Starting phenix.real_space_refine
on Fri Aug 22 13:19:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g92_29860/08_2025/8g92_29860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g92_29860/08_2025/8g92_29860.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g92_29860/08_2025/8g92_29860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g92_29860/08_2025/8g92_29860.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g92_29860/08_2025/8g92_29860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g92_29860/08_2025/8g92_29860.map"
  }
  resolution = 3.6
  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=   0.002 sd=   0.050
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      17      5.16       5
     C    2117      2.51       5
     N     529      2.21       5
     O     548      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3211
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3186
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 12, 'TRANS': 402}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'YUX': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.18, per 1000 atoms: 0.37
  Number of scatterers: 3211
  At special positions: 0
  Unit cell: (69.72, 64.74, 81.34, 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      17     16.00
     O     548      8.00
     N     529      7.00
     C    2117      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: 0.32
  Conformation dependent library (CDL) restraints added in 159.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  758

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      93.3% 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 100 through 125
      removed outlier: 3.854A  pdb=" N   ALA A 106 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ALA A 123 " --> pdb=" O   ARG A 119 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 136 through 165
      removed outlier: 3.883A  pdb=" N   ALA A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 153 " --> pdb=" O   CYS A 149 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
      removed outlier: 3.712A  pdb=" N   ASP A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   PHE A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 186
      removed outlier: 4.049A  pdb=" N   ILE A 170 " --> pdb=" O   ASN A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 222
      removed outlier: 3.600A  pdb=" N   TYR A 210 " --> pdb=" O   GLY A 206 " (cutoff:3.500A)
      Proline residue:  A 215  - end of helix
      removed outlier: 3.955A  pdb=" N   PHE A 222 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 257
      Proline residue:  A 239  - end of helix
      removed outlier: 4.239A  pdb=" N   TYR A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 265
      removed outlier: 4.045A  pdb=" N   LEU A 263 " --> pdb=" O   TRP A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 280
      removed outlier: 3.947A  pdb=" N   ILE A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 312
    Processing helix  chain 'A' and resid 313 through 347
      Proline residue:  A 337  - end of helix
    Processing helix  chain 'A' and resid 361 through 389
      removed outlier: 4.673A  pdb=" N   PHE A 375 " --> pdb=" O   CYS A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 419
      removed outlier: 3.533A  pdb=" N   LEU A 398 " --> pdb=" O   ARG A 394 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   PHE A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   VAL A 416 " --> pdb=" O   CYS A 412 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LYS A 419 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 442
      removed outlier: 3.723A  pdb=" N   SER A 438 " --> pdb=" O   THR A 434 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ASN A 439 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   TRP A 440 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE A 442 " --> pdb=" O   SER A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 451
      removed outlier: 3.629A  pdb=" N   ILE A 446 " --> pdb=" O   ILE A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 470
    Processing helix  chain 'A' and resid 474 through 489
      removed outlier: 3.644A  pdb=" N   SER A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 506
    Processing helix  chain 'A' and resid 506 through 539
      removed outlier: 4.255A  pdb=" N   PHE A 510 " --> pdb=" O   MET A 506 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE A 525 " --> pdb=" O   ALA A 521 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   VAL A 527 " --> pdb=" O   ALA A 523 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   SER A 528 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN A 539 " --> pdb=" O   GLN A 535 " (cutoff:3.500A)

    274 hydrogen bonds defined for protein.
