Starting phenix.real_space_refine
on Fri Oct 10 10:17:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uip_42301/10_2025/8uip_42301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uip_42301/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uip_42301/10_2025/8uip_42301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uip_42301/10_2025/8uip_42301.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uip_42301/10_2025/8uip_42301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uip_42301/10_2025/8uip_42301.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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:
    B, C
  Time building chain proxies: 0.62, per 1000 atoms: 0.27
  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: 0.20
  Conformation dependent library (CDL) restraints added in 111.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.10
  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: 0.41

  Time building geometry restraints manager: 0.27 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             2.080
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     4.470
  Find NCS groups from input model:        0.030
  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:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.260
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 TYR   0.006   0.001   TYR A  77 
 PHE   0.016   0.002   PHE B  74 
 HIS   0.004   0.002   HIS A  40 

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

*********************** 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  : 0.085 
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: 0.0569
  time to fit residues: 4.8334
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  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    0.0970
   chunk 12 optimal weight:    9.9990
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    6.9990
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0970
   chunk 15 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.3976

-------------------------------------------------------------------------------
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 = 0.5433 r_free = 0.5433 target = 0.293427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5367 r_free = 0.5367 target = 0.278844 restraints weight = 9594.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5375 r_free = 0.5375 target = 0.280275 restraints weight = 7276.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5390 r_free = 0.5390 target = 0.281407 restraints weight = 5866.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.5397 r_free = 0.5397 target = 0.282159 restraints weight = 4924.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.5407 r_free = 0.5407 target = 0.282832 restraints weight = 4295.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.4939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5146
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2358  Z= 0.152
  Angle     :  0.721   9.845   3210  Z= 0.373
  Chirality :  0.042   0.150    411
  Planarity :  0.004   0.032    390
  Dihedral  :  5.902  16.465    309
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 19.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 12.94 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.46), residues: 297
  helix: -1.16 (0.33), residues: 207
  sheet:  None (None), residues: 0
  loop : -2.43 (0.68), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.001   TYR A  77 
 PHE   0.018   0.001   PHE A 127 
 HIS   0.005   0.001   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 2358)
  covalent geometry    : angle       0.72064 ( 3210)
  hydrogen bonds       : bond        0.05909 (  144)
  hydrogen bonds       : angle       5.88297 (  432)

*********************** 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
  59 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 GLN cc_start: 0.8368 (mt0) cc_final: 0.8079 (mt0)
REVERT: A  127 PHE cc_start: 0.7688 (m-10) cc_final: 0.7406 (m-10)
REVERT: B   91 GLN cc_start: 0.7970 (mt0) cc_final: 0.7600 (mt0)
REVERT: C  127 PHE cc_start: 0.7924 (m-10) cc_final: 0.7629 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0506
  time to fit residues: 3.6029
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  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0980
   chunk 6 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 13 optimal weight:    0.5980
   chunk 2 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.5036 r_free = 0.5036 target = 0.221863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.181684 restraints weight = 5885.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.183972 restraints weight = 5197.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.185413 restraints weight = 4678.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.187245 restraints weight = 4321.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.188351 restraints weight = 4006.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.4630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5559
moved from start:          0.3931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2358  Z= 0.159
  Angle     :  0.751   6.990   3210  Z= 0.377
  Chirality :  0.044   0.158    411
  Planarity :  0.004   0.028    390
  Dihedral  :  5.830  17.630    309
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 21.53
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.60 (0.45), residues: 297
  helix: -1.23 (0.32), residues: 207
  sheet:  None (None), residues: 0
  loop : -2.64 (0.70), residues: 90

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 2358)
  covalent geometry    : angle       0.75137 ( 3210)
  hydrogen bonds       : bond        0.05537 (  144)
  hydrogen bonds       : angle       5.74033 (  432)

