Starting phenix.real_space_refine
on Wed Mar  5 15:31:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uip_42301/03_2025/8uip_42301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uip_42301/03_2025/8uip_42301.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uip_42301/03_2025/8uip_42301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uip_42301/03_2025/8uip_42301.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uip_42301/03_2025/8uip_42301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uip_42301/03_2025/8uip_42301.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    1548      2.51       5
     N     363      2.21       5
     O     399      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2316
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 772
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 3, 'TRANS': 97}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 1.85, per 1000 atoms: 0.80
  Number of scatterers: 2316
  At special positions: 0
  Unit cell: (54.45, 58.575, 92.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       6     16.00
     O     399      8.00
     N     363      7.00
     C    1548      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: 0.57
  Conformation dependent library (CDL) restraints added in 288.3 milliseconds
  

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  582

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 0 sheets defined
      75.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 49
    Processing helix  chain 'A' and resid 54 through 70
      removed outlier: 3.559A  pdb=" N   MET A  58 " --> pdb=" O   ILE A  54 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLN A  70 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 100
      removed outlier: 3.601A  pdb=" N   ILE A  84 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   VAL A  89 " --> pdb=" O   SER A  85 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LEU A  90 " --> pdb=" O   ILE A  86 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ILE A  92 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   GLY A  93 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   PHE A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 139
      removed outlier: 4.229A  pdb=" N   LYS A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   LEU A 121 " --> pdb=" O   PHE A 117 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLY A 124 " --> pdb=" O   ASN A 120 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 49
    Processing helix  chain 'B' and resid 54 through 70
      removed outlier: 3.560A  pdb=" N   MET B  58 " --> pdb=" O   ILE B  54 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   GLN B  70 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 100
      removed outlier: 3.601A  pdb=" N   ILE B  84 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   VAL B  89 " --> pdb=" O   SER B  85 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LEU B  90 " --> pdb=" O   ILE B  86 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ILE B  92 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   GLY B  93 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   PHE B 100 " --> pdb=" O   VAL B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 139
      removed outlier: 4.230A  pdb=" N   LYS B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   LEU B 121 " --> pdb=" O   PHE B 117 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLY B 124 " --> pdb=" O   ASN B 120 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ILE B 128 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 49
    Processing helix  chain 'C' and resid 54 through 70
      removed outlier: 3.559A  pdb=" N   MET C  58 " --> pdb=" O   ILE C  54 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLN C  70 " --> pdb=" O   ALA C  66 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 100
      removed outlier: 3.601A  pdb=" N   ILE C  84 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
      removed outlier: 4.735A  pdb=" N   VAL C  89 " --> pdb=" O   SER C  85 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU C  90 " --> pdb=" O   ILE C  86 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ILE C  92 " --> pdb=" O   LEU C  88 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   GLY C  93 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   PHE C 100 " --> pdb=" O   VAL C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 139
      removed outlier: 4.230A  pdb=" N   LYS C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   LEU C 121 " --> pdb=" O   PHE C 117 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLY C 124 " --> pdb=" O   ASN C 120 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ILE C 128 " --> pdb=" O   GLY C 124 " (cutoff:3.500A)

    144 hydrogen bonds defined for protein.
    432 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: 0.53

