Starting phenix.real_space_refine
on Fri May  9 14:04:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uip_42301/05_2025/8uip_42301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uip_42301/05_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_42301/05_2025/8uip_42301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uip_42301/05_2025/8uip_42301.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uip_42301/05_2025/8uip_42301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uip_42301/05_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-5687/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: 1.98, per 1000 atoms: 0.85
  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: 0.96
  Conformation dependent library (CDL) restraints added in 485.0 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: 0.61

  Time building geometry restraints manager: 1.04 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:                  0.010
  Normalize map: mean=0, sd=1:             1.160
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.780
  Find NCS groups from input model:        0.040
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.070
-------------------------------------------------------------------------------
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= 0.215
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17580 (  144)
  hydrogen bonds       : angle       6.60196 (  432)
  covalent geometry    : bond        0.00351 ( 2358)
  covalent geometry    : angle       0.79321 ( 3210)

*********************** 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  : 0.224 
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: 0.1264
  time to fit residues: 10.6258
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  : 0.273 
-------------------------------------------------------------------------------
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 = 51)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.174265 restraints weight = 5426.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.177731 restraints weight = 4674.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.180627 restraints weight = 4115.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.4539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5687
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= 0.161
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06154 (  144)
  hydrogen bonds       : angle       5.98346 (  432)
  covalent geometry    : bond        0.00323 ( 2358)
  covalent geometry    : angle       0.73015 ( 3210)

*********************** 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  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLN cc_start: 0.8134 (mt0) cc_final: 0.7890 (mt0)
REVERT: A  127 PHE cc_start: 0.7869 (m-10) cc_final: 0.7584 (m-80)
REVERT: B   86 ILE cc_start: 0.8205 (mt) cc_final: 0.7990 (mm)
REVERT: B   91 GLN cc_start: 0.8037 (mt0) cc_final: 0.7681 (mt0)
REVERT: B  115 LEU cc_start: 0.8415 (mp) cc_final: 0.7895 (mp)
REVERT: B  119 ASN cc_start: 0.6607 (t0) cc_final: 0.6218 (m-40)
REVERT: C  117 PHE cc_start: 0.8483 (t80) cc_final: 0.8248 (t80)
REVERT: C  127 PHE cc_start: 0.8016 (m-10) cc_final: 0.7751 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.1307
  time to fit residues: 9.4422
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  : 0.240 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 10 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   overall best weight:    1.1986

-------------------------------------------------------------------------------
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 = 0.4982 r_free = 0.4982 target = 0.216059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.170352 restraints weight = 5485.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.173042 restraints weight = 4779.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.175362 restraints weight = 4267.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.4504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5802
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   2358  Z= 0.208
  Angle     :  0.851   8.194   3210  Z= 0.434
  Chirality :  0.050   0.380    411
  Planarity :  0.005   0.031    390
  Dihedral  :  6.175  17.402    309
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 23.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  6.27 %
    Favored  : 93.33 %
  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: -3.10 (0.44), residues: 297
  helix: -1.64 (0.31), residues: 219
  sheet:  None (None), residues: 0
  loop : -2.79 (0.72), residues: 78

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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06557 (  144)
  hydrogen bonds       : angle       6.21151 (  432)
  covalent geometry    : bond        0.00397 ( 2358)
  covalent geometry    : angle       0.85129 ( 3210)

*********************** 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
  61 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8161 (mptt) cc_final: 0.7930 (tmmt)
REVERT: B   91 GLN cc_start: 0.8063 (mt0) cc_final: 0.7586 (mt0)
REVERT: B  115 LEU cc_start: 0.8572 (mp) cc_final: 0.8006 (mp)
REVERT: C   91 GLN cc_start: 0.7658 (mt0) cc_final: 0.7088 (mt0)
REVERT: C  117 PHE cc_start: 0.8488 (t80) cc_final: 0.8172 (t80)
REVERT: C  127 PHE cc_start: 0.8000 (m-10) cc_final: 0.7752 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 61
  average time/residue: 0.1156
  time to fit residues: 8.5241
Evaluate side-chains
  53 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0870
   chunk 0 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0770
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.5004 r_free = 0.5004 target = 0.219718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.174841 restraints weight = 5433.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.177852 restraints weight = 4741.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.180335 restraints weight = 4222.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5675
moved from start:          0.4929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2358  Z= 0.152
  Angle     :  0.749   7.321   3210  Z= 0.376
  Chirality :  0.043   0.164    411
  Planarity :  0.004   0.028    390
  Dihedral  :  5.946  21.025    309
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 22.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  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: -2.95 (0.45), residues: 297
  helix: -1.43 (0.32), residues: 216
  sheet:  None (None), residues: 0
  loop : -3.05 (0.70), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C  40 
 PHE   0.012   0.001   PHE A 127 
 TYR   0.004   0.001   TYR A  41 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05372 (  144)
  hydrogen bonds       : angle       5.78641 (  432)
  covalent geometry    : bond        0.00307 ( 2358)
  covalent geometry    : angle       0.74914 ( 3210)

