.039   0.002   PHE A 358 
 TYR   0.014   0.001   TYR A 128 
 ARG   0.006   0.001   ARG A 248 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  575)
  hydrogen bonds       : angle       4.43099 ( 1761)
  covalent geometry    : bond        0.00364 (10283)
  covalent geometry    : angle       0.67467 (13920)

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

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

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2474 Ramachandran restraints generated.
    1237 Oldfield, 0 Emsley, 1237 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 259
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 HIS cc_start: 0.7727 (m90) cc_final: 0.7476 (m90)
REVERT: A    9 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7647 (ttp80)
REVERT: A   12 ASN cc_start: 0.8082 (t0) cc_final: 0.7768 (t0)
REVERT: A   14 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7640 (tmmt)
REVERT: A   17 PHE cc_start: 0.8064 (m-80) cc_final: 0.7850 (m-10)
REVERT: A   31 ASP cc_start: 0.7050 (m-30) cc_final: 0.6809 (m-30)
REVERT: A  123 GLU cc_start: 0.7420 (mp0) cc_final: 0.6897 (pt0)
REVERT: A  202 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7575 (t70)
REVERT: A  220 ASP cc_start: 0.7374 (t0) cc_final: 0.6918 (t0)
REVERT: A  288 ARG cc_start: 0.8128 (ttt180) cc_final: 0.7812 (ttt-90)
REVERT: A  345 GLU cc_start: 0.7281 (pp20) cc_final: 0.6818 (pp20)
REVERT: A  376 GLN cc_start: 0.7229 (tt0) cc_final: 0.6983 (mt0)
REVERT: A  416 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6756 (mp0)
REVERT: A  561 SER cc_start: 0.8598 (m) cc_final: 0.8108 (t)
REVERT: A  567 GLU cc_start: 0.7853 (mp0) cc_final: 0.7596 (mm-30)
REVERT: A  595 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8099 (tmmt)
REVERT: A  615 LYS cc_start: 0.8184 (tppt) cc_final: 0.7837 (tptp)
REVERT: A  643 MET cc_start: 0.8569 (mmm) cc_final: 0.8263 (mmm)
REVERT: A  663 MET cc_start: 0.7566 (tmm) cc_final: 0.7298 (tmm)
REVERT: A  695 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.7666 (mmm-85)
REVERT: A  754 GLU cc_start: 0.8128 (tp30) cc_final: 0.7853 (tm-30)
REVERT: A  803 ASN cc_start: 0.7824 (m-40) cc_final: 0.7564 (m110)
REVERT: A  811 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6270 (tm-30)
REVERT: A  819 ARG cc_start: 0.7696 (mpp80) cc_final: 0.7467 (mtm-85)
REVERT: A  836 TYR cc_start: 0.7829 (m-10) cc_final: 0.7474 (m-10)
REVERT: A  847 ASP cc_start: 0.7434 (p0) cc_final: 0.6999 (p0)
REVERT: A  870 GLN cc_start: 0.7518 (mm-40) cc_final: 0.6966 (mm-40)
REVERT: A  873 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6822 (pp20)
REVERT: A  885 LYS cc_start: 0.8116 (pmmt) cc_final: 0.7904 (pmtt)
REVERT: A  888 SER cc_start: 0.8162 (t) cc_final: 0.7927 (p)
REVERT: B  122 LYS cc_start: 0.8241 (tmmt) cc_final: 0.7871 (tmmt)
REVERT: B  143 TYR cc_start: 0.8518 (p90) cc_final: 0.7895 (p90)
REVERT: B  165 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7777 (m)
REVERT: B  168 VAL cc_start: 0.8470 (p) cc_final: 0.8261 (m)
REVERT: C   13 ASN cc_start: 0.8510 (p0) cc_final: 0.8158 (p0)
REVERT: C   14 LYS cc_start: 0.8488 (mtpm) cc_final: 0.8273 (mtmt)
REVERT: C   43 MET cc_start: 0.8589 (tmm) cc_final: 0.8332 (ttp)
REVERT: C   52 SER cc_start: 0.7394 (t) cc_final: 0.7161 (m)
REVERT: C   66 VAL cc_start: 0.8234 (m) cc_final: 0.7941 (p)