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 705
        1.34 -     1.46: 342
        1.46 -     1.57: 1299
        1.57 -     1.69: 0
        1.69 -     1.80: 12
  Bond restraints: 2358
  Sorted by residual:
  bond pdb=" N   PRO B  72 "
       pdb=" CA  PRO B  72 "
    ideal  model  delta    sigma   weight residual
    1.474  1.465  0.009 7.40e-03 1.83e+04 1.41e+00
  bond pdb=" N   PRO A  72 "
       pdb=" CA  PRO A  72 "
    ideal  model  delta    sigma   weight residual
    1.474  1.465  0.009 7.40e-03 1.83e+04 1.37e+00
  bond pdb=" N   PRO C  72 "
       pdb=" CA  PRO C  72 "
    ideal  model  delta    sigma   weight residual
    1.474  1.466  0.008 7.40e-03 1.83e+04 1.32e+00
  bond pdb=" N   GLY C  95 "
       pdb=" CA  GLY C  95 "
    ideal  model  delta    sigma   weight residual
    1.454  1.442  0.012 1.24e-02 6.50e+03 9.50e-01
  bond pdb=" CA  ASN C 119 "
       pdb=" C   ASN C 119 "
    ideal  model  delta    sigma   weight residual
    1.522  1.509  0.014 1.40e-02 5.10e+03 9.38e-01
  ... (remaining 2353 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 3092
        1.73 -     3.47: 91
        3.47 -     5.20: 21
        5.20 -     6.94: 3
        6.94 -     8.67: 3
  Bond angle restraints: 3210
  Sorted by residual:
  angle pdb=" C   SER B  50 "
        pdb=" N   MET B  51 "
        pdb=" CA  MET B  51 "
      ideal   model   delta    sigma   weight residual
     121.54  127.41   -5.87 1.91e+00 2.74e-01 9.44e+00
  angle pdb=" C   SER A  50 "
        pdb=" N   MET A  51 "
        pdb=" CA  MET A  51 "
      ideal   model   delta    sigma   weight residual
     121.54  127.33   -5.79 1.91e+00 2.74e-01 9.20e+00
  angle pdb=" C   SER C  50 "
        pdb=" N   MET C  51 "
        pdb=" CA  MET C  51 "
      ideal   model   delta    sigma   weight residual
     121.54  127.33   -5.79 1.91e+00 2.74e-01 9.19e+00
  angle pdb=" C   GLU C  69 "
        pdb=" N   GLN C  70 "
        pdb=" CA  GLN C  70 "
      ideal   model   delta    sigma   weight residual
     121.54  126.52   -4.98 1.91e+00 2.74e-01 6.81e+00
  angle pdb=" C   GLU B  69 "
        pdb=" N   GLN B  70 "
        pdb=" CA  GLN B  70 "
      ideal   model   delta    sigma   weight residual
     121.54  126.52   -4.98 1.91e+00 2.74e-01 6.79e+00
  ... (remaining 3205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 1235
       17.95 -    35.89: 124
       35.89 -    53.84: 39
       53.84 -    71.78: 0
       71.78 -    89.73: 3
  Dihedral angle restraints: 1401
    sinusoidal: 510
      harmonic: 891
  Sorted by residual:
  dihedral pdb=" CB  GLU B  49 "
           pdb=" CG  GLU B  49 "
           pdb=" CD  GLU B  49 "
           pdb=" OE1 GLU B  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU C  49 "
           pdb=" CG  GLU C  49 "
           pdb=" CD  GLU C  49 "
           pdb=" OE1 GLU C  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.72  -89.72     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A  49 "
           pdb=" CG  GLU A  49 "
           pdb=" CD  GLU A  49 "
           pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.70  -89.70     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 1398 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 174
       0.022 -    0.043: 103
       0.043 -    0.065: 77
       0.065 -    0.087: 42
       0.087 -    0.109: 15
  Chirality restraints: 411
  Sorted by residual:
  chirality pdb=" CA  ASN C 119 "
            pdb=" N   ASN C 119 "
            pdb=" C   ASN C 119 "
            pdb=" CB  ASN C 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.95e-01
  chirality pdb=" CA  ILE A 129 "
            pdb=" N   ILE A 129 "
            pdb=" C   ILE A 129 "
            pdb=" CB  ILE A 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.87e-01
  chirality pdb=" CA  ASN B 119 "
            pdb=" N   ASN B 119 "
            pdb=" C   ASN B 119 "
            pdb=" CB  ASN B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.40    0.11 2.00e-01 2.50e+01 2.85e-01
  ... (remaining 408 not shown)

