Starting phenix.real_space_refine
on Tue Mar  3 12:05:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ouc_20202/03_2026/6ouc_20202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ouc_20202/03_2026/6ouc_20202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ouc_20202/03_2026/6ouc_20202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ouc_20202/03_2026/6ouc_20202.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ouc_20202/03_2026/6ouc_20202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ouc_20202/03_2026/6ouc_20202.map"
  }
  resolution = 2.8
  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=  -0.001 sd=   0.041
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      15      5.16       5
     C    2421      2.51       5
     N     642      2.21       5
     O     820      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 3899
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 483, 3774
          Classifications: {'peptide': 483}
          Link IDs: {'PTRANS': 46, 'TRANS': 436}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 125
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1, 'water': 124}
          Link IDs: {None: 124}
  Time building chain proxies: 1.13, per 1000 atoms: 0.29
  Number of scatterers: 3899
  At special positions: 0
  Unit cell: (95.23, 95.23, 78.11, 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      15     16.00
     O     820      8.00
     N     642      7.00
     C    2421      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: 0.29
  Conformation dependent library (CDL) restraints added in 129.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A 299 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS A 293 "


  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  900

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 9 sheets defined
      6.2% alpha, 28.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 85
      removed outlier: 3.522A  pdb=" N   LEU A  85 " --> pdb=" O   GLY A  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 82 through 85'
    Processing helix  chain 'A' and resid 86 through 93
    Processing helix  chain 'A' and resid 136 through 141
      removed outlier: 3.628A  pdb=" N   THR A 139 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE A 141 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 467
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58
    Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 58
      removed outlier: 4.053A  pdb=" N   SER A 199 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 80
      removed outlier: 6.342A  pdb=" N   ALA A 180 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ASN A  78 " --> pdb=" O   ILE A 178 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE A 178 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 168
    Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 116
    Processing sheet with id=AA6, first strand: chain 'A' and resid 450 through 453
      removed outlier: 4.853A  pdb=" N   MET A 249 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 450 through 453
      removed outlier: 4.743A  pdb=" N   MET A 499 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   PHE A 489 " --> pdb=" O   TYR A 479 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL A 474 " --> pdb=" O   TRP A 522 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   TRP A 522 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LEU A 476 " --> pdb=" O   ASP A 520 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 265 through 266
      removed outlier: 4.565A  pdb=" N   ARG A 265 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 360
      removed outlier: 7.700A  pdb=" N   ARG A 331 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   LEU A 396 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   PHE A 333 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ARG A 339 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   PHE A 286 " --> pdb=" O   PHE A 391 " (cutoff:3.500A)

    100 hydrogen bonds defined for protein.
    258 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: 0.60

  Time building geometry restraints manager: 0.38 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: 969
        1.33 -     1.45: 735
        1.45 -     1.56: 2154
        1.56 -     1.68: 0
        1.68 -     1.80: 25
  Bond restraints: 3883
  Sorted by residual:
  bond pdb=" CA  TYR A 214 "
       pdb=" C   TYR A 214 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.032 1.22e-02 6.72e+03 6.77e+00
  bond pdb=" CA  GLN A 170 "
       pdb=" C   GLN A 170 "
    ideal  model  delta    sigma   weight residual
    1.528  1.561 -0.033 1.33e-02 5.65e+03 6.30e+00
  bond pdb=" N   TRP A 378 "
       pdb=" CA  TRP A 378 "
    ideal  model  delta    sigma   weight residual
    1.459  1.430  0.029 1.24e-02 6.50e+03 5.52e+00
  bond pdb=" CG  LEU A 455 "
       pdb=" CD1 LEU A 455 "