REVERT: C   79 VAL cc_start: 0.8880 (t) cc_final: 0.8521 (m)
REVERT: C   80 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8393 (mmmt)
REVERT: C  112 VAL cc_start: 0.8758 (p) cc_final: 0.8547 (t)
REVERT: C  134 THR cc_start: 0.7895 (p) cc_final: 0.7672 (m)
REVERT: C  210 GLU cc_start: 0.8062 (pt0) cc_final: 0.7560 (pt0)
  outliers start: 29
  outliers final: 12
  residues processed: 272
  average time/residue: 1.2326
  time to fit residues: 358.7817
Evaluate side-chains
  272 residues out of total 1134 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 256
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  344 MET
Chi-restraints excluded: chain A residue  379 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  532 HIS
Chi-restraints excluded: chain A residue  581 VAL
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain B residue   95 ILE
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain C residue  143 SER
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  173 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 58.036 > 50:
  distance: 23 - 46:  27.153
  distance: 26 - 43:   9.496
  distance: 35 - 43:  10.168
  distance: 36 - 138:   3.269
  distance: 43 - 44:   8.086
  distance: 44 - 45:  23.199
  distance: 44 - 47:   9.052
  distance: 45 - 46:   9.187
  distance: 45 - 51:  15.024
  distance: 47 - 48:   9.238
  distance: 48 - 49:  12.688
  distance: 48 - 50:   7.954
  distance: 51 - 52:  23.243
  distance: 52 - 53:  11.738
  distance: 52 - 55:   7.063
  distance: 53 - 54:   8.014
  distance: 53 - 59:   4.781
  distance: 55 - 56:  10.811
  distance: 56 - 57:  17.706
  distance: 56 - 58:  23.651
  distance: 59 - 60:  15.565
  distance: 60 - 61:   7.809
  distance: 60 - 63:  11.643
  distance: 61 - 62:  13.606
  distance: 61 - 65:  17.094
  distance: 63 - 64:  15.085
  distance: 65 - 66:  10.715
  distance: 66 - 67:  12.126
  distance: 66 - 69:  12.154
  distance: 67 - 68:  17.817
  distance: 67 - 72:   9.703
  distance: 69 - 70:   4.873
  distance: 69 - 71:   5.906
  distance: 72 - 73:   5.207
  distance: 73 - 74:   8.284
  distance: 74 - 75:   4.912
  distance: 74 - 80:  10.237
  distance: 76 - 77:  11.021
  distance: 77 - 78:   9.986
  distance: 77 - 79:   9.041
  distance: 80 - 81:  20.794
  distance: 81 - 84:   8.082
  distance: 82 - 83:   9.992
  distance: 82 - 86:  13.484
  distance: 84 - 85:  31.813
  distance: 86 - 87:  23.498
  distance: 87 - 88:  13.186
  distance: 87 - 90:  15.319
  distance: 88 - 89:   9.981
  distance: 88 - 93:  32.552
  distance: 90 - 91:  22.153
  distance: 90 - 92:  20.035
  distance: 93 - 94:  16.380
  distance: 94 - 95:  26.649
  distance: 94 - 97:  27.128
  distance: 95 - 96:  24.133
  distance: 95 - 101:   8.305
  distance: 97 - 98:  22.672
  distance: 97 - 99:  19.245
  distance: 98 - 100:  25.730
  distance: 101 - 102:  21.081
  distance: 102 - 103:  18.447
  distance: 102 - 105:  11.400
  distance: 103 - 104:  11.884
  distance: 103 - 108:  17.961
  distance: 105 - 106:  12.837
  distance: 105 - 107:  21.137
  distance: 108 - 109:  12.282
  distance: 109 - 110:  17.863
  distance: 109 - 112:  18.014
  distance: 110 - 111:  18.097
  distance: 110 - 117:  18.654
  distance: 112 - 113:   5.292
  distance: 113 - 114:  11.235
  distance: 114 - 115:   5.843
  distance: 114 - 116:   6.251