    822 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.53

  Time building geometry restraints manager: 0.42 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: 967
        1.34 -     1.46: 545
        1.46 -     1.57: 1748
        1.57 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 3286
  Sorted by residual:
  bond pdb=" C07 YUX A 601 "
       pdb=" C08 YUX A 601 "
    ideal  model  delta    sigma   weight residual
    1.460  1.532 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C04 YUX A 601 "
       pdb=" C05 YUX A 601 "
    ideal  model  delta    sigma   weight residual
    1.481  1.530 -0.049 2.00e-02 2.50e+03 6.03e+00
  bond pdb=" C05 YUX A 601 "
       pdb=" N06 YUX A 601 "
    ideal  model  delta    sigma   weight residual
    1.291  1.335 -0.044 2.00e-02 2.50e+03 4.88e+00
  bond pdb=" C11 YUX A 601 "
       pdb=" C12 YUX A 601 "
    ideal  model  delta    sigma   weight residual
    1.500  1.537 -0.037 2.00e-02 2.50e+03 3.33e+00
  bond pdb=" N24 YUX A 601 "
       pdb=" O25 YUX A 601 "
    ideal  model  delta    sigma   weight residual
    1.367  1.339  0.028 2.00e-02 2.50e+03 1.99e+00
  ... (remaining 3281 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 4315
        1.56 -     3.11: 114
        3.11 -     4.67: 18
        4.67 -     6.23: 9
        6.23 -     7.79: 2
  Bond angle restraints: 4458
  Sorted by residual:
  angle pdb=" CA  TRP A 178 "
        pdb=" CB  TRP A 178 "
        pdb=" CG  TRP A 178 "
      ideal   model   delta    sigma   weight residual
     113.60  121.39   -7.79 1.90e+00 2.77e-01 1.68e+01
  angle pdb=" C   THR A 121 "
        pdb=" N   VAL A 122 "
        pdb=" CA  VAL A 122 "
      ideal   model   delta    sigma   weight residual
     121.19  116.43    4.76 1.59e+00 3.96e-01 8.96e+00
  angle pdb=" C   PHE A 177 "
        pdb=" N   TRP A 178 "
        pdb=" CA  TRP A 178 "
      ideal   model   delta    sigma   weight residual
     120.31  116.15    4.16 1.52e+00 4.33e-01 7.48e+00
  angle pdb=" C04 YUX A 601 "
        pdb=" C05 YUX A 601 "
        pdb=" O25 YUX A 601 "
      ideal   model   delta    sigma   weight residual
     119.00  126.78   -7.78 3.00e+00 1.11e-01 6.73e+00
  angle pdb=" C   ALA A 395 "
        pdb=" N   ASP A 396 "
        pdb=" CA  ASP A 396 "
      ideal   model   delta    sigma   weight residual
     120.97  124.39   -3.42 1.48e+00 4.57e-01 5.34e+00
  ... (remaining 4453 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.28: 1635
       14.28 -    28.55: 193
       28.55 -    42.83: 53
       42.83 -    57.10: 9
       57.10 -    71.38: 3
  Dihedral angle restraints: 1893
    sinusoidal: 710
      harmonic: 1183
  Sorted by residual:
  dihedral pdb=" CA  ARG A 264 "
           pdb=" C   ARG A 264 "
           pdb=" N   VAL A 265 "
           pdb=" CA  VAL A 265 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.16  -16.84     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CG  ARG A 227 "
           pdb=" CD  ARG A 227 "
           pdb=" NE  ARG A 227 "
           pdb=" CZ  ARG A 227 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.97   44.97     2      1.50e+01 4.44e-03 1.07e+01
  dihedral pdb=" CA  TYR A 235 "
           pdb=" C   TYR A 235 "
           pdb=" N   PHE A 236 "
           pdb=" CA  PHE A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.90   16.10     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 1890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 340
       0.036 -    0.071: 145
       0.071 -    0.107: 29
       0.107 -    0.143: 7
       0.143 -    0.178: 1
  Chirality restraints: 522
  Sorted by residual:
  chirality pdb=" CA  TRP A 178 "
            pdb=" N   TRP A 178 "
            pdb=" C   TRP A 178 "
            pdb=" CB  TRP A 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.96e-01
  chirality pdb=" CB  VAL A 125 "
            pdb=" CA  VAL A 125 "
            pdb=" CG1 VAL A 125 "
            pdb=" CG2 VAL A 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.67e-01
  chirality pdb=" CA  ILE A 452 "
            pdb=" N   ILE A 452 "
            pdb=" C   ILE A 452 "
            pdb=" CB  ILE A 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 519 not shown)

  Planarity restraints: 542
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 178 "   -0.018 2.00e-02 2.50e+03   1.23e-02 3.80e+00
        pdb=" CG  TRP A 178 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 178 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 178 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 178 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 178 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 178 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 178 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 266 "    0.026 5.00e-02 4.00e+02   3.85e-02 2.37e+00