    ideal  model  delta    sigma   weight residual
    1.521  1.447  0.074 3.30e-02 9.18e+02 5.06e+00
  bond pdb=" CA  GLN A 170 "
       pdb=" CB  GLN A 170 "
    ideal  model  delta    sigma   weight residual
    1.527  1.498  0.029 1.44e-02 4.82e+03 3.96e+00
  ... (remaining 3878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.39: 5207
        3.39 -     6.79: 93
        6.79 -    10.18: 8
       10.18 -    13.57: 6
       13.57 -    16.97: 1
  Bond angle restraints: 5315
  Sorted by residual:
  angle pdb=" N   GLY A  62 "
        pdb=" CA  GLY A  62 "
        pdb=" C   GLY A  62 "
      ideal   model   delta    sigma   weight residual
     112.73  129.70  -16.97 1.20e+00 6.94e-01 2.00e+02
  angle pdb=" N   THR A 213 "
        pdb=" CA  THR A 213 "
        pdb=" C   THR A 213 "
      ideal   model   delta    sigma   weight residual
     112.68  125.51  -12.83 1.33e+00 5.65e-01 9.31e+01
  angle pdb=" N   ASN A 297 "
        pdb=" CA  ASN A 297 "
        pdb=" C   ASN A 297 "
      ideal   model   delta    sigma   weight residual
     111.28  101.34    9.94 1.09e+00 8.42e-01 8.32e+01
  angle pdb=" N   TYR A 301 "
        pdb=" CA  TYR A 301 "
        pdb=" C   TYR A 301 "
      ideal   model   delta    sigma   weight residual
     111.02  121.74  -10.72 1.25e+00 6.40e-01 7.36e+01
  angle pdb=" N   LEU A 300 "
        pdb=" CA  LEU A 300 "
        pdb=" C   LEU A 300 "
      ideal   model   delta    sigma   weight residual
     114.04  123.08   -9.04 1.24e+00 6.50e-01 5.31e+01
  ... (remaining 5310 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.63: 2184
       13.63 -    27.25: 101
       27.25 -    40.87: 25
       40.87 -    54.49: 3
       54.49 -    68.11: 2
  Dihedral angle restraints: 2315
    sinusoidal: 917
      harmonic: 1398
  Sorted by residual:
  dihedral pdb=" C   LEU A 300 "
           pdb=" N   LEU A 300 "
           pdb=" CA  LEU A 300 "
           pdb=" CB  LEU A 300 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.63   16.03     0      2.50e+00 1.60e-01 4.11e+01
  dihedral pdb=" CA  ALA A 344 "
           pdb=" C   ALA A 344 "
           pdb=" N   ALA A 345 "
           pdb=" CA  ALA A 345 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.63  -29.37     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" N   LEU A 300 "
           pdb=" C   LEU A 300 "
           pdb=" CA  LEU A 300 "
           pdb=" CB  LEU A 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.25  -14.45     0      2.50e+00 1.60e-01 3.34e+01
  ... (remaining 2312 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.161: 574
       0.161 -    0.321: 11
       0.321 -    0.482: 1
       0.482 -    0.642: 1
       0.642 -    0.802: 1
  Chirality restraints: 588
  Sorted by residual:
  chirality pdb=" CA  LEU A 300 "
            pdb=" N   LEU A 300 "
            pdb=" C   LEU A 300 "
            pdb=" CB  LEU A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.71    0.80 2.00e-01 2.50e+01 1.61e+01
  chirality pdb=" CA  TYR A 301 "
            pdb=" N   TYR A 301 "
            pdb=" C   TYR A 301 "
            pdb=" CB  TYR A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.45e+00
  chirality pdb=" CA  THR A 213 "
            pdb=" N   THR A 213 "
            pdb=" C   THR A 213 "
            pdb=" CB  THR A 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.09    0.43 2.00e-01 2.50e+01 4.66e+00
  ... (remaining 585 not shown)

  Planarity restraints: 708
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  51 "    0.020 2.00e-02 2.50e+03   1.84e-02 8.44e+00
        pdb=" CG  TRP A  51 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  51 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  51 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  51 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  51 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  51 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  51 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  51 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  51 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 405 "   -0.010 2.00e-02 2.50e+03   1.45e-02 5.23e+00
        pdb=" CG  TRP A 405 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 405 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 405 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 405 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 405 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 405 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 405 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 405 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 405 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  49 "    0.038 5.00e-02 4.00e+02   5.68e-02 5.17e+00
        pdb=" N   PRO A  50 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A  50 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  50 "    0.031 5.00e-02 4.00e+02
  ... (remaining 705 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 158