  Planarity restraints: 390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  71 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO A  72 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A  72 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A  72 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 108 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO A 109 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 109 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 109 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 108 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO B 109 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 109 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 109 "    0.019 5.00e-02 4.00e+02
  ... (remaining 387 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 37
        2.65 -     3.21: 2589
        3.21 -     3.77: 3798
        3.77 -     4.34: 5186
        4.34 -     4.90: 7439
  Nonbonded interactions: 19049
  Sorted by model distance:
  nonbonded pdb=" O   ALA C  42 "
            pdb=" OG  SER C  46 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" O   ALA A  42 "
            pdb=" OG  SER A  46 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" O   ALA B  42 "
            pdb=" OG  SER B  46 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" O   PHE B 117 "
            pdb=" ND2 ASN B 120 "
     model   vdw
     2.147 3.120
  nonbonded pdb=" O   PHE A 117 "
            pdb=" ND2 ASN A 120 "
     model   vdw
     2.148 3.120
  ... (remaining 19044 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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 group one per residue
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:             1.170
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.480
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.010
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5683
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2358  Z= 0.217
  Angle     :  0.793   8.672   3210  Z= 0.438
  Chirality :  0.042   0.109    411
  Planarity :  0.005   0.034    390
  Dihedral  : 16.554  89.725    819
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 25.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.13 %
    Favored  : 86.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.46), residues: 297
  helix: -1.15 (0.34), residues: 192
  sheet:  None (None), residues: 0
  loop : -2.41 (0.62), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS A  40 
 PHE   0.016   0.002   PHE B  74 
 TYR   0.006   0.001   TYR A  77 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 VAL cc_start: 0.6897 (t) cc_final: 0.6695 (t)
REVERT: A  127 PHE cc_start: 0.7957 (m-10) cc_final: 0.7655 (m-80)
REVERT: B   58 MET cc_start: 0.5886 (tmm) cc_final: 0.5575 (tmm)
REVERT: B   91 GLN cc_start: 0.8229 (mt0) cc_final: 0.7851 (mt0)
REVERT: B   96 VAL cc_start: 0.8465 (m) cc_final: 0.8258 (p)
REVERT: B  119 ASN cc_start: 0.6612 (t0) cc_final: 0.6220 (t0)
REVERT: C   45 LYS cc_start: 0.6834 (tppt) cc_final: 0.6158 (tppt)
REVERT: C  101 LEU cc_start: 0.7762 (mt) cc_final: 0.7418 (mt)
REVERT: C  116 ASP cc_start: 0.8281 (m-30) cc_final: 0.8023 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1338
  time to fit residues: 11.2371
Evaluate side-chains
  66 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 12 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0170
   chunk 9 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0970
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5616