*********************** 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
  58 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: B   91 GLN cc_start: 0.8138 (mt0) cc_final: 0.7702 (mt0)
REVERT: C   91 GLN cc_start: 0.7737 (mt0) cc_final: 0.7162 (mt0)
REVERT: C  117 PHE cc_start: 0.8332 (t80) cc_final: 0.7973 (t80)
REVERT: C  127 PHE cc_start: 0.7993 (m-10) cc_final: 0.7721 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.1253
  time to fit residues: 8.7166
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  : 0.243 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 19 optimal weight:    0.4980
   chunk 1 optimal weight:    0.2980
   chunk 21 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.4961 r_free = 0.4961 target = 0.217051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.170868 restraints weight = 5667.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.173839 restraints weight = 4859.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.176063 restraints weight = 4269.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.4507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5662
moved from start:          0.5719

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= 0.170
  Angle     :  0.787   7.796   3210  Z= 0.396
  Chirality :  0.045   0.200    411
  Planarity :  0.004   0.033    390
  Dihedral  :  5.981  24.879    309
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 22.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  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 : 0.00 %

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: -2.61 (0.47), residues: 297
  helix: -1.23 (0.33), residues: 210
  sheet:  None (None), residues: 0
  loop : -2.66 (0.73), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  40 
 PHE   0.007   0.001   PHE A 127 
 TYR   0.012   0.001   TYR A  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05639 (  144)
  hydrogen bonds       : angle       5.87070 (  432)
  covalent geometry    : bond        0.00335 ( 2358)
  covalent geometry    : angle       0.78710 ( 3210)

*********************** 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
  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 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   51 MET cc_start: 0.1702 (mtt) cc_final: 0.1435 (mtt)
REVERT: B   91 GLN cc_start: 0.8043 (mt0) cc_final: 0.7585 (mt0)
REVERT: C   91 GLN cc_start: 0.7754 (mt0) cc_final: 0.7150 (mt0)
REVERT: C  117 PHE cc_start: 0.8406 (t80) cc_final: 0.8006 (t80)
REVERT: C  127 PHE cc_start: 0.7937 (m-10) cc_final: 0.7626 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.1035
  time to fit residues: 7.0625
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  : 0.240 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 29 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0270
   chunk 8 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0030
   chunk 10 optimal weight:    0.0980
   overall best weight:    0.2648

-------------------------------------------------------------------------------
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 = 0.5005 r_free = 0.5005 target = 0.221696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.176929 restraints weight = 5600.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.179658 restraints weight = 4811.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.182653 restraints weight = 4252.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.4553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5543
moved from start:          0.6201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2358  Z= 0.143
  Angle     :  0.730   7.996   3210  Z= 0.363
  Chirality :  0.045   0.226    411
  Planarity :  0.004   0.028    390
  Dihedral  :  5.646  24.377    309
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 19.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.52 (0.46), residues: 297
  helix: -1.09 (0.33), residues: 210
  sheet:  None (None), residues: 0
  loop : -2.87 (0.68), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  40 
 PHE   0.013   0.001   PHE B 127 
 TYR   0.007   0.001   TYR B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05200 (  144)
  hydrogen bonds       : angle       5.50196 (  432)
  covalent geometry    : bond        0.00284 ( 2358)
  covalent geometry    : angle       0.73033 ( 3210)

*********************** 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
  50 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: B   51 MET cc_start: 0.1331 (mtt) cc_final: 0.1061 (mtt)
REVERT: B   58 MET cc_start: 0.5698 (tmm) cc_final: 0.5475 (tmm)
REVERT: B   91 GLN cc_start: 0.8052 (mt0) cc_final: 0.7612 (mt0)
REVERT: C  117 PHE cc_start: 0.8400 (t80) cc_final: 0.8018 (t80)
REVERT: C  127 PHE cc_start: 0.7803 (m-10) cc_final: 0.7528 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1058
  time to fit residues: 6.6428
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  : 0.252 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0980
   chunk 28 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4957 r_free = 0.4957 target = 0.217267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.171814 restraints weight = 5716.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.174872 restraints weight = 4869.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.177466 restraints weight = 4290.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.4513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5664
moved from start:          0.6633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2358  Z= 0.156
  Angle     :  0.743  10.742   3210  Z= 0.370
  Chirality :  0.045   0.210    411
  Planarity :  0.004   0.030    390
  Dihedral  :  5.596  22.724    309
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 20.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  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: -2.46 (0.47), residues: 297
  helix: -1.14 (0.33), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.61 (0.77), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  40 
 PHE   0.007   0.001   PHE A 127 
 TYR   0.006   0.001   TYR A  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05486 (  144)
  hydrogen bonds       : angle       5.64344 (  432)
  covalent geometry    : bond        0.00301 ( 2358)
  covalent geometry    : angle       0.74305 ( 3210)

