Starting phenix.real_space_refine
on Wed Mar  5 18:04:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g92_29860/03_2025/8g92_29860.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g92_29860/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g92_29860/03_2025/8g92_29860.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g92_29860/03_2025/8g92_29860.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g92_29860/03_2025/8g92_29860.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g92_29860/03_2025/8g92_29860.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.15, per 1000 atoms: 0.98
  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: 0.81
  Conformation dependent library (CDL) restraints added in 370.7 milliseconds
  

  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: 0.30
  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: 0.96

  Time building geometry restraints manager: 0.97 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:             1.070
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.500
  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:3.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.290
-------------------------------------------------------------------------------
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= 0.340
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.034   0.002   TRP A 178 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.019   0.002   PHE A 234 
 TYR   0.009   0.001   TYR A 246 
 ARG   0.004   0.000   ARG A 227 

*********************** 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  : 0.331 
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: 0.1595
  time to fit residues: 16.9695
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  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0970
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 539 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.166795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.127116 restraints weight = 4290.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.131340 restraints weight = 2598.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.134023 restraints weight = 1914.078|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3286  Z= 0.226
  Angle     :  0.612   7.310   4458  Z= 0.324
  Chirality :  0.040   0.164    522
  Planarity :  0.004   0.039    542
  Dihedral  :  5.584  43.643    459
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.67 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.42), residues: 409
  helix:  0.88 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.93 (0.91), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.016   0.002   PHE A 234 
 TYR   0.018   0.002   TYR A 426 
 ARG   0.005   0.001   ARG A 227 

*********************** 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
  80 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7625 (mptt) cc_final: 0.7142 (mttp)
REVERT: A  192 TYR cc_start: 0.7495 (m-80) cc_final: 0.7272 (m-80)
REVERT: A  394 ARG cc_start: 0.5788 (mtt180) cc_final: 0.5552 (mtt180)
REVERT: A  422 ILE cc_start: 0.8097 (tt) cc_final: 0.7703 (mm)
REVERT: A  481 PHE cc_start: 0.8897 (t80) cc_final: 0.8594 (t80)
REVERT: A  530 ARG cc_start: 0.7130 (ttt-90) cc_final: 0.6740 (tmt-80)
  outliers start: 8
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1117
  time to fit residues: 10.7088
Evaluate side-chains
  68 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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 16 optimal weight:    0.0980
   chunk 13 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0570
   chunk 11 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
A 254 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.169412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.131070 restraints weight = 4338.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.135333 restraints weight = 2651.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.138104 restraints weight = 1948.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3286  Z= 0.177
  Angle     :  0.571   6.631   4458  Z= 0.294
  Chirality :  0.038   0.148    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.326  45.898    459
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.35 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.43), residues: 409
  helix:  1.49 (0.28), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.52 (0.95), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 178 
 HIS   0.006   0.001   HIS A 341 
 PHE   0.014   0.001   PHE A 234 
 TYR   0.012   0.001   TYR A 120 
 ARG   0.004   0.000   ARG A 227 

*********************** 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
  79 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7464 (mptt) cc_final: 0.6694 (mtmm)
REVERT: A  161 LEU cc_start: 0.8237 (mp) cc_final: 0.7963 (mp)
REVERT: A  192 TYR cc_start: 0.7464 (m-80) cc_final: 0.7243 (m-80)
REVERT: A  394 ARG cc_start: 0.5879 (mtt180) cc_final: 0.5631 (mtt180)
REVERT: A  407 SER cc_start: 0.8790 (t) cc_final: 0.8452 (p)
REVERT: A  422 ILE cc_start: 0.7957 (tt) cc_final: 0.7507 (mm)
REVERT: A  481 PHE cc_start: 0.8853 (t80) cc_final: 0.8578 (t80)
REVERT: A  530 ARG cc_start: 0.7137 (ttt-90) cc_final: 0.6779 (tmt-80)
  outliers start: 8
  outliers final: 6
  residues processed: 74
  average time/residue: 0.1303
  time to fit residues: 12.1606
Evaluate side-chains
  69 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 SER
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 14 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3939 r_free = 0.3939 target = 0.168182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.129082 restraints weight = 4442.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.133084 restraints weight = 2784.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.135672 restraints weight = 2086.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3286  Z= 0.238
  Angle     :  0.626   9.574   4458  Z= 0.319
  Chirality :  0.042   0.323    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.568  50.491    459
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 18.75 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.43), residues: 409
  helix:  1.50 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.01 (1.05), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 178 
 HIS   0.007   0.002   HIS A 341 
 PHE   0.015   0.002   PHE A 234 
 TYR   0.017   0.001   TYR A 426 
 ARG   0.004   0.001   ARG A 200 

