Starting phenix.real_space_refine
on Tue Mar  3 11:32:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zh3_14720/03_2026/7zh3_14720.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zh3_14720/03_2026/7zh3_14720.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zh3_14720/03_2026/7zh3_14720.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zh3_14720/03_2026/7zh3_14720.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zh3_14720/03_2026/7zh3_14720.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zh3_14720/03_2026/7zh3_14720.map"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.186
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      14      5.16       5
     C    2082      2.51       5
     N     538      2.21       5
     O     666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3301
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 607
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "D"
      Number of atoms: 2655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2655
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 316}
          Chain breaks: 5
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 32
          Classifications: {'water': 32}
          Link IDs: {None: 31}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1793  SG  CYS D 440      37.260  78.151  22.375  1.00  6.35           S
  ATOM   1816  SG  CYS D 443      38.958  78.902  19.208  1.00  6.36           S
  ATOM   2191  SG  CYS D 506      40.949  77.487  22.051  1.00  6.09           S
  ATOM   2214  SG  CYS D 509      39.607  81.273  22.115  1.00  6.77           S

  Time building chain proxies: 0.74, per 1000 atoms: 0.22
  Number of scatterers: 3301
  At special positions: 0
  Unit cell: (69.96, 92.22, 58.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      14     16.00
     O     666      8.00
     N     538      7.00
     C    2082      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: 0.21
  Conformation dependent library (CDL) restraints added in 87.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D1000 "
        pdb="ZN    ZN D1000 " - pdb=" SG  CYS D 443 "
        pdb="ZN    ZN D1000 " - pdb=" SG  CYS D 440 "
        pdb="ZN    ZN D1000 " - pdb=" SG  CYS D 506 "
        pdb="ZN    ZN D1000 " - pdb=" SG  CYS D 509 "
      Number of angles added : 6


  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 8 sheets defined
      39.1% alpha, 29.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'C' and resid 22 through 35
    Processing helix  chain 'C' and resid 37 through 41
    Processing helix  chain 'D' and resid 89 through 101
      removed outlier: 3.717A  pdb=" N   ILE D  95 " --> pdb=" O   TYR D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 122
    Processing helix  chain 'D' and resid 143 through 166
    Processing helix  chain 'D' and resid 178 through 189
    Processing helix  chain 'D' and resid 190 through 193
    Processing helix  chain 'D' and resid 200 through 222
    Processing helix  chain 'D' and resid 424 through 431
      removed outlier: 3.542A  pdb=" N   GLN D 431 " --> pdb=" O   GLU D 427 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 484 through 494
    Processing helix  chain 'D' and resid 499 through 503
      removed outlier: 3.763A  pdb=" N   LYS D 503 " --> pdb=" O   GLY D 500 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 564 through 568
    Processing helix  chain 'D' and resid 737 through 742
      removed outlier: 3.867A  pdb=" N   GLU D 742 " --> pdb=" O   SER D 739 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 759 through 768
      removed outlier: 3.649A  pdb=" N   SER D 768 " --> pdb=" O   LEU D 764 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 12 through 17
    Processing sheet with id=AA2, first strand: chain 'C' and resid 74 through 75
    Processing sheet with id=AA3, first strand: chain 'D' and resid 82 through 83
      removed outlier: 6.505A  pdb=" N   GLY D  82 " --> pdb=" O   THR D 176 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'D' and resid 446 through 453
    Processing sheet with id=AA5, first strand: chain 'D' and resid 456 through 459
      removed outlier: 5.876A  pdb=" N   TYR D 778 " --> pdb=" O   LEU D 532 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL D 582 " --> pdb=" O   TYR D 778 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   LEU D 780 " --> pdb=" O   ALA D 580 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ALA D 580 " --> pdb=" O   LEU D 780 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TYR D 782 " --> pdb=" O   LEU D 578 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU D 578 " --> pdb=" O   TYR D 782 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LYS D 784 " --> pdb=" O   TYR D 576 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   TYR D 576 " --> pdb=" O   LYS D 784 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 456 through 459
      removed outlier: 5.876A  pdb=" N   TYR D 778 " --> pdb=" O   LEU D 532 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL D 582 " --> pdb=" O   TYR D 778 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   LEU D 780 " --> pdb=" O   ALA D 580 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ALA D 580 " --> pdb=" O   LEU D 780 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   TYR D 782 " --> pdb=" O   LEU D 578 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU D 578 " --> pdb=" O   TYR D 782 " (cutoff:3.500A)
      removed outlier: 6.692A  pdb=" N   LYS D 784 " --> pdb=" O   TYR D 576 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   TYR D 576 " --> pdb=" O   LYS D 784 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   PHE D 579 " --> pdb=" O   LYS D 599 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 504 through 506
    Processing sheet with id=AA8, first strand: chain 'D' and resid 535 through 536

    187 hydrogen bonds defined for protein.