*********************** 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
  58 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: A   91 GLN cc_start: 0.8180 (mt0) cc_final: 0.7899 (mt0)
REVERT: A  127 PHE cc_start: 0.7798 (m-10) cc_final: 0.7526 (m-10)
REVERT: B   91 GLN cc_start: 0.8128 (mt0) cc_final: 0.7748 (mt0)
REVERT: B  115 LEU cc_start: 0.8435 (mp) cc_final: 0.8005 (mp)
REVERT: B  119 ASN cc_start: 0.6769 (t0) cc_final: 0.6372 (m-40)
REVERT: C  117 PHE cc_start: 0.8440 (t80) cc_final: 0.8140 (t80)
REVERT: C  127 PHE cc_start: 0.7900 (m-10) cc_final: 0.7659 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0534
  time to fit residues: 3.7434
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  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 22 optimal weight:    6.9990
   chunk 3 optimal weight:    0.6980
   chunk 1 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0070
   chunk 2 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6998

-------------------------------------------------------------------------------
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 = 0.5011 r_free = 0.5011 target = 0.219206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.173315 restraints weight = 5560.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4559 r_free = 0.4559 target = 0.175621 restraints weight = 4938.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.177598 restraints weight = 4491.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.178851 restraints weight = 4150.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.180625 restraints weight = 3903.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.4556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5645
moved from start:          0.4763

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= 0.155
  Angle     :  0.724   6.534   3210  Z= 0.368
  Chirality :  0.043   0.175    411
  Planarity :  0.004   0.030    390
  Dihedral  :  5.858  17.942    309
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 20.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.44 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.63 (0.47), residues: 297
  helix: -1.25 (0.33), residues: 216
  sheet:  None (None), residues: 0
  loop : -2.74 (0.73), residues: 81

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 2358)
  covalent geometry    : angle       0.72415 ( 3210)
  hydrogen bonds       : bond        0.05398 (  144)
  hydrogen bonds       : angle       5.61185 (  432)

*********************** 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
  53 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: B   86 ILE cc_start: 0.8120 (mt) cc_final: 0.7866 (mm)
REVERT: B   91 GLN cc_start: 0.7880 (mt0) cc_final: 0.7361 (mt0)
REVERT: B  115 LEU cc_start: 0.8458 (mp) cc_final: 0.8090 (mt)
REVERT: B  119 ASN cc_start: 0.6853 (t0) cc_final: 0.6435 (m-40)
REVERT: C  117 PHE cc_start: 0.8315 (t80) cc_final: 0.7978 (t80)
REVERT: C  127 PHE cc_start: 0.8002 (m-10) cc_final: 0.7718 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 53
  average time/residue: 0.0490
  time to fit residues: 3.2412
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  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0970
   chunk 22 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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 = 0.5032 r_free = 0.5032 target = 0.220604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.176108 restraints weight = 5561.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.179240 restraints weight = 4822.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.181615 restraints weight = 4269.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.183486 restraints weight = 3879.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.184977 restraints weight = 3563.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.4599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5560
moved from start:          0.5308

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= 0.154
  Angle     :  0.750   7.420   3210  Z= 0.376
  Chirality :  0.046   0.201    411
  Planarity :  0.004   0.031    390
  Dihedral  :  5.806  24.799    309
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.46), residues: 297
  helix: -1.26 (0.32), residues: 219
  sheet:  None (None), residues: 0
  loop : -2.86 (0.72), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.001   TYR B  77 
 PHE   0.008   0.001   PHE A 127 
 HIS   0.005   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 2358)
  covalent geometry    : angle       0.74970 ( 3210)
  hydrogen bonds       : bond        0.05348 (  144)
  hydrogen bonds       : angle       5.64472 (  432)

*********************** 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
  51 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: B   51 MET cc_start: 0.1673 (mtt) cc_final: 0.1365 (mtt)
REVERT: B   86 ILE cc_start: 0.8038 (mt) cc_final: 0.7814 (mm)
REVERT: B   91 GLN cc_start: 0.7937 (mt0) cc_final: 0.7448 (mt0)
REVERT: B  115 LEU cc_start: 0.8459 (mp) cc_final: 0.8049 (mt)
REVERT: B  119 ASN cc_start: 0.6958 (t0) cc_final: 0.6584 (m-40)
REVERT: C  117 PHE cc_start: 0.8324 (t80) cc_final: 0.7964 (t80)
REVERT: C  127 PHE cc_start: 0.7849 (m-10) cc_final: 0.7526 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.0432
  time to fit residues: 2.7904
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  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 7 optimal weight:    0.0870
   chunk 27 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0970
   chunk 14 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.4556