        2.68 -     3.24: 3304
        3.24 -     3.79: 5839
        3.79 -     4.35: 8181
        4.35 -     4.90: 13624
  Nonbonded interactions: 31106
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 243 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OE1 GLU A  84 "
            pdb=" O   HOH A 702 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" O   ALA A 496 "
            pdb=" O   HOH A 703 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   MET A 532 "
            pdb=" O   HOH A 704 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OD1 ASP A 211 "
            pdb=" N   PHE A 212 "
     model   vdw
     2.197 3.120
  ... (remaining 31101 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.170
  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:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.370
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:6.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
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   0.284   3885  Z= 0.417
  Angle     :  1.153  16.966   5315  Z= 0.699
  Chirality :  0.081   0.802    588
  Planarity :  0.010   0.057    708
  Dihedral  :  9.030  68.110   1415
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.22 %
  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: -2.32 (0.31), residues: 479
  helix: -3.43 (0.57), residues: 27
  sheet: -0.80 (0.41), residues: 130
  loop : -1.78 (0.27), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG A 495 
 TYR   0.025   0.004   TYR A 410 
 PHE   0.035   0.004   PHE A 498 
 TRP   0.048   0.006   TRP A  51 
 HIS   0.013   0.002   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00821 ( 3883)
  covalent geometry    : angle       1.15326 ( 5315)
  hydrogen bonds       : bond        0.16176 (   94)
  hydrogen bonds       : angle       7.18390 (  258)
  metal coordination   : bond        0.27823 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7265 (mp0) cc_final: 0.7054 (mp0)
REVERT: A  155 LEU cc_start: 0.8987 (mt) cc_final: 0.8739 (mt)
REVERT: A  356 ASP cc_start: 0.8347 (m-30) cc_final: 0.8122 (m-30)
REVERT: A  379 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7605 (mm110)
REVERT: A  443 LYS cc_start: 0.9112 (tttm) cc_final: 0.8849 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.5140
  time to fit residues: 59.4465
Evaluate side-chains
  100 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
A 167 HIS
A 189 ASN
A 347 GLN
A 386 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.107305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.091595 restraints weight = 5091.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 1.63
r_work: 0.2823 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3885  Z= 0.136
  Angle     :  0.580   6.755   5315  Z= 0.304
  Chirality :  0.046   0.132    588
  Planarity :  0.007   0.040    708
  Dihedral  :  5.273  21.258    519
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  7.69 %
    Favored  : 90.62 %
  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: -1.28 (0.34), residues: 479
  helix: -1.81 (0.81), residues: 27
  sheet: -0.35 (0.40), residues: 153
  loop : -1.02 (0.31), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 495 
 TYR   0.012   0.001   TYR A 168 
 PHE   0.015   0.002   PHE A  64 
 TRP   0.016   0.002   TRP A  51 
 HIS   0.005   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 3883)
  covalent geometry    : angle       0.57978 ( 5315)
  hydrogen bonds       : bond        0.03798 (   94)
  hydrogen bonds       : angle       5.96810 (  258)
  metal coordination   : bond        0.00327 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  398 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8478 (p0)
REVERT: A  443 LYS cc_start: 0.9206 (tttm) cc_final: 0.8905 (tttm)
  outliers start: 7
  outliers final: 1
  residues processed: 101
  average time/residue: 0.5085
  time to fit residues: 53.0261
Evaluate side-chains
  91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  398 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0980
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
A 386 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.105661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.089980 restraints weight = 4938.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 1.58
r_work: 0.2801 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8818
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.197   3885  Z= 0.190
  Angle     :  0.586   6.572   5315  Z= 0.300
  Chirality :  0.047   0.132    588
  Planarity :  0.006   0.037    708
  Dihedral  :  5.058  20.608    519
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.58 %
    Favored  : 87.26 %
  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 (0.35), residues: 479
  helix: -1.65 (0.80), residues: 33
  sheet: -0.16 (0.42), residues: 144
  loop : -0.84 (0.31), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 201 