        pdb=" N   PRO A 267 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 178 "    0.007 2.00e-02 2.50e+03   1.36e-02 1.84e+00
        pdb=" C   TRP A 178 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   TRP A 178 "    0.009 2.00e-02 2.50e+03
        pdb=" N   SER A 179 "    0.008 2.00e-02 2.50e+03
  ... (remaining 539 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 604
        2.75 -     3.29: 3321
        3.29 -     3.83: 5533
        3.83 -     4.36: 6354
        4.36 -     4.90: 10830
  Nonbonded interactions: 26642
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 219 "
            pdb=" NH1 ARG A 227 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OH  TYR A 246 "
            pdb=" O   GLY A 333 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" NH2 ARG A 487 "
            pdb=" OD2 ASP A 492 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OG  SER A 250 "
            pdb=" OG  SER A 363 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" NH1 ARG A 530 "
            pdb=" OE2 GLU A 534 "
     model   vdw
     2.332 3.120
  ... (remaining 26637 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.840
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.810
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
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      :  0.005   0.072   3286  Z= 0.240
  Angle     :  0.675   7.787   4458  Z= 0.381
  Chirality :  0.040   0.178    522
  Planarity :  0.004   0.038    542
  Dihedral  : 13.627  71.381   1135
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.38), residues: 409
  helix: -0.45 (0.25), residues: 356
  sheet:  None (None), residues: 0
  loop : -1.68 (0.82), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 227 
 TYR   0.009   0.001   TYR A 246 
 PHE   0.019   0.002   PHE A 234 
 TRP   0.034   0.002   TRP A 178 
 HIS   0.003   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 3286)
  covalent geometry    : angle       0.67540 ( 4458)
  hydrogen bonds       : bond        0.10746 (  274)
  hydrogen bonds       : angle       5.05483 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7741 (mptt) cc_final: 0.7058 (mtmm)
REVERT: A  192 TYR cc_start: 0.7513 (m-80) cc_final: 0.7310 (m-80)
REVERT: A  394 ARG cc_start: 0.5818 (mtt180) cc_final: 0.5562 (mtt180)
REVERT: A  481 PHE cc_start: 0.8928 (t80) cc_final: 0.8634 (t80)
REVERT: A  530 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6856 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0615
  time to fit residues: 6.5508
Evaluate side-chains
  64 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0070
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
A 190 GLN
A 254 GLN
A 539 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.168383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.128894 restraints weight = 4324.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.133156 restraints weight = 2587.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.136038 restraints weight = 1896.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.137612 restraints weight = 1561.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.139045 restraints weight = 1386.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3286  Z= 0.153
  Angle     :  0.597   7.129   4458  Z= 0.316
  Chirality :  0.039   0.160    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.480  42.893    459
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.07 %
    Favored  : 81.55 %
  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:  0.97 (0.42), residues: 409
  helix:  0.90 (0.27), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.81 (0.93), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 227 
 TYR   0.018   0.002   TYR A 426 
 PHE   0.016   0.001   PHE A 234 
 TRP   0.028   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3286)
  covalent geometry    : angle       0.59679 ( 4458)
  hydrogen bonds       : bond        0.05119 (  274)
  hydrogen bonds       : angle       4.20594 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7577 (mptt) cc_final: 0.7105 (mttp)
REVERT: A  192 TYR cc_start: 0.7461 (m-80) cc_final: 0.7243 (m-80)
REVERT: A  394 ARG cc_start: 0.5871 (mtt180) cc_final: 0.5631 (mtt180)
REVERT: A  422 ILE cc_start: 0.8005 (tt) cc_final: 0.7615 (mm)
REVERT: A  481 PHE cc_start: 0.8895 (t80) cc_final: 0.8576 (t80)
REVERT: A  530 ARG cc_start: 0.7097 (ttt-90) cc_final: 0.6751 (tmt-80)
  outliers start: 8
  outliers final: 5
  residues processed: 75
  average time/residue: 0.0484
  time to fit residues: 4.7277
Evaluate side-chains