    489 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: 0.57

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 803
        1.33 -     1.45: 598
        1.45 -     1.57: 1897
        1.57 -     1.69: 0
        1.69 -     1.81: 19
  Bond restraints: 3317
  Sorted by residual:
  bond pdb=" C   SER D 775 "
       pdb=" N   THR D 776 "
    ideal  model  delta    sigma   weight residual
    1.331  1.286  0.045 1.63e-02 3.76e+03 7.78e+00
  bond pdb=" CB  ARG D 186 "
       pdb=" CG  ARG D 186 "
    ideal  model  delta    sigma   weight residual
    1.520  1.467  0.053 3.00e-02 1.11e+03 3.14e+00
  bond pdb=" CB  LEU D 159 "
       pdb=" CG  LEU D 159 "
    ideal  model  delta    sigma   weight residual
    1.530  1.495  0.035 2.00e-02 2.50e+03 3.07e+00
  bond pdb=" CG  LYS D 551 "
       pdb=" CD  LYS D 551 "
    ideal  model  delta    sigma   weight residual
    1.520  1.473  0.047 3.00e-02 1.11e+03 2.49e+00
  bond pdb=" CA  ASP D 751 "
       pdb=" CB  ASP D 751 "
    ideal  model  delta    sigma   weight residual
    1.536  1.474  0.062 4.10e-02 5.95e+02 2.31e+00
  ... (remaining 3312 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 4226
        1.65 -     3.31: 214
        3.31 -     4.96: 29
        4.96 -     6.62: 6
        6.62 -     8.27: 2
  Bond angle restraints: 4477
  Sorted by residual:
  angle pdb=" CA  LEU C  15 "
        pdb=" CB  LEU C  15 "
        pdb=" CG  LEU C  15 "
      ideal   model   delta    sigma   weight residual
     116.30  124.57   -8.27 3.50e+00 8.16e-02 5.59e+00
  angle pdb=" C   PHE D 535 "
        pdb=" CA  PHE D 535 "
        pdb=" CB  PHE D 535 "
      ideal   model   delta    sigma   weight residual
     110.16  114.38   -4.22 1.83e+00 2.99e-01 5.32e+00
  angle pdb=" CA  GLN D 433 "
        pdb=" CB  GLN D 433 "
        pdb=" CG  GLN D 433 "
      ideal   model   delta    sigma   weight residual
     114.10  118.69   -4.59 2.00e+00 2.50e-01 5.28e+00
  angle pdb=" C   GLU D 424 "
        pdb=" CA  GLU D 424 "
        pdb=" CB  GLU D 424 "
      ideal   model   delta    sigma   weight residual
     110.42  114.98   -4.56 1.99e+00 2.53e-01 5.26e+00
  angle pdb=" N   ASP D 172 "
        pdb=" CA  ASP D 172 "
        pdb=" C   ASP D 172 "
      ideal   model   delta    sigma   weight residual
     111.24  114.11   -2.87 1.29e+00 6.01e-01 4.94e+00
  ... (remaining 4472 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.58: 1819
       15.58 -    31.16: 158
       31.16 -    46.74: 34
       46.74 -    62.32: 11
       62.32 -    77.89: 4
  Dihedral angle restraints: 2026
    sinusoidal: 838
      harmonic: 1188
  Sorted by residual:
  dihedral pdb=" CA  PRO D 555 "
           pdb=" C   PRO D 555 "
           pdb=" N   LEU D 556 "
           pdb=" CA  LEU D 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.21   16.79     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CG  ARG D 486 "
           pdb=" CD  ARG D 486 "
           pdb=" NE  ARG D 486 "
           pdb=" CZ  ARG D 486 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -46.72  -43.28     2      1.50e+01 4.44e-03 1.00e+01
  dihedral pdb=" CB  LYS D 428 "
           pdb=" CG  LYS D 428 "
           pdb=" CD  LYS D 428 "
           pdb=" CE  LYS D 428 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  118.40  -58.40     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 2023 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 434
       0.074 -    0.149: 83
       0.149 -    0.223: 1
       0.223 -    0.297: 0
       0.297 -    0.371: 1
  Chirality restraints: 519
  Sorted by residual:
  chirality pdb=" CG  LEU D 519 "
            pdb=" CB  LEU D 519 "
            pdb=" CD1 LEU D 519 "
            pdb=" CD2 LEU D 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.22   -0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CB  VAL D 755 "
            pdb=" CA  VAL D 755 "
            pdb=" CG1 VAL D 755 "
            pdb=" CG2 VAL D 755 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.61e-01
  chirality pdb=" CA  PHE D 535 "
            pdb=" N   PHE D 535 "
            pdb=" C   PHE D 535 "
            pdb=" CB  PHE D 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.89e-01
  ... (remaining 516 not shown)

  Planarity restraints: 566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 189 "   -0.032 5.00e-02 4.00e+02   4.88e-02 3.82e+00
        pdb=" N   PRO D 190 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO D 190 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 190 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN D 177 "   -0.032 5.00e-02 4.00e+02   4.81e-02 3.70e+00