 TYR   0.012   0.001   TYR A 214 
 PHE   0.014   0.002   PHE A  64 
 TRP   0.008   0.001   TRP A  51 
 HIS   0.005   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 3883)
  covalent geometry    : angle       0.58605 ( 5315)
  hydrogen bonds       : bond        0.03800 (   94)
  hydrogen bonds       : angle       5.77178 (  258)
  metal coordination   : bond        0.13931 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  187 ARG cc_start: 0.8058 (mtm180) cc_final: 0.7540 (mtp85)
REVERT: A  443 LYS cc_start: 0.9202 (tttm) cc_final: 0.8956 (tttm)
REVERT: A  525 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7759 (pm20)
  outliers start: 9
  outliers final: 5
  residues processed: 96
  average time/residue: 0.5157
  time to fit residues: 51.1268
Evaluate side-chains
  95 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 45 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.104341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.088564 restraints weight = 4995.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 1.59
r_work: 0.2821 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3885  Z= 0.159
  Angle     :  0.566   6.582   5315  Z= 0.289
  Chirality :  0.047   0.134    588
  Planarity :  0.006   0.041    708
  Dihedral  :  4.892  21.569    519
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.26 %
    Favored  : 85.34 %
  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: -0.86 (0.35), residues: 479
  helix: -1.42 (0.83), residues: 33
  sheet: -0.17 (0.41), residues: 154
  loop : -0.65 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 437 
 TYR   0.012   0.001   TYR A 214 
 PHE   0.013   0.002   PHE A  64 
 TRP   0.005   0.001   TRP A  51 
 HIS   0.005   0.001   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 3883)
  covalent geometry    : angle       0.56648 ( 5315)
  hydrogen bonds       : bond        0.03735 (   94)
  hydrogen bonds       : angle       5.67007 (  258)
  metal coordination   : bond        0.00592 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  187 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7584 (mtp85)
REVERT: A  204 THR cc_start: 0.9321 (p) cc_final: 0.9094 (m)
REVERT: A  398 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8567 (p0)
REVERT: A  443 LYS cc_start: 0.9162 (tttm) cc_final: 0.8937 (tttm)
REVERT: A  525 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7793 (pm20)
  outliers start: 10
  outliers final: 5
  residues processed: 98
  average time/residue: 0.5192
  time to fit residues: 52.4662
Evaluate side-chains
  99 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    0.4980
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.107781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.092138 restraints weight = 4969.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 1.60
r_work: 0.2848 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3885  Z= 0.092
  Angle     :  0.495   6.588   5315  Z= 0.251
  Chirality :  0.044   0.129    588
  Planarity :  0.005   0.041    708
  Dihedral  :  4.445  21.492    519
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 12.74 %
    Favored  : 84.86 %
  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: -0.65 (0.36), residues: 479
  helix: -0.95 (0.89), residues: 33
  sheet: -0.08 (0.42), residues: 153
  loop : -0.50 (0.33), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 437 
 TYR   0.009   0.001   TYR A 168 
 PHE   0.011   0.001   PHE A  64 
 TRP   0.006   0.001   TRP A 522 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 3883)
  covalent geometry    : angle       0.49476 ( 5315)
  hydrogen bonds       : bond        0.02949 (   94)
  hydrogen bonds       : angle       5.34366 (  258)
  metal coordination   : bond        0.00234 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  187 ARG cc_start: 0.8070 (mtm180) cc_final: 0.7701 (mtp85)
REVERT: A  238 SER cc_start: 0.9166 (m) cc_final: 0.8944 (p)
REVERT: A  443 LYS cc_start: 0.9125 (tttm) cc_final: 0.8889 (tttm)
  outliers start: 10
  outliers final: 5
  residues processed: 101
  average time/residue: 0.5005
  time to fit residues: 52.1551
Evaluate side-chains
  95 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0970
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
A 386 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.103596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.087357 restraints weight = 4949.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 1.68
r_work: 0.2711 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2608 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3885  Z= 0.211
  Angle     :  0.604   6.572   5315  Z= 0.307
  Chirality :  0.048   0.142    588
  Planarity :  0.006   0.039    708
  Dihedral  :  4.918  20.585    519
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.98 %
    Favored  : 84.86 %
  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: -0.65 (0.35), residues: 479