  67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  362 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 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 = 0.3875 r_free = 0.3875 target = 0.164339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.124825 restraints weight = 4395.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.128842 restraints weight = 2700.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.131362 restraints weight = 2008.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.133322 restraints weight = 1674.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.134187 restraints weight = 1482.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3286  Z= 0.179
  Angle     :  0.621   7.463   4458  Z= 0.322
  Chirality :  0.040   0.172    522
  Planarity :  0.004   0.037    542
  Dihedral  :  5.644  49.326    459
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 17.56 %
    Favored  : 78.87 %
  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:  1.57 (0.42), residues: 409
  helix:  1.30 (0.28), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.57 (0.94), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 227 
 TYR   0.011   0.002   TYR A 246 
 PHE   0.015   0.002   PHE A 234 
 TRP   0.031   0.002   TRP A 178 
 HIS   0.007   0.002   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 3286)
  covalent geometry    : angle       0.62115 ( 4458)
  hydrogen bonds       : bond        0.05334 (  274)
  hydrogen bonds       : angle       4.24427 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7562 (mptt) cc_final: 0.6955 (mtmm)
REVERT: A  161 LEU cc_start: 0.8308 (mp) cc_final: 0.8004 (mp)
REVERT: A  192 TYR cc_start: 0.7444 (m-80) cc_final: 0.7226 (m-80)
REVERT: A  394 ARG cc_start: 0.5888 (mtt180) cc_final: 0.5643 (mtt180)
REVERT: A  407 SER cc_start: 0.8835 (t) cc_final: 0.8497 (p)
REVERT: A  422 ILE cc_start: 0.7987 (tt) cc_final: 0.7580 (mm)
REVERT: A  481 PHE cc_start: 0.8905 (t80) cc_final: 0.8594 (t80)
REVERT: A  530 ARG cc_start: 0.7119 (ttt-90) cc_final: 0.6768 (tmt-80)
  outliers start: 12
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0438
  time to fit residues: 4.3102
Evaluate side-chains
  73 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  484 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 GLN ** 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 = 0.3943 r_free = 0.3943 target = 0.168728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.129561 restraints weight = 4416.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.133578 restraints weight = 2791.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.136179 restraints weight = 2095.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137670 restraints weight = 1753.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.138932 restraints weight = 1571.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3286  Z= 0.158
  Angle     :  0.617  10.310   4458  Z= 0.312
  Chirality :  0.041   0.317    522
  Planarity :  0.004   0.037    542
  Dihedral  :  5.594  51.828    459
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 20.24 %
    Favored  : 77.68 %
  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:  1.94 (0.43), residues: 409
  helix:  1.50 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.13 (1.00), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 200 
 TYR   0.017   0.001   TYR A 426 
 PHE   0.015   0.001   PHE A 234 
 TRP   0.029   0.001   TRP A 178 
 HIS   0.004   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3286)
  covalent geometry    : angle       0.61716 ( 4458)
  hydrogen bonds       : bond        0.05063 (  274)
  hydrogen bonds       : angle       4.13601 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7462 (mptt) cc_final: 0.6878 (mtmm)
REVERT: A  161 LEU cc_start: 0.8288 (mp) cc_final: 0.7977 (mp)
REVERT: A  192 TYR cc_start: 0.7396 (m-80) cc_final: 0.7181 (m-80)
REVERT: A  407 SER cc_start: 0.8811 (t) cc_final: 0.8514 (p)
REVERT: A  422 ILE cc_start: 0.7776 (tt) cc_final: 0.7322 (mm)
REVERT: A  481 PHE cc_start: 0.8881 (t80) cc_final: 0.8586 (t80)
REVERT: A  530 ARG cc_start: 0.7030 (ttt-90) cc_final: 0.6713 (tmt-80)
  outliers start: 7
  outliers final: 6
  residues processed: 72
  average time/residue: 0.0521
  time to fit residues: 4.9143
Evaluate side-chains
  67 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  363 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.0060