        pdb=" N   PRO D 178 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D 178 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 178 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 505 "   -0.020 2.00e-02 2.50e+03   1.34e-02 3.14e+00
        pdb=" CG  PHE D 505 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 505 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 505 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 505 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 505 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 505 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 563 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 451
        2.75 -     3.29: 2912
        3.29 -     3.82: 5767
        3.82 -     4.36: 7330
        4.36 -     4.90: 11851
  Nonbonded interactions: 28311
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN D 454 "
            pdb=" O   HOH D1101 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ALA C  46 "
            pdb=" O   HOH C 101 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" NZ  LYS C  33 "
            pdb=" OD1 ASP D 502 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" O   LEU C  73 "
            pdb=" OH  TYR D 594 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   HOH D1131 "
            pdb=" O   HOH D1132 "
     model   vdw
     2.329 3.040
  ... (remaining 28306 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:             2.920
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.330
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:6.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
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      :  0.010   0.103   3321  Z= 0.424
  Angle     :  0.846   8.273   4483  Z= 0.451
  Chirality :  0.055   0.371    519
  Planarity :  0.007   0.060    566
  Dihedral  : 13.327  77.893   1252
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.40 (0.37), residues: 393
  helix: -0.49 (0.40), residues: 130
  sheet: -0.68 (0.44), residues: 100
  loop : -1.31 (0.44), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG C  42 
 TYR   0.021   0.004   TYR D 195 
 PHE   0.027   0.005   PHE D 505 
 TRP   0.013   0.004   TRP D 487 
 HIS   0.006   0.002   HIS D 593 

Details of bonding type rmsd
  covalent geometry    : bond        0.00990 ( 3317)
  covalent geometry    : angle       0.84196 ( 4477)
  hydrogen bonds       : bond        0.13752 (  175)
  hydrogen bonds       : angle       6.01219 (  489)
  metal coordination   : bond        0.06860 (    4)
  metal coordination   : angle       2.39840 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.127 
Fit side-chains
REVERT: D  455 ASP cc_start: 0.8188 (p0) cc_final: 0.7885 (p0)
REVERT: D  524 MET cc_start: 0.8540 (mmm) cc_final: 0.8316 (tpt)
  outliers start: 0
  outliers final: 1
  residues processed: 68
  average time/residue: 0.7244
  time to fit residues: 50.3200
Evaluate side-chains
  62 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  115 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 210 ASN
D 216 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.128101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.102110 restraints weight = 3059.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 1.36
r_work: 0.2913 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3321  Z= 0.130
  Angle     :  0.513   5.675   4483  Z= 0.271
  Chirality :  0.038   0.128    519
  Planarity :  0.004   0.036    566
  Dihedral  :  5.255  34.101    432
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  6.68 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.41), residues: 393
  helix:  1.38 (0.45), residues: 130
  sheet: -0.36 (0.44), residues: 104
  loop : -0.45 (0.50), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 486 
 TYR   0.011   0.002   TYR D 195 
 PHE   0.012   0.002   PHE D 505 
 TRP   0.004   0.001   TRP D 487 
 HIS   0.002   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3317)
  covalent geometry    : angle       0.50578 ( 4477)
  hydrogen bonds       : bond        0.04002 (  175)
  hydrogen bonds       : angle       4.27639 (  489)
  metal coordination   : bond        0.00274 (    4)
  metal coordination   : angle       2.46985 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: D  158 GLN cc_start: 0.8323 (mt0) cc_final: 0.7960 (mt0)
REVERT: D  424 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7233 (pm20)
REVERT: D  565 GLU cc_start: 0.8582 (tt0) cc_final: 0.8260 (tt0)
  outliers start: 6
  outliers final: 3
  residues processed: 68
  average time/residue: 0.6924
  time to fit residues: 48.1570
Evaluate side-chains
  64 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 SER
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  424 GLU