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

Flipped N/Q/H residues before XYZ refinement:
B 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5042 r_free = 0.5042 target = 0.222727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.174249 restraints weight = 5426.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.177728 restraints weight = 4676.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.180907 restraints weight = 4117.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5675
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2358  Z= 0.217
  Angle     :  0.730   9.713   3210  Z= 0.379
  Chirality :  0.042   0.147    411
  Planarity :  0.004   0.034    390
  Dihedral  :  5.920  16.504    309
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 21.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.55 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.47), residues: 297
  helix: -1.19 (0.33), residues: 207
  sheet:  None (None), residues: 0
  loop : -2.30 (0.72), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 112 
 PHE   0.017   0.001   PHE A 127 
 TYR   0.006   0.001   TYR A  77 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLN cc_start: 0.8116 (mt0) cc_final: 0.7878 (mt0)
REVERT: A  127 PHE cc_start: 0.7864 (m-10) cc_final: 0.7581 (m-80)
REVERT: B   86 ILE cc_start: 0.8210 (mt) cc_final: 0.7994 (mm)
REVERT: B   91 GLN cc_start: 0.8034 (mt0) cc_final: 0.7676 (mt0)
REVERT: B  115 LEU cc_start: 0.8416 (mp) cc_final: 0.7902 (mp)
REVERT: B  119 ASN cc_start: 0.6614 (t0) cc_final: 0.6217 (m-40)
REVERT: C  117 PHE cc_start: 0.8496 (t80) cc_final: 0.8257 (t80)
REVERT: C  127 PHE cc_start: 0.8016 (m-10) cc_final: 0.7754 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1241
  time to fit residues: 8.9699
Evaluate side-chains
  54 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** C  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4980 r_free = 0.4980 target = 0.215750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.170333 restraints weight = 5440.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.173062 restraints weight = 4705.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.175756 restraints weight = 4206.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.4510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5791
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   2358  Z= 0.255
  Angle     :  0.846   7.997   3210  Z= 0.434
  Chirality :  0.050   0.400    411
  Planarity :  0.005   0.032    390
  Dihedral  :  6.155  17.374    309
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 24.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  5.88 %
    Favored  : 93.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.45), residues: 297
  helix: -1.55 (0.32), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.50 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B  40 
 PHE   0.010   0.001   PHE A 127 
 TYR   0.008   0.001   TYR A  77 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8150 (mptt) cc_final: 0.7901 (tmmt)
REVERT: B   91 GLN cc_start: 0.8026 (mt0) cc_final: 0.7558 (mt0)
REVERT: B  115 LEU cc_start: 0.8540 (mp) cc_final: 0.7961 (mp)
REVERT: C   91 GLN cc_start: 0.7662 (mt0) cc_final: 0.7089 (mt0)
REVERT: C  117 PHE cc_start: 0.8492 (t80) cc_final: 0.8188 (t80)
REVERT: C  127 PHE cc_start: 0.8009 (m-10) cc_final: 0.7762 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.1152
  time to fit residues: 8.2683
Evaluate side-chains
  52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4976 r_free = 0.4976 target = 0.217015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.173990 restraints weight = 5545.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.176729 restraints weight = 4832.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.179101 restraints weight = 4309.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.4526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5715
moved from start:          0.4954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2358  Z= 0.201
  Angle     :  0.760   7.032   3210  Z= 0.383
  Chirality :  0.044   0.147    411
  Planarity :  0.004   0.029    390
  Dihedral  :  5.983  21.929    309
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 24.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.45), residues: 297
  helix: -1.42 (0.32), residues: 213
  sheet:  None (None), residues: 0
  loop : -3.07 (0.67), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C  40 
 PHE   0.012   0.001   PHE A 127 
 TYR   0.004   0.001   TYR C  41 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8065 (mptt) cc_final: 0.7819 (tmmt)
REVERT: B   91 GLN cc_start: 0.8051 (mt0) cc_final: 0.7662 (mt0)
REVERT: B  115 LEU cc_start: 0.8257 (mp) cc_final: 0.8036 (mp)
REVERT: C   91 GLN cc_start: 0.7769 (mt0) cc_final: 0.7196 (mt0)
REVERT: C  117 PHE cc_start: 0.8339 (t80) cc_final: 0.7963 (t80)
REVERT: C  127 PHE cc_start: 0.7956 (m-10) cc_final: 0.7646 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.1389
  time to fit residues: 9.4978
Evaluate side-chains
  50 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 1 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0010
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6988

-------------------------------------------------------------------------------
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 = 0.4975 r_free = 0.4975 target = 0.216736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.174904 restraints weight = 5639.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.177813 restraints weight = 4823.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.180429 restraints weight = 4239.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5652
moved from start:          0.5587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2358  Z= 0.203
  Angle     :  0.763   7.662   3210  Z= 0.382
  Chirality :  0.047   0.211    411
  Planarity :  0.004   0.033    390
  Dihedral  :  5.888  22.388    309
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 20.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.45), residues: 297
  helix: -1.44 (0.31), residues: 219
  sheet:  None (None), residues: 0
  loop : -2.74 (0.72), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  40 
 PHE   0.007   0.001   PHE B 127 
 TYR   0.011   0.001   TYR A  77 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 MET cc_start: 0.1716 (mtt) cc_final: 0.1443 (mtt)
REVERT: B   91 GLN cc_start: 0.8005 (mt0) cc_final: 0.7567 (mt0)
REVERT: C   91 GLN cc_start: 0.7708 (mt0) cc_final: 0.7113 (mt0)
REVERT: C  117 PHE cc_start: 0.8275 (t80) cc_final: 0.7905 (t80)
REVERT: C  127 PHE cc_start: 0.7863 (m-10) cc_final: 0.7514 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1188
  time to fit residues: 7.9400
Evaluate side-chains
  49 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0040
   chunk 29 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6192