*********************** 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  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: B   51 MET cc_start: 0.1291 (mtt) cc_final: 0.1067 (mtt)
REVERT: B   91 GLN cc_start: 0.7986 (mt0) cc_final: 0.7553 (mt0)
REVERT: B   98 LEU cc_start: 0.7051 (pp) cc_final: 0.4856 (tt)
REVERT: B  126 VAL cc_start: 0.7574 (p) cc_final: 0.7189 (m)
REVERT: C   91 GLN cc_start: 0.7764 (mt0) cc_final: 0.7183 (mt0)
REVERT: C  117 PHE cc_start: 0.8338 (t80) cc_final: 0.7941 (t80)
REVERT: C  127 PHE cc_start: 0.7761 (m-10) cc_final: 0.7509 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1183
  time to fit residues: 7.5076
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  : 0.238 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0020
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0980
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 = 0.5374 r_free = 0.5374 target = 0.286048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.5310 r_free = 0.5310 target = 0.271474 restraints weight = 10104.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5322 r_free = 0.5322 target = 0.272920 restraints weight = 7656.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.5332 r_free = 0.5332 target = 0.274114 restraints weight = 6045.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.4823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5191
moved from start:          0.7018

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= 0.145
  Angle     :  0.733   8.945   3210  Z= 0.362
  Chirality :  0.043   0.141    411
  Planarity :  0.004   0.028    390
  Dihedral  :  5.609  23.143    309
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 18.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  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: -2.47 (0.47), residues: 297
  helix: -1.04 (0.33), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.94 (0.74), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  40 
 PHE   0.008   0.001   PHE A 127 
 TYR   0.010   0.001   TYR B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05157 (  144)
  hydrogen bonds       : angle       5.49928 (  432)
  covalent geometry    : bond        0.00289 ( 2358)
  covalent geometry    : angle       0.73267 ( 3210)

*********************** 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
  51 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.2978 (tmm) cc_final: 0.2670 (tmm)
REVERT: B   51 MET cc_start: 0.0743 (mtt) cc_final: 0.0520 (mtt)
REVERT: B   91 GLN cc_start: 0.7872 (mt0) cc_final: 0.7493 (mt0)
REVERT: B   98 LEU cc_start: 0.6785 (pp) cc_final: 0.4453 (tt)
REVERT: B  111 LYS cc_start: 0.8099 (ptpt) cc_final: 0.7786 (pttt)
REVERT: B  126 VAL cc_start: 0.7505 (p) cc_final: 0.7141 (m)
REVERT: C   91 GLN cc_start: 0.7714 (mt0) cc_final: 0.7145 (mt0)
REVERT: C  117 PHE cc_start: 0.8285 (t80) cc_final: 0.7909 (t80)
REVERT: C  127 PHE cc_start: 0.7579 (m-10) cc_final: 0.7283 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1166
  time to fit residues: 7.3488
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  : 0.254 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0040
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0020
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.5400

-------------------------------------------------------------------------------
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 = 0.5363 r_free = 0.5363 target = 0.285234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5301 r_free = 0.5301 target = 0.270872 restraints weight = 9713.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5313 r_free = 0.5313 target = 0.272377 restraints weight = 7294.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.5320 r_free = 0.5320 target = 0.273052 restraints weight = 5898.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.4828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5193
moved from start:          0.7418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2358  Z= 0.147
  Angle     :  0.746   9.717   3210  Z= 0.365
  Chirality :  0.044   0.190    411
  Planarity :  0.004   0.030    390
  Dihedral  :  5.569  22.961    309
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 17.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -0.89 (0.33), residues: 210
  sheet:  None (None), residues: 0
  loop : -3.20 (0.70), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  40 
 PHE   0.007   0.001   PHE B 127 
 TYR   0.006   0.001   TYR B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05209 (  144)
  hydrogen bonds       : angle       5.45608 (  432)
  covalent geometry    : bond        0.00302 ( 2358)
  covalent geometry    : angle       0.74629 ( 3210)