Chi-restraints excluded: chain D residue  772 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0370
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    1.8064

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 216 GLN
D 454 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.125545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.099461 restraints weight = 3034.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 1.36
r_work: 0.2878 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3321  Z= 0.220
  Angle     :  0.592   6.389   4483  Z= 0.304
  Chirality :  0.041   0.126    519
  Planarity :  0.005   0.038    566
  Dihedral  :  5.371  31.919    432
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  :  9.36 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.42), residues: 393
  helix:  1.74 (0.46), residues: 130
  sheet: -0.19 (0.45), residues: 102
  loop : -0.34 (0.51), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 450 
 TYR   0.014   0.002   TYR D 195 
 PHE   0.020   0.003   PHE D 505 
 TRP   0.007   0.002   TRP D 487 
 HIS   0.003   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 3317)
  covalent geometry    : angle       0.58646 ( 4477)
  hydrogen bonds       : bond        0.04500 (  175)
  hydrogen bonds       : angle       4.36901 (  489)
  metal coordination   : bond        0.00543 (    4)
  metal coordination   : angle       2.35918 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.137 
Fit side-chains
REVERT: D  565 GLU cc_start: 0.8568 (tt0) cc_final: 0.8182 (tt0)
  outliers start: 7
  outliers final: 7
  residues processed: 63
  average time/residue: 0.6770
  time to fit residues: 43.6033
Evaluate side-chains
  67 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   63 LYS
Chi-restraints excluded: chain D residue  107 SER
Chi-restraints excluded: chain D residue  424 GLU
Chi-restraints excluded: chain D residue  462 GLU
Chi-restraints excluded: chain D residue  483 LYS
Chi-restraints excluded: chain D residue  535 PHE
Chi-restraints excluded: chain D residue  772 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0010
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 216 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.128155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.102330 restraints weight = 3041.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 1.37
r_work: 0.2930 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3321  Z= 0.108
  Angle     :  0.474   4.958   4483  Z= 0.246
  Chirality :  0.037   0.127    519
  Planarity :  0.004   0.032    566
  Dihedral  :  4.571  26.655    430
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.16 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.42), residues: 393
  helix:  2.29 (0.46), residues: 130
  sheet: -0.08 (0.44), residues: 104
  loop : -0.18 (0.52), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 450 
 TYR   0.008   0.001   TYR D 195 
 PHE   0.009   0.001   PHE D 505 
 TRP   0.003   0.001   TRP D 747 
 HIS   0.002   0.001   HIS D 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3317)
  covalent geometry    : angle       0.46756 ( 4477)
  hydrogen bonds       : bond        0.03422 (  175)
  hydrogen bonds       : angle       3.93686 (  489)
  metal coordination   : bond        0.00373 (    4)
  metal coordination   : angle       2.15184 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.104 
Fit side-chains
REVERT: D  158 GLN cc_start: 0.8363 (mt0) cc_final: 0.8007 (mt0)
REVERT: D  565 GLU cc_start: 0.8513 (tt0) cc_final: 0.8098 (tt0)
REVERT: D  758 THR cc_start: 0.7705 (m) cc_final: 0.7303 (p)
  outliers start: 9
  outliers final: 5
  residues processed: 68
  average time/residue: 0.7022
  time to fit residues: 48.7666
Evaluate side-chains
  69 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 SER
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  424 GLU
Chi-restraints excluded: chain D residue  495 VAL
Chi-restraints excluded: chain D residue  772 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 1 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 216 GLN
D 454 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.128263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.102755 restraints weight = 3085.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.33
r_work: 0.2929 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3321  Z= 0.117
  Angle     :  0.467   4.445   4483  Z= 0.245
  Chirality :  0.037   0.128    519
  Planarity :  0.003   0.031    566
  Dihedral  :  4.478  23.836    430
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 10.43 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.43), residues: 393