-------------------------------------------------------------------------------
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 = 0.5410 r_free = 0.5410 target = 0.290309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5345 r_free = 0.5345 target = 0.275416 restraints weight = 9591.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5352 r_free = 0.5352 target = 0.276900 restraints weight = 7384.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5368 r_free = 0.5368 target = 0.278047 restraints weight = 6030.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.5374 r_free = 0.5374 target = 0.278840 restraints weight = 5057.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.5388 r_free = 0.5388 target = 0.279524 restraints weight = 4407.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.4887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5161
moved from start:          0.5831

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= 0.141
  Angle     :  0.723   8.104   3210  Z= 0.358
  Chirality :  0.046   0.249    411
  Planarity :  0.004   0.028    390
  Dihedral  :  5.585  24.665    309
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 19.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (0.46), residues: 297
  helix: -1.00 (0.33), residues: 213
  sheet:  None (None), residues: 0
  loop : -3.09 (0.65), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR B  77 
 PHE   0.011   0.001   PHE A 127 
 HIS   0.003   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 2358)
  covalent geometry    : angle       0.72343 ( 3210)
  hydrogen bonds       : bond        0.05107 (  144)
  hydrogen bonds       : angle       5.41346 (  432)

*********************** 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  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: B   51 MET cc_start: 0.0941 (mtt) cc_final: 0.0599 (mtt)
REVERT: B   86 ILE cc_start: 0.7966 (mt) cc_final: 0.7720 (mm)
REVERT: B   91 GLN cc_start: 0.7962 (mt0) cc_final: 0.7472 (mt0)
REVERT: B   98 LEU cc_start: 0.6598 (pp) cc_final: 0.4719 (tt)
REVERT: B  115 LEU cc_start: 0.8402 (mp) cc_final: 0.7989 (mt)
REVERT: C  117 PHE cc_start: 0.8306 (t80) cc_final: 0.7964 (t80)
REVERT: C  127 PHE cc_start: 0.7705 (m-10) cc_final: 0.7352 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0476
  time to fit residues: 2.9519
Evaluate side-chains
  46 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 22 optimal weight:    4.9990
   chunk 7 optimal weight:    0.0060
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 = 0.5406 r_free = 0.5406 target = 0.288893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5337 r_free = 0.5337 target = 0.273752 restraints weight = 9943.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5342 r_free = 0.5342 target = 0.275135 restraints weight = 7717.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.5353 r_free = 0.5353 target = 0.276265 restraints weight = 6221.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.5368 r_free = 0.5368 target = 0.277174 restraints weight = 5276.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5373 r_free = 0.5373 target = 0.277771 restraints weight = 4520.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.4875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5198
moved from start:          0.6237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2358  Z= 0.144
  Angle     :  0.733  10.423   3210  Z= 0.367
  Chirality :  0.044   0.181    411
  Planarity :  0.004   0.032    390
  Dihedral  :  5.536  26.920    309
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 18.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.50 (0.45), residues: 297
  helix: -1.11 (0.32), residues: 219
  sheet:  None (None), residues: 0
  loop : -2.89 (0.66), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR A  77 
 PHE   0.009   0.001   PHE A 127 
 HIS   0.007   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 2358)
  covalent geometry    : angle       0.73271 ( 3210)
  hydrogen bonds       : bond        0.05091 (  144)
  hydrogen bonds       : angle       5.54642 (  432)