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 23 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.3970 r_free = 0.3970 target = 0.170894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.131608 restraints weight = 4460.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.135647 restraints weight = 2803.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.138394 restraints weight = 2103.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.140019 restraints weight = 1746.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.140893 restraints weight = 1561.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3286  Z= 0.146
  Angle     :  0.604   9.274   4458  Z= 0.305
  Chirality :  0.039   0.156    522
  Planarity :  0.004   0.037    542
  Dihedral  :  5.546  52.598    459
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.43 %
    Favored  : 75.30 %
  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:  2.17 (0.43), residues: 409
  helix:  1.65 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop :  0.04 (1.03), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 200 
 TYR   0.013   0.001   TYR A 426 
 PHE   0.014   0.001   PHE A 234 
 TRP   0.028   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3286)
  covalent geometry    : angle       0.60421 ( 4458)
  hydrogen bonds       : bond        0.04856 (  274)
  hydrogen bonds       : angle       4.05068 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.088 
Fit side-chains
REVERT: A  102 LYS cc_start: 0.7409 (mptt) cc_final: 0.6838 (mtmm)
REVERT: A  161 LEU cc_start: 0.8231 (mp) cc_final: 0.7900 (mp)
REVERT: A  407 SER cc_start: 0.8805 (t) cc_final: 0.8495 (p)
REVERT: A  413 LEU cc_start: 0.8885 (mm) cc_final: 0.8579 (tt)
REVERT: A  422 ILE cc_start: 0.7708 (tt) cc_final: 0.7203 (mm)
REVERT: A  481 PHE cc_start: 0.8866 (t80) cc_final: 0.8609 (t80)
REVERT: A  530 ARG cc_start: 0.7039 (ttt-90) cc_final: 0.6697 (tmt-80)
  outliers start: 11
  outliers final: 10
  residues processed: 79
  average time/residue: 0.0486
  time to fit residues: 5.0080
Evaluate side-chains
  70 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  484 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.167271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.128276 restraints weight = 4426.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.132187 restraints weight = 2839.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.134395 restraints weight = 2152.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.136095 restraints weight = 1825.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136767 restraints weight = 1630.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3286  Z= 0.178
  Angle     :  0.658   9.532   4458  Z= 0.334
  Chirality :  0.041   0.216    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.761  55.325    459
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.51 %
    Favored  : 73.51 %
  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:  2.11 (0.43), residues: 409
  helix:  1.60 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop :  0.13 (1.06), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 200 
 TYR   0.012   0.002   TYR A 426 
 PHE   0.014   0.002   PHE A 234 
 TRP   0.032   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 3286)
  covalent geometry    : angle       0.65764 ( 4458)
  hydrogen bonds       : bond        0.05250 (  274)
  hydrogen bonds       : angle       4.16152 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  102 LYS cc_start: 0.7457 (mptt) cc_final: 0.6818 (mtmm)
REVERT: A  161 LEU cc_start: 0.8237 (mp) cc_final: 0.7887 (mp)
REVERT: A  407 SER cc_start: 0.8814 (t) cc_final: 0.8513 (p)
REVERT: A  413 LEU cc_start: 0.8908 (mm) cc_final: 0.8593 (tt)
REVERT: A  481 PHE cc_start: 0.8875 (t80) cc_final: 0.8582 (t80)
REVERT: A  530 ARG cc_start: 0.7007 (ttt-90) cc_final: 0.6648 (tmt-80)
  outliers start: 10
  outliers final: 10
  residues processed: 75
  average time/residue: 0.0498
  time to fit residues: 4.9043
Evaluate side-chains
  75 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  484 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.169328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.130382 restraints weight = 4507.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.134286 restraints weight = 2860.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.136927 restraints weight = 2160.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.138380 restraints weight = 1810.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.139577 restraints weight = 1625.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3286  Z= 0.156
  Angle     :  0.625   8.477   4458  Z= 0.316
  Chirality :  0.040   0.181    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.686  55.171    459
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.51 %
    Favored  : 73.21 %
  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:  2.26 (0.43), residues: 409