  helix:  2.48 (0.45), residues: 130
  sheet:  0.01 (0.45), residues: 104
  loop : -0.11 (0.52), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 486 
 TYR   0.009   0.001   TYR D 195 
 PHE   0.012   0.002   PHE D 505 
 TRP   0.003   0.001   TRP D 487 
 HIS   0.002   0.001   HIS D 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 3317)
  covalent geometry    : angle       0.46181 ( 4477)
  hydrogen bonds       : bond        0.03432 (  175)
  hydrogen bonds       : angle       3.90159 (  489)
  metal coordination   : bond        0.00360 (    4)
  metal coordination   : angle       2.00154 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.078 
Fit side-chains
REVERT: C   54 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8426 (mmm-85)
REVERT: D  450 ARG cc_start: 0.8305 (mtt90) cc_final: 0.7860 (mtt180)
REVERT: D  565 GLU cc_start: 0.8530 (tt0) cc_final: 0.8084 (tt0)
REVERT: D  758 THR cc_start: 0.7567 (OUTLIER) cc_final: 0.7206 (p)
REVERT: D  764 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7361 (mm)
  outliers start: 10
  outliers final: 6
  residues processed: 68
  average time/residue: 0.6720
  time to fit residues: 46.7352
Evaluate side-chains
  71 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 SER
Chi-restraints excluded: chain D residue  424 GLU
Chi-restraints excluded: chain D residue  495 VAL
Chi-restraints excluded: chain D residue  535 PHE
Chi-restraints excluded: chain D residue  758 THR
Chi-restraints excluded: chain D residue  764 LEU
Chi-restraints excluded: chain D residue  768 SER
Chi-restraints excluded: chain D residue  772 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 216 GLN
D 454 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.124130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.098632 restraints weight = 3069.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.33
r_work: 0.2891 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3321  Z= 0.214
  Angle     :  0.579   6.615   4483  Z= 0.296
  Chirality :  0.041   0.125    519
  Planarity :  0.004   0.035    566
  Dihedral  :  4.907  25.931    430
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 10.43 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.42), residues: 393
  helix:  2.20 (0.45), residues: 130
  sheet: -0.03 (0.45), residues: 102
  loop : -0.13 (0.52), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 486 
 TYR   0.014   0.002   TYR D 195 
 PHE   0.020   0.003   PHE D 505 
 TRP   0.007   0.002   TRP D 487 
 HIS   0.004   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 3317)
  covalent geometry    : angle       0.57317 ( 4477)
  hydrogen bonds       : bond        0.04241 (  175)
  hydrogen bonds       : angle       4.18642 (  489)
  metal coordination   : bond        0.00516 (    4)
  metal coordination   : angle       2.35401 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.126 
Fit side-chains
REVERT: C   54 ARG cc_start: 0.8713 (mmm-85) cc_final: 0.8496 (mmm-85)
REVERT: D  450 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7765 (mtp85)
REVERT: D  764 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7421 (mm)
  outliers start: 12
  outliers final: 8
  residues processed: 70
  average time/residue: 0.6863
  time to fit residues: 49.0492
Evaluate side-chains
  75 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 SER
Chi-restraints excluded: chain D residue  424 GLU
Chi-restraints excluded: chain D residue  495 VAL
Chi-restraints excluded: chain D residue  535 PHE
Chi-restraints excluded: chain D residue  757 VAL
Chi-restraints excluded: chain D residue  758 THR
Chi-restraints excluded: chain D residue  764 LEU
Chi-restraints excluded: chain D residue  768 SER
Chi-restraints excluded: chain D residue  772 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    0.1980
   chunk 19 optimal weight:    3.9990
   chunk 39 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 216 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.127255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.101894 restraints weight = 3149.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.32
r_work: 0.2934 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3321  Z= 0.112
  Angle     :  0.472   4.538   4483  Z= 0.246
  Chirality :  0.037   0.128    519
  Planarity :  0.003   0.030    566
  Dihedral  :  4.480  23.171    430
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 10.96 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.43), residues: 393
  helix:  2.54 (0.45), residues: 130
  sheet:  0.01 (0.45), residues: 104
  loop : -0.04 (0.52), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 486 
 TYR   0.009   0.001   TYR D 195 
 PHE   0.010   0.001   PHE D 505 