*********************** 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
  48 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: B   51 MET cc_start: 0.0815 (mtt) cc_final: 0.0539 (mtt)
REVERT: B   86 ILE cc_start: 0.7997 (mt) cc_final: 0.7762 (mm)
REVERT: B   91 GLN cc_start: 0.7951 (mt0) cc_final: 0.7492 (mt0)
REVERT: B   98 LEU cc_start: 0.6637 (pp) cc_final: 0.4673 (tt)
REVERT: B  111 LYS cc_start: 0.8077 (ptpt) cc_final: 0.7750 (pttt)
REVERT: C  117 PHE cc_start: 0.8307 (t80) cc_final: 0.7978 (t80)
REVERT: C  127 PHE cc_start: 0.7689 (m-10) cc_final: 0.7410 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0448
  time to fit residues: 2.7383
Evaluate side-chains
  46 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 19 optimal weight:    0.0870
   chunk 18 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 24 optimal weight:    0.0870
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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 = 0.5409 r_free = 0.5409 target = 0.290286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5340 r_free = 0.5340 target = 0.275371 restraints weight = 9723.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5351 r_free = 0.5351 target = 0.276829 restraints weight = 7344.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.5364 r_free = 0.5364 target = 0.277955 restraints weight = 5989.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.5368 r_free = 0.5368 target = 0.278366 restraints weight = 5024.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.5383 r_free = 0.5383 target = 0.279368 restraints weight = 4533.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.4905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5130
moved from start:          0.6662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2358  Z= 0.135
  Angle     :  0.700   8.227   3210  Z= 0.349
  Chirality :  0.043   0.167    411
  Planarity :  0.004   0.029    390
  Dihedral  :  5.430  26.017    309
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.35 (0.45), residues: 297
  helix: -0.86 (0.34), residues: 213
  sheet:  None (None), residues: 0
  loop : -3.16 (0.61), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.001   TYR B  77 
 PHE   0.012   0.001   PHE A 127 
 HIS   0.003   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 2358)
  covalent geometry    : angle       0.70016 ( 3210)
  hydrogen bonds       : bond        0.04967 (  144)
  hydrogen bonds       : angle       5.35369 (  432)

*********************** 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
  46 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: B   51 MET cc_start: 0.0648 (mtt) cc_final: 0.0381 (mtt)
REVERT: B   86 ILE cc_start: 0.7950 (mt) cc_final: 0.7704 (mm)
REVERT: B   91 GLN cc_start: 0.8004 (mt0) cc_final: 0.7563 (mt0)
REVERT: B   98 LEU cc_start: 0.6464 (pp) cc_final: 0.4471 (tt)
REVERT: B  111 LYS cc_start: 0.8112 (ptpt) cc_final: 0.7829 (pttt)
REVERT: C  117 PHE cc_start: 0.8234 (t80) cc_final: 0.7875 (t80)
REVERT: C  127 PHE cc_start: 0.7614 (m-10) cc_final: 0.7338 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0449
  time to fit residues: 2.6289
Evaluate side-chains
  46 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0870
   chunk 28 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
C  60 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5377 r_free = 0.5377 target = 0.287369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.5305 r_free = 0.5305 target = 0.271998 restraints weight = 9922.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5314 r_free = 0.5314 target = 0.273348 restraints weight = 7540.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.5323 r_free = 0.5323 target = 0.274352 restraints weight = 6168.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.5331 r_free = 0.5331 target = 0.275218 restraints weight = 5266.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.5340 r_free = 0.5340 target = 0.275820 restraints weight = 4626.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.4849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5227
moved from start:          0.7132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2358  Z= 0.153
  Angle     :  0.737  11.141   3210  Z= 0.367
  Chirality :  0.043   0.169    411
  Planarity :  0.004   0.032    390
  Dihedral  :  5.502  25.707    309
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.30 (0.45), residues: 297
  helix: -0.78 (0.33), residues: 213
  sheet:  None (None), residues: 0
  loop : -3.29 (0.63), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR B  77 
 PHE   0.011   0.001   PHE B 127 
 HIS   0.003   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2358)
  covalent geometry    : angle       0.73681 ( 3210)
  hydrogen bonds       : bond        0.05156 (  144)
  hydrogen bonds       : angle       5.45822 (  432)