-------------------------------------------------------------------------------
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 = 0.4972 r_free = 0.4972 target = 0.218482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.175426 restraints weight = 5541.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.178171 restraints weight = 4749.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.180403 restraints weight = 4195.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.4528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5614
moved from start:          0.6057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2358  Z= 0.203
  Angle     :  0.730   6.035   3210  Z= 0.370
  Chirality :  0.046   0.281    411
  Planarity :  0.004   0.028    390
  Dihedral  :  5.646  22.583    309
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 21.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.45), residues: 297
  helix: -1.22 (0.33), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.90 (0.67), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  40 
 PHE   0.009   0.001   PHE B 127 
 TYR   0.006   0.001   TYR C  77 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 MET cc_start: 0.1552 (mtt) cc_final: 0.1269 (mtt)
REVERT: B   58 MET cc_start: 0.5816 (tmm) cc_final: 0.5587 (tmm)
REVERT: B   91 GLN cc_start: 0.8003 (mt0) cc_final: 0.7586 (mt0)
REVERT: B  126 VAL cc_start: 0.7392 (t) cc_final: 0.7108 (m)
REVERT: C   91 GLN cc_start: 0.7784 (mt0) cc_final: 0.7171 (mt0)
REVERT: C  117 PHE cc_start: 0.8337 (t80) cc_final: 0.7921 (t80)
REVERT: C  127 PHE cc_start: 0.7806 (m-10) cc_final: 0.7522 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1142
  time to fit residues: 7.6576
Evaluate side-chains
  52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5356 r_free = 0.5356 target = 0.284068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5289 r_free = 0.5289 target = 0.269233 restraints weight = 9714.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5302 r_free = 0.5302 target = 0.270620 restraints weight = 7385.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.5308 r_free = 0.5308 target = 0.271762 restraints weight = 5964.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.4788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5284
moved from start:          0.6594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2358  Z= 0.215
  Angle     :  0.752   9.988   3210  Z= 0.377
  Chirality :  0.046   0.196    411
  Planarity :  0.004   0.029    390
  Dihedral  :  5.791  32.001    309
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 21.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.46), residues: 297
  helix: -1.23 (0.33), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.76 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS B  40 
 PHE   0.010   0.001   PHE A 127 
 TYR   0.006   0.001   TYR A  77 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.2989 (tmm) cc_final: 0.2655 (tmm)
REVERT: B   51 MET cc_start: 0.0964 (mtt) cc_final: 0.0729 (mtt)
REVERT: B   91 GLN cc_start: 0.7944 (mt0) cc_final: 0.7584 (mt0)
REVERT: B  126 VAL cc_start: 0.7279 (t) cc_final: 0.7004 (m)
REVERT: C   91 GLN cc_start: 0.7715 (mt0) cc_final: 0.7145 (mt0)
REVERT: C  117 PHE cc_start: 0.8367 (t80) cc_final: 0.7986 (t80)
REVERT: C  127 PHE cc_start: 0.7674 (m-10) cc_final: 0.7356 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1065
  time to fit residues: 6.6886
Evaluate side-chains
  52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 8 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4966 r_free = 0.4966 target = 0.219227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.174542 restraints weight = 5833.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.177872 restraints weight = 4867.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.180731 restraints weight = 4208.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.4522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5624
moved from start:          0.7036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2358  Z= 0.198
  Angle     :  0.737   8.674   3210  Z= 0.365
  Chirality :  0.044   0.139    411
  Planarity :  0.004   0.028    390
  Dihedral  :  5.693  24.224    309
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 21.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.46), residues: 297
  helix: -1.15 (0.33), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.92 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS B  40 
 PHE   0.011   0.001   PHE B  76 
 TYR   0.010   0.001   TYR B  77 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.3042 (tmm) cc_final: 0.2720 (tmm)
REVERT: B   58 MET cc_start: 0.5885 (tmm) cc_final: 0.5673 (tmm)
REVERT: B   91 GLN cc_start: 0.7922 (mt0) cc_final: 0.7556 (mt0)
REVERT: B   98 LEU cc_start: 0.7056 (pp) cc_final: 0.4665 (tt)
REVERT: B  126 VAL cc_start: 0.7469 (t) cc_final: 0.7179 (m)
REVERT: C   91 GLN cc_start: 0.7797 (mt0) cc_final: 0.7253 (mt0)
REVERT: C  117 PHE cc_start: 0.8283 (t80) cc_final: 0.7886 (t80)
REVERT: C  127 PHE cc_start: 0.7594 (m-10) cc_final: 0.7296 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1271
  time to fit residues: 8.2987
Evaluate side-chains
  50 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    0.3980
   chunk 26 optimal weight:    0.4980
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0070
   chunk 6 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.4798