  helix: -1.21 (0.83), residues: 33
  sheet:  0.04 (0.41), residues: 154
  loop : -0.55 (0.32), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 149 
 TYR   0.016   0.002   TYR A 214 
 PHE   0.013   0.002   PHE A  64 
 TRP   0.003   0.001   TRP A  51 
 HIS   0.005   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 3883)
  covalent geometry    : angle       0.60418 ( 5315)
  hydrogen bonds       : bond        0.04147 (   94)
  hydrogen bonds       : angle       5.65380 (  258)
  metal coordination   : bond        0.00934 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A  114 PHE cc_start: 0.8329 (m-80) cc_final: 0.8042 (m-80)
REVERT: A  171 LYS cc_start: 0.8299 (tppt) cc_final: 0.7771 (mmmt)
REVERT: A  398 ASP cc_start: 0.8519 (p0) cc_final: 0.8125 (p0)
REVERT: A  443 LYS cc_start: 0.9252 (tttm) cc_final: 0.9046 (tttm)
  outliers start: 9
  outliers final: 7
  residues processed: 103
  average time/residue: 0.5082
  time to fit residues: 54.0429
Evaluate side-chains
  99 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  397 ASN
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 7 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.105429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.089733 restraints weight = 4986.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 1.59
r_work: 0.2887 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3885  Z= 0.122
  Angle     :  0.532   6.442   5315  Z= 0.270
  Chirality :  0.045   0.136    588
  Planarity :  0.006   0.042    708
  Dihedral  :  4.625  20.185    519
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.46 %
    Favored  : 84.38 %
  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: -0.49 (0.36), residues: 479
  helix: -0.92 (0.87), residues: 33
  sheet:  0.11 (0.42), residues: 154
  loop : -0.43 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 409 
 TYR   0.009   0.001   TYR A 168 
 PHE   0.012   0.001   PHE A  64 
 TRP   0.006   0.001   TRP A 522 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3883)
  covalent geometry    : angle       0.53159 ( 5315)
  hydrogen bonds       : bond        0.03387 (   94)
  hydrogen bonds       : angle       5.45174 (  258)
  metal coordination   : bond        0.00660 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  114 PHE cc_start: 0.8240 (m-80) cc_final: 0.7972 (m-80)
REVERT: A  187 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7599 (ttp80)
REVERT: A  238 SER cc_start: 0.9178 (m) cc_final: 0.8897 (p)
REVERT: A  294 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8322 (mp)
REVERT: A  398 ASP cc_start: 0.8527 (p0) cc_final: 0.8285 (p0)
REVERT: A  443 LYS cc_start: 0.9217 (tttm) cc_final: 0.9017 (tttm)
REVERT: A  525 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7858 (pm20)
  outliers start: 9
  outliers final: 6
  residues processed: 99
  average time/residue: 0.5117
  time to fit residues: 52.2954
Evaluate side-chains
  102 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  294 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0030
   chunk 39 optimal weight:    5.9990
   chunk 45 optimal weight:    4.9990
   chunk 12 optimal weight:    0.3980
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.8794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.106614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.091050 restraints weight = 4871.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 1.58
r_work: 0.2837 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2742 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3885  Z= 0.097
  Angle     :  0.505   6.392   5315  Z= 0.254
  Chirality :  0.044   0.131    588
  Planarity :  0.005   0.042    708
  Dihedral  :  4.367  19.812    519
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.94 %
    Favored  : 84.13 %
  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: -0.32 (0.36), residues: 479
  helix: -0.71 (0.90), residues: 33
  sheet:  0.21 (0.42), residues: 152
  loop : -0.32 (0.33), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 409 
 TYR   0.009   0.001   TYR A 168 
 PHE   0.011   0.001   PHE A  64 
 TRP   0.006   0.001   TRP A 522 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 3883)
  covalent geometry    : angle       0.50452 ( 5315)
  hydrogen bonds       : bond        0.03050 (   94)
  hydrogen bonds       : angle       5.22988 (  258)
  metal coordination   : bond        0.00392 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A  114 PHE cc_start: 0.8208 (m-80) cc_final: 0.7967 (m-80)
REVERT: A  187 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7673 (ttp80)
REVERT: A  238 SER cc_start: 0.9179 (m) cc_final: 0.8967 (p)
REVERT: A  384 LYS cc_start: 0.8362 (mttt) cc_final: 0.8095 (mttt)
REVERT: A  398 ASP cc_start: 0.8556 (p0) cc_final: 0.8124 (p0)
REVERT: A  525 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7853 (pm20)
  outliers start: 8
  outliers final: 6
  residues processed: 102
  average time/residue: 0.5321