*********************** 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
  45 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 MET cc_start: 0.2948 (tmm) cc_final: 0.2644 (tmm)
REVERT: B   86 ILE cc_start: 0.8082 (mt) cc_final: 0.7847 (mm)
REVERT: B   91 GLN cc_start: 0.7959 (mt0) cc_final: 0.7485 (mt0)
REVERT: B   98 LEU cc_start: 0.6664 (pp) cc_final: 0.4604 (tt)
REVERT: B  111 LYS cc_start: 0.7993 (ptpt) cc_final: 0.7685 (pttt)
REVERT: C   91 GLN cc_start: 0.7734 (mt0) cc_final: 0.7164 (mt0)
REVERT: C   97 LEU cc_start: 0.8417 (mt) cc_final: 0.8147 (mt)
REVERT: C  117 PHE cc_start: 0.8242 (t80) cc_final: 0.7880 (t80)
REVERT: C  127 PHE cc_start: 0.7491 (m-10) cc_final: 0.7205 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.0423
  time to fit residues: 2.4184
Evaluate side-chains
  44 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 10 optimal weight:    0.1980
   chunk 3 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.5329 r_free = 0.5329 target = 0.282650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.5248 r_free = 0.5248 target = 0.266069 restraints weight = 9880.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.267516 restraints weight = 7665.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.5269 r_free = 0.5269 target = 0.268598 restraints weight = 6282.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.5275 r_free = 0.5275 target = 0.269223 restraints weight = 5308.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.5280 r_free = 0.5280 target = 0.269908 restraints weight = 4761.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.4759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5363
moved from start:          0.7712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2358  Z= 0.197
  Angle     :  0.787   8.446   3210  Z= 0.408
  Chirality :  0.045   0.188    411
  Planarity :  0.005   0.035    390
  Dihedral  :  6.070  26.820    309
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 20.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.12 %
    Favored  : 87.88 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.79 (0.43), residues: 297
  helix: -1.11 (0.31), residues: 216
  sheet:  None (None), residues: 0
  loop : -3.65 (0.61), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR C  41 
 PHE   0.015   0.001   PHE A 127 
 HIS   0.004   0.002   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 2358)
  covalent geometry    : angle       0.78712 ( 3210)
  hydrogen bonds       : bond        0.05836 (  144)
  hydrogen bonds       : angle       5.93565 (  432)

********************** 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
  52 residues out of total 255 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 LYS cc_start: 0.7053 (ptpp) cc_final: 0.6690 (ptmt)
REVERT: B   86 ILE cc_start: 0.8049 (mt) cc_final: 0.7845 (mm)
REVERT: B   91 GLN cc_start: 0.7912 (mt0) cc_final: 0.7467 (mt0)
REVERT: B   98 LEU cc_start: 0.7045 (pp) cc_final: 0.4680 (tt)
REVERT: B  111 LYS cc_start: 0.7907 (ptpt) cc_final: 0.7617 (pttt)
REVERT: B  126 VAL cc_start: 0.7089 (t) cc_final: 0.6803 (m)
REVERT: C   91 GLN cc_start: 0.7797 (mt0) cc_final: 0.7257 (mt0)
REVERT: C   97 LEU cc_start: 0.8413 (mt) cc_final: 0.8162 (mt)
REVERT: C  117 PHE cc_start: 0.8346 (t80) cc_final: 0.7951 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0363
  time to fit residues: 2.4008
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  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    0.4980
   chunk 27 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.5324 r_free = 0.5324 target = 0.282765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.267275 restraints weight = 9924.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.5268 r_free = 0.5268 target = 0.268568 restraints weight = 7498.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.5279 r_free = 0.5279 target = 0.269552 restraints weight = 6140.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.5287 r_free = 0.5287 target = 0.270364 restraints weight = 5251.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.5291 r_free = 0.5291 target = 0.270903 restraints weight = 4604.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.4775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5318
moved from start:          0.8082

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= 0.171
  Angle     :  0.768   9.842   3210  Z= 0.387
  Chirality :  0.045   0.179    411
  Planarity :  0.005   0.064    390
  Dihedral  :  5.950  26.163    309
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 19.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.73 (0.44), residues: 297
  helix: -1.05 (0.32), residues: 216
  sheet:  None (None), residues: 0
  loop : -3.70 (0.61), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR B  77 
 PHE   0.009   0.001   PHE A 127 
 HIS   0.007   0.002   HIS C  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2358)
  covalent geometry    : angle       0.76817 ( 3210)
  hydrogen bonds       : bond        0.05401 (  144)
  hydrogen bonds       : angle       5.75738 (  432)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 670.56 seconds
wall clock time: 12 minutes 14.05 seconds (734.05 seconds total)