-------------------------------------------------------------------------------
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 = 0.5357 r_free = 0.5357 target = 0.285824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.5298 r_free = 0.5298 target = 0.270976 restraints weight = 9721.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5312 r_free = 0.5312 target = 0.272547 restraints weight = 7327.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5326 r_free = 0.5326 target = 0.273698 restraints weight = 5822.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.4850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5170
moved from start:          0.7414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2358  Z= 0.210
  Angle     :  0.769   8.891   3210  Z= 0.375
  Chirality :  0.044   0.159    411
  Planarity :  0.004   0.032    390
  Dihedral  :  5.725  26.207    309
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 20.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.47), residues: 297
  helix: -0.98 (0.33), residues: 210
  sheet:  None (None), residues: 0
  loop : -3.24 (0.70), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  40 
 PHE   0.009   0.001   PHE B 127 
 TYR   0.009   0.001   TYR C  77 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.3063 (tmm) cc_final: 0.2728 (tmm)
REVERT: B   91 GLN cc_start: 0.7887 (mt0) cc_final: 0.7587 (mt0)
REVERT: C   91 GLN cc_start: 0.7677 (mt0) cc_final: 0.7129 (mt0)
REVERT: C  117 PHE cc_start: 0.8262 (t80) cc_final: 0.7905 (t80)
REVERT: C  127 PHE cc_start: 0.7438 (m-10) cc_final: 0.7112 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1166
  time to fit residues: 7.0609
Evaluate side-chains
  47 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.1988

-------------------------------------------------------------------------------
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 = 0.5305 r_free = 0.5305 target = 0.280296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5231 r_free = 0.5231 target = 0.264037 restraints weight = 9589.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5242 r_free = 0.5242 target = 0.265336 restraints weight = 7508.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.5257 r_free = 0.5257 target = 0.266587 restraints weight = 6253.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.4741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5371
moved from start:          0.7928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2358  Z= 0.255
  Angle     :  0.813   7.542   3210  Z= 0.408
  Chirality :  0.047   0.190    411
  Planarity :  0.005   0.034    390
  Dihedral  :  6.011  23.997    309
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 22.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.12 %
    Favored  : 87.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.46), residues: 297
  helix: -1.21 (0.32), residues: 216
  sheet:  None (None), residues: 0
  loop : -3.53 (0.72), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B  40 
 PHE   0.016   0.001   PHE B 127 
 TYR   0.005   0.001   TYR C  77 

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

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

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  594 Ramachandran restraints generated.
    297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   91 GLN cc_start: 0.7726 (mt0) cc_final: 0.7469 (mt0)
REVERT: B  126 VAL cc_start: 0.7623 (p) cc_final: 0.7247 (m)
REVERT: C   91 GLN cc_start: 0.7710 (mt0) cc_final: 0.7196 (mt0)
REVERT: C  117 PHE cc_start: 0.8342 (t80) cc_final: 0.7956 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 49
  average time/residue: 0.1251
  time to fit residues: 7.5019
Evaluate side-chains
  48 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 0 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0270
   chunk 9 optimal weight:    6.9990
   chunk 2 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.9840

-------------------------------------------------------------------------------
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 = 0.5312 r_free = 0.5312 target = 0.281605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5282 r_free = 0.5282 target = 0.266225 restraints weight = 9834.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5261 r_free = 0.5261 target = 0.267867 restraints weight = 7954.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.5271 r_free = 0.5271 target = 0.268918 restraints weight = 5926.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.4794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5305
moved from start:          0.8189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2358  Z= 0.226
  Angle     :  0.772   8.031   3210  Z= 0.385
  Chirality :  0.045   0.149    411
  Planarity :  0.004   0.029    390
  Dihedral  :  5.955  24.147    309
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 23.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.46), residues: 297
  helix: -1.13 (0.32), residues: 216
  sheet:  None (None), residues: 0
  loop : -3.67 (0.70), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B  40 
 PHE   0.012   0.001   PHE A 127 
 TYR   0.008   0.001   TYR C  77 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1149.73 seconds
wall clock time: 20 minutes 39.84 seconds (1239.84 seconds total)