 TRP   0.004   0.001   TRP D 747 
 HIS   0.002   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 3317)
  covalent geometry    : angle       0.46528 ( 4477)
  hydrogen bonds       : bond        0.03391 (  175)
  hydrogen bonds       : angle       3.90438 (  489)
  metal coordination   : bond        0.00378 (    4)
  metal coordination   : angle       2.16928 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.126 
Fit side-chains
REVERT: C   54 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8445 (mmm-85)
REVERT: D  450 ARG cc_start: 0.8361 (mtt90) cc_final: 0.8099 (mtt90)
REVERT: D  565 GLU cc_start: 0.8539 (tt0) cc_final: 0.8170 (tt0)
REVERT: D  758 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7232 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 69
  average time/residue: 0.6775
  time to fit residues: 47.7759
Evaluate side-chains
  72 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 SER
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  424 GLU
Chi-restraints excluded: chain D residue  495 VAL
Chi-restraints excluded: chain D residue  535 PHE
Chi-restraints excluded: chain D residue  758 THR
Chi-restraints excluded: chain D residue  764 LEU
Chi-restraints excluded: chain D residue  768 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 10 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 216 GLN
D 454 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.125342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.099622 restraints weight = 3178.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 1.34
r_work: 0.2895 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3321  Z= 0.183
  Angle     :  0.548   6.042   4483  Z= 0.282
  Chirality :  0.039   0.126    519
  Planarity :  0.004   0.033    566
  Dihedral  :  4.770  24.420    430
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 10.70 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.42), residues: 393
  helix:  2.32 (0.45), residues: 130
  sheet: -0.00 (0.45), residues: 102
  loop : -0.11 (0.51), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 486 
 TYR   0.013   0.002   TYR D 195 
 PHE   0.017   0.002   PHE D 505 
 TRP   0.006   0.002   TRP D 487 
 HIS   0.003   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 3317)
  covalent geometry    : angle       0.54244 ( 4477)
  hydrogen bonds       : bond        0.03993 (  175)
  hydrogen bonds       : angle       4.09477 (  489)
  metal coordination   : bond        0.00444 (    4)
  metal coordination   : angle       2.11862 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.116 
Fit side-chains
REVERT: C   54 ARG cc_start: 0.8686 (mmm-85) cc_final: 0.8410 (mmm-85)
REVERT: D  450 ARG cc_start: 0.8383 (mtt90) cc_final: 0.8118 (mtt180)
REVERT: D  526 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8146 (mm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 69
  average time/residue: 0.6641
  time to fit residues: 46.7973
Evaluate side-chains
  73 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 SER
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  424 GLU
Chi-restraints excluded: chain D residue  495 VAL
Chi-restraints excluded: chain D residue  535 PHE
Chi-restraints excluded: chain D residue  758 THR
Chi-restraints excluded: chain D residue  764 LEU
Chi-restraints excluded: chain D residue  768 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 216 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.127678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.102043 restraints weight = 3129.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.33
r_work: 0.2921 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2801 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3321  Z= 0.126
  Angle     :  0.487   6.187   4483  Z= 0.254
  Chirality :  0.037   0.127    519
  Planarity :  0.003   0.029    566
  Dihedral  :  4.521  22.740    430
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 11.50 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.42), residues: 393
  helix:  2.51 (0.45), residues: 130
  sheet:  0.03 (0.45), residues: 104
  loop : -0.03 (0.51), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 486 
 TYR   0.010   0.002   TYR D 195 
 PHE   0.012   0.002   PHE D 505 
 TRP   0.004   0.001   TRP D 487 
 HIS   0.002   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3317)
  covalent geometry    : angle       0.48149 ( 4477)
  hydrogen bonds       : bond        0.03505 (  175)
  hydrogen bonds       : angle       3.93095 (  489)
  metal coordination   : bond        0.00385 (    4)
  metal coordination   : angle       2.13939 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.101 
Fit side-chains