  time to fit residues: 56.0493
Evaluate side-chains
  103 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 15 optimal weight:    0.1980
   chunk 22 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.6186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.106834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.091202 restraints weight = 4929.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 1.58
r_work: 0.2846 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3885  Z= 0.143
  Angle     :  0.548   6.284   5315  Z= 0.277
  Chirality :  0.046   0.134    588
  Planarity :  0.006   0.041    708
  Dihedral  :  4.597  19.551    519
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.70 %
    Favored  : 84.13 %
  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: -0.34 (0.36), residues: 479
  helix: -0.86 (0.88), residues: 33
  sheet:  0.22 (0.42), residues: 154
  loop : -0.33 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 409 
 TYR   0.012   0.001   TYR A 214 
 PHE   0.012   0.001   PHE A  64 
 TRP   0.003   0.001   TRP A 522 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 3883)
  covalent geometry    : angle       0.54839 ( 5315)
  hydrogen bonds       : bond        0.03505 (   94)
  hydrogen bonds       : angle       5.36906 (  258)
  metal coordination   : bond        0.00806 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  114 PHE cc_start: 0.8256 (m-80) cc_final: 0.7995 (m-80)
REVERT: A  176 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8562 (ttm)
REVERT: A  187 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7687 (ttp80)
REVERT: A  398 ASP cc_start: 0.8564 (p0) cc_final: 0.8116 (p0)
REVERT: A  525 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7857 (pm20)
  outliers start: 9
  outliers final: 6
  residues processed: 97
  average time/residue: 0.5476
  time to fit residues: 54.8055
Evaluate side-chains
  101 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  176 MET
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.106067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.090480 restraints weight = 4884.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 1.57
r_work: 0.2867 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3885  Z= 0.124
  Angle     :  0.530   6.289   5315  Z= 0.268
  Chirality :  0.045   0.134    588
  Planarity :  0.006   0.041    708
  Dihedral  :  4.520  19.483    519
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.94 %
    Favored  : 84.13 %
  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: -0.29 (0.36), residues: 479
  helix: -0.80 (0.88), residues: 33
  sheet:  0.24 (0.42), residues: 154
  loop : -0.29 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 409 
 TYR   0.010   0.001   TYR A 362 
 PHE   0.011   0.001   PHE A  64 
 TRP   0.005   0.001   TRP A 522 
 HIS   0.003   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3883)
  covalent geometry    : angle       0.53031 ( 5315)
  hydrogen bonds       : bond        0.03321 (   94)
  hydrogen bonds       : angle       5.28776 (  258)
  metal coordination   : bond        0.00675 (    2)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  187 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7761 (mtp85)
REVERT: A  398 ASP cc_start: 0.8548 (p0) cc_final: 0.8142 (p0)
REVERT: A  525 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.7855 (pm20)
  outliers start: 8
  outliers final: 6
  residues processed: 99
  average time/residue: 0.5158
  time to fit residues: 52.7702
Evaluate side-chains
  100 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   overall best weight:    2.7388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.120727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.105444 restraints weight = 4508.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 1.61
r_work: 0.2740 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2636 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3885  Z= 0.221
  Angle     :  0.611   6.261   5315  Z= 0.311
  Chirality :  0.048   0.144    588
  Planarity :  0.006   0.040    708
  Dihedral  :  4.893  19.326    519
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.42 %
    Favored  : 83.65 %
  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: -0.49 (0.35), residues: 479
  helix: -1.09 (0.85), residues: 33
  sheet:  0.12 (0.42), residues: 152
  loop : -0.43 (0.32), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 437 
 TYR   0.016   0.002   TYR A 362 
 PHE   0.013   0.002   PHE A  64 
 TRP   0.004   0.001   TRP A 378 
 HIS   0.004   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 3883)
  covalent geometry    : angle       0.61124 ( 5315)
  hydrogen bonds       : bond        0.04158 (   94)
  hydrogen bonds       : angle       5.54833 (  258)
  metal coordination   : bond        0.01042 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1740.44 seconds
wall clock time: 30 minutes 15.57 seconds (1815.57 seconds total)