  helix:  1.72 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.01 (1.01), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 200 
 TYR   0.017   0.002   TYR A 426 
 PHE   0.014   0.001   PHE A 234 
 TRP   0.029   0.001   TRP A 178 
 HIS   0.001   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3286)
  covalent geometry    : angle       0.62495 ( 4458)
  hydrogen bonds       : bond        0.04973 (  274)
  hydrogen bonds       : angle       4.12022 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.127 
Fit side-chains
REVERT: A  102 LYS cc_start: 0.7374 (mptt) cc_final: 0.6743 (mtmm)
REVERT: A  126 LEU cc_start: 0.8260 (tp) cc_final: 0.7672 (mt)
REVERT: A  161 LEU cc_start: 0.8198 (mp) cc_final: 0.7834 (mp)
REVERT: A  407 SER cc_start: 0.8798 (t) cc_final: 0.8521 (p)
REVERT: A  413 LEU cc_start: 0.8916 (mm) cc_final: 0.8599 (tt)
REVERT: A  481 PHE cc_start: 0.8858 (t80) cc_final: 0.8604 (t80)
REVERT: A  530 ARG cc_start: 0.6921 (ttt-90) cc_final: 0.6603 (tmt-80)
  outliers start: 11
  outliers final: 10
  residues processed: 71
  average time/residue: 0.0567
  time to fit residues: 5.1182
Evaluate side-chains
  71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  484 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 36 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3937 r_free = 0.3937 target = 0.168073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.129090 restraints weight = 4536.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.133110 restraints weight = 2853.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.135621 restraints weight = 2136.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.137379 restraints weight = 1781.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137955 restraints weight = 1592.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3286  Z= 0.168
  Angle     :  0.640   8.498   4458  Z= 0.322
  Chirality :  0.041   0.200    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.730  55.833    459
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.51 %
    Favored  : 73.21 %
  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:  2.21 (0.42), residues: 409
  helix:  1.72 (0.28), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.19 (0.93), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 200 
 TYR   0.015   0.002   TYR A 426 
 PHE   0.014   0.001   PHE A 234 
 TRP   0.032   0.002   TRP A 178 
 HIS   0.002   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 3286)
  covalent geometry    : angle       0.63954 ( 4458)
  hydrogen bonds       : bond        0.05104 (  274)
  hydrogen bonds       : angle       4.15982 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7351 (mptt) cc_final: 0.6735 (mtmm)
REVERT: A  161 LEU cc_start: 0.8258 (mp) cc_final: 0.7895 (mp)
REVERT: A  407 SER cc_start: 0.8770 (t) cc_final: 0.8503 (p)
REVERT: A  413 LEU cc_start: 0.8918 (mm) cc_final: 0.8606 (tt)
REVERT: A  481 PHE cc_start: 0.8862 (t80) cc_final: 0.8600 (t80)
REVERT: A  530 ARG cc_start: 0.6901 (ttt-90) cc_final: 0.6604 (tmt-80)
  outliers start: 11
  outliers final: 11
  residues processed: 72
  average time/residue: 0.0616
  time to fit residues: 5.5589
Evaluate side-chains
  71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  484 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0670
   chunk 26 optimal weight:    0.4980
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.170327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.131995 restraints weight = 4520.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136011 restraints weight = 2812.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.138730 restraints weight = 2103.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.140307 restraints weight = 1745.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.141488 restraints weight = 1555.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3286  Z= 0.146
  Angle     :  0.615   8.702   4458  Z= 0.308
  Chirality :  0.039   0.183    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.592  55.089    459
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 23.51 %
    Favored  : 72.92 %
  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:  2.34 (0.43), residues: 409
  helix:  1.84 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -0.45 (0.90), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 200 
 TYR   0.012   0.001   TYR A 246 
 PHE   0.015   0.001   PHE A 234 
 TRP   0.028   0.001   TRP A 178 
 HIS   0.001   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3286)
  covalent geometry    : angle       0.61484 ( 4458)
  hydrogen bonds       : bond        0.04728 (  274)
  hydrogen bonds       : angle       4.09695 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7372 (mptt) cc_final: 0.6783 (mtmm)