*********************** 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
  52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.3006 (tmm) cc_final: 0.2675 (tmm)
REVERT: B   91 GLN cc_start: 0.7785 (mt0) cc_final: 0.7427 (mt0)
REVERT: B   98 LEU cc_start: 0.6903 (pp) cc_final: 0.4961 (tt)
REVERT: B  111 LYS cc_start: 0.7953 (ptpt) cc_final: 0.7638 (pttt)
REVERT: B  126 VAL cc_start: 0.7538 (p) cc_final: 0.7157 (m)
REVERT: C   91 GLN cc_start: 0.7742 (mt0) cc_final: 0.7207 (mt0)
REVERT: C   97 LEU cc_start: 0.8334 (mt) cc_final: 0.8027 (mt)
REVERT: C  117 PHE cc_start: 0.8183 (t80) cc_final: 0.7859 (t80)
REVERT: C  127 PHE cc_start: 0.7497 (m-10) cc_final: 0.7186 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1143
  time to fit residues: 7.3378
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  : 0.260 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0000
   chunk 5 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7386

-------------------------------------------------------------------------------
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 = 0.5348 r_free = 0.5348 target = 0.284356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.5287 r_free = 0.5287 target = 0.269120 restraints weight = 9714.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.5297 r_free = 0.5297 target = 0.270577 restraints weight = 7298.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.5305 r_free = 0.5305 target = 0.271577 restraints weight = 5799.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.4819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5234
moved from start:          0.7860

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= 0.154
  Angle     :  0.744   8.533   3210  Z= 0.366
  Chirality :  0.044   0.144    411
  Planarity :  0.004   0.028    390
  Dihedral  :  5.636  23.609    309
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 18.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  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: -2.38 (0.47), residues: 297
  helix: -0.91 (0.33), residues: 213
  sheet:  None (None), residues: 0
  loop : -3.12 (0.73), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS C  40 
 PHE   0.009   0.001   PHE A 127 
 TYR   0.006   0.001   TYR B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05202 (  144)
  hydrogen bonds       : angle       5.52272 (  432)
  covalent geometry    : bond        0.00309 ( 2358)
  covalent geometry    : angle       0.74393 ( 3210)

********************** 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
  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 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 LYS cc_start: 0.6654 (ptpp) cc_final: 0.6333 (ptmt)
REVERT: B   91 GLN cc_start: 0.7748 (mt0) cc_final: 0.7412 (mt0)
REVERT: B   98 LEU cc_start: 0.6756 (pp) cc_final: 0.4838 (tp)
REVERT: B  111 LYS cc_start: 0.7917 (ptpt) cc_final: 0.7630 (pttt)
REVERT: B  126 VAL cc_start: 0.7520 (p) cc_final: 0.7120 (m)
REVERT: C   91 GLN cc_start: 0.7780 (mt0) cc_final: 0.7280 (mt0)
REVERT: C   97 LEU cc_start: 0.8375 (mt) cc_final: 0.8064 (mt)
REVERT: C  117 PHE cc_start: 0.8222 (t80) cc_final: 0.7883 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1346
  time to fit residues: 7.9296
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  : 0.273 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 2 optimal weight:    8.9990
   chunk 23 optimal weight:    0.4980
   chunk 27 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0970
   chunk 24 optimal weight:    0.0470
   overall best weight:    0.4276

-------------------------------------------------------------------------------
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 = 0.5354 r_free = 0.5354 target = 0.285568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5292 r_free = 0.5292 target = 0.270345 restraints weight = 9932.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.5306 r_free = 0.5306 target = 0.271899 restraints weight = 7345.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.5318 r_free = 0.5318 target = 0.273057 restraints weight = 5825.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.4841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5165
moved from start:          0.8124

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= 0.143
  Angle     :  0.730   9.154   3210  Z= 0.357
  Chirality :  0.043   0.143    411
  Planarity :  0.005   0.067    390
  Dihedral  :  5.663  22.863    309
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 18.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  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: -2.36 (0.48), residues: 297
  helix: -0.87 (0.33), residues: 213
  sheet:  None (None), residues: 0
  loop : -3.18 (0.75), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C  40 
 PHE   0.008   0.001   PHE B 127 
 TYR   0.011   0.001   TYR C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04908 (  144)
  hydrogen bonds       : angle       5.37478 (  432)
  covalent geometry    : bond        0.00292 ( 2358)
  covalent geometry    : angle       0.72983 ( 3210)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1246.03 seconds
wall clock time: 22 minutes 44.40 seconds (1364.40 seconds total)