REVERT: C   54 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8437 (mmm-85)
REVERT: D  450 ARG cc_start: 0.8388 (mtt90) cc_final: 0.8174 (mtp85)
REVERT: D  526 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8171 (mm-30)
REVERT: D  565 GLU cc_start: 0.8634 (tt0) cc_final: 0.8375 (tt0)
REVERT: D  758 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7242 (p)
  outliers start: 9
  outliers final: 7
  residues processed: 68
  average time/residue: 0.6616
  time to fit residues: 46.0122
Evaluate side-chains
  70 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 SER
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  424 GLU
Chi-restraints excluded: chain D residue  495 VAL
Chi-restraints excluded: chain D residue  535 PHE
Chi-restraints excluded: chain D residue  758 THR
Chi-restraints excluded: chain D residue  764 LEU
Chi-restraints excluded: chain D residue  768 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 33 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 216 GLN
D 454 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.127103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.101412 restraints weight = 3106.921|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.33
r_work: 0.2921 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2802 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3321  Z= 0.143
  Angle     :  0.516   6.417   4483  Z= 0.266
  Chirality :  0.038   0.126    519
  Planarity :  0.004   0.032    566
  Dihedral  :  4.591  22.412    430
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 12.03 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.42), residues: 393
  helix:  2.42 (0.45), residues: 130
  sheet:  0.04 (0.45), residues: 104
  loop : -0.00 (0.51), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 486 
 TYR   0.011   0.002   TYR D 195 
 PHE   0.014   0.002   PHE D 505 
 TRP   0.005   0.001   TRP D 487 
 HIS   0.002   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3317)
  covalent geometry    : angle       0.51036 ( 4477)
  hydrogen bonds       : bond        0.03674 (  175)
  hydrogen bonds       : angle       3.99416 (  489)
  metal coordination   : bond        0.00384 (    4)
  metal coordination   : angle       2.05586 (    6)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.173 
Fit side-chains
REVERT: C   54 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8379 (mmm-85)
REVERT: D  450 ARG cc_start: 0.8378 (mtt90) cc_final: 0.8066 (mtp85)
REVERT: D  526 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8146 (mm-30)
REVERT: D  565 GLU cc_start: 0.8561 (tt0) cc_final: 0.8318 (tt0)
  outliers start: 9
  outliers final: 9
  residues processed: 67
  average time/residue: 0.6754
  time to fit residues: 46.2756
Evaluate side-chains
  72 residues out of total 374 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  107 SER
Chi-restraints excluded: chain D residue  115 ILE
Chi-restraints excluded: chain D residue  424 GLU
Chi-restraints excluded: chain D residue  495 VAL
Chi-restraints excluded: chain D residue  535 PHE
Chi-restraints excluded: chain D residue  757 VAL
Chi-restraints excluded: chain D residue  758 THR
Chi-restraints excluded: chain D residue  764 LEU
Chi-restraints excluded: chain D residue  768 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
C  25 ASN
C  60 ASN
C  62 GLN
D 177 GLN
D 216 GLN
D 454 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.124811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.098612 restraints weight = 3166.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 1.37
r_work: 0.2880 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3321  Z= 0.232
  Angle     :  0.605   7.150   4483  Z= 0.310
  Chirality :  0.042   0.126    519
  Planarity :  0.004   0.034    566
  Dihedral  :  4.962  25.610    430
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.76 %
    Favored  : 86.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.42), residues: 393
  helix:  2.02 (0.45), residues: 130
  sheet:  0.00 (0.45), residues: 102
  loop : -0.06 (0.51), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 486 
 TYR   0.015   0.002   TYR D 195 
 PHE   0.020   0.003   PHE D 505 
 TRP   0.007   0.002   TRP D 487 
 HIS   0.003   0.001   HIS C  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 3317)
  covalent geometry    : angle       0.59907 ( 4477)
  hydrogen bonds       : bond        0.04365 (  175)
  hydrogen bonds       : angle       4.25767 (  489)
  metal coordination   : bond        0.00516 (    4)
  metal coordination   : angle       2.34996 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1555.41 seconds
wall clock time: 27 minutes 18.62 seconds (1638.62 seconds total)