REVERT: A  126 LEU cc_start: 0.8129 (tp) cc_final: 0.7841 (tp)
REVERT: A  161 LEU cc_start: 0.8175 (mp) cc_final: 0.7780 (mp)
REVERT: A  407 SER cc_start: 0.8788 (t) cc_final: 0.8498 (p)
REVERT: A  413 LEU cc_start: 0.8898 (mm) cc_final: 0.8601 (tt)
REVERT: A  481 PHE cc_start: 0.8844 (t80) cc_final: 0.8599 (t80)
REVERT: A  530 ARG cc_start: 0.6880 (ttt-90) cc_final: 0.6557 (tmt-80)
  outliers start: 12
  outliers final: 12
  residues processed: 72
  average time/residue: 0.0671
  time to fit residues: 5.9757
Evaluate side-chains
  78 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  304 ARG
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  484 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0870
   chunk 4 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 7 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0970
   chunk 39 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0370
   chunk 26 optimal weight:    9.9990
   overall best weight:    0.2834

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.174073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.136067 restraints weight = 4454.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.140045 restraints weight = 2752.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.143094 restraints weight = 2055.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.144884 restraints weight = 1695.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.145933 restraints weight = 1496.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3286  Z= 0.131
  Angle     :  0.613   9.102   4458  Z= 0.307
  Chirality :  0.038   0.158    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.332  52.557    459
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.11 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.42), residues: 409
  helix:  1.86 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -0.48 (0.87), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 200 
 TYR   0.012   0.001   TYR A 120 
 PHE   0.013   0.001   PHE A 234 
 TRP   0.024   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3286)
  covalent geometry    : angle       0.61268 ( 4458)
  hydrogen bonds       : bond        0.04439 (  274)
  hydrogen bonds       : angle       4.00851 (  822)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7277 (mptt) cc_final: 0.6682 (mtmm)
REVERT: A  126 LEU cc_start: 0.8029 (tp) cc_final: 0.7785 (tp)
REVERT: A  161 LEU cc_start: 0.8108 (mp) cc_final: 0.7746 (mp)
REVERT: A  407 SER cc_start: 0.8785 (t) cc_final: 0.8515 (p)
REVERT: A  413 LEU cc_start: 0.8884 (mm) cc_final: 0.8620 (tt)
REVERT: A  481 PHE cc_start: 0.8793 (t80) cc_final: 0.8539 (t80)
REVERT: A  530 ARG cc_start: 0.6856 (ttt-90) cc_final: 0.6538 (tmt-80)
  outliers start: 11
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0708
  time to fit residues: 6.3009
Evaluate side-chains
  71 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  225 ASN
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  304 ARG
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  484 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    0.1980
   chunk 9 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.3986 r_free = 0.3986 target = 0.172871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.134455 restraints weight = 4490.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.138623 restraints weight = 2772.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.141544 restraints weight = 2052.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.143187 restraints weight = 1693.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.144504 restraints weight = 1501.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3286  Z= 0.137
  Angle     :  0.619   8.876   4458  Z= 0.307
  Chirality :  0.039   0.164    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.289  50.732    459
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 25.89 %
    Favored  : 71.43 %
  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:  2.38 (0.42), residues: 409
  helix:  1.86 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -0.45 (0.83), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 200 
 TYR   0.011   0.001   TYR A 120 
 PHE   0.016   0.001   PHE A 234 
 TRP   0.027   0.001   TRP A 178 
 HIS   0.001   0.000   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3286)
  covalent geometry    : angle       0.61924 ( 4458)
  hydrogen bonds       : bond        0.04498 (  274)
  hydrogen bonds       : angle       4.03287 (  822)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 802.47 seconds
wall clock time: 14 minutes 35.77 seconds (875.77 seconds total)