*********************** 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
  78 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7502 (mptt) cc_final: 0.6853 (mtmm)
REVERT: A  161 LEU cc_start: 0.8286 (mp) cc_final: 0.7974 (mp)
REVERT: A  192 TYR cc_start: 0.7430 (m-80) cc_final: 0.7227 (m-80)
REVERT: A  407 SER cc_start: 0.8823 (t) cc_final: 0.8511 (p)
REVERT: A  422 ILE cc_start: 0.7807 (tt) cc_final: 0.7355 (mm)
REVERT: A  481 PHE cc_start: 0.8865 (t80) cc_final: 0.8566 (t80)
REVERT: A  530 ARG cc_start: 0.7107 (ttt-90) cc_final: 0.6745 (tmt-80)
  outliers start: 11
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1335
  time to fit residues: 12.2933
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  : 0.358 
-------------------------------------------------------------------------------
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  199 SER
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  304 ARG
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 341 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.169034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.130375 restraints weight = 4467.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.134294 restraints weight = 2822.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.136657 restraints weight = 2122.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2110

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= 0.219
  Angle     :  0.626   8.373   4458  Z= 0.319
  Chirality :  0.040   0.166    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.591  52.171    459
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.62 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.43), residues: 409
  helix:  1.61 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop :  0.00 (1.02), residues: 45

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 178 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.014   0.001   PHE A 234 
 TYR   0.013   0.001   TYR A 426 
 ARG   0.004   0.000   ARG A 200 

*********************** 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
  75 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  102 LYS cc_start: 0.7465 (mptt) cc_final: 0.6826 (mtmm)
REVERT: A  161 LEU cc_start: 0.8225 (mp) cc_final: 0.7874 (mp)
REVERT: A  192 TYR cc_start: 0.7426 (m-80) cc_final: 0.7224 (m-80)
REVERT: A  407 SER cc_start: 0.8818 (t) cc_final: 0.8499 (p)
REVERT: A  413 LEU cc_start: 0.8884 (mm) cc_final: 0.8589 (tt)
REVERT: A  481 PHE cc_start: 0.8851 (t80) cc_final: 0.8555 (t80)
REVERT: A  530 ARG cc_start: 0.7080 (ttt-90) cc_final: 0.6709 (tmt-80)
  outliers start: 10
  outliers final: 10
  residues processed: 71
  average time/residue: 0.1323
  time to fit residues: 11.9182
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  : 0.289 
-------------------------------------------------------------------------------
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  303 LEU
Chi-restraints excluded: chain A residue  304 ARG
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 31 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0870
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.171294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.132432 restraints weight = 4515.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.136485 restraints weight = 2787.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.138957 restraints weight = 2078.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2312

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= 0.197
  Angle     :  0.605   8.516   4458  Z= 0.306
  Chirality :  0.039   0.172    522
  Planarity :  0.004   0.037    542
  Dihedral  :  5.512  52.833    459
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 22.92 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.43), residues: 409
  helix:  1.79 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -0.45 (0.92), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 178 
 HIS   0.001   0.001   HIS A 468 
 PHE   0.013   0.001   PHE A 234 
 TYR   0.016   0.001   TYR A 426 
 ARG   0.004   0.000   ARG A 200 

*********************** 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
  80 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  102 LYS cc_start: 0.7407 (mptt) cc_final: 0.6830 (mtmm)
REVERT: A  161 LEU cc_start: 0.8163 (mp) cc_final: 0.7788 (mp)
REVERT: A  192 TYR cc_start: 0.7423 (m-80) cc_final: 0.7222 (m-80)
REVERT: A  407 SER cc_start: 0.8806 (t) cc_final: 0.8490 (p)
REVERT: A  413 LEU cc_start: 0.8910 (mm) cc_final: 0.8589 (tt)
REVERT: A  481 PHE cc_start: 0.8825 (t80) cc_final: 0.8575 (t80)
REVERT: A  530 ARG cc_start: 0.7021 (ttt-90) cc_final: 0.6636 (tmt-80)
  outliers start: 11
  outliers final: 10
  residues processed: 76
  average time/residue: 0.1361
  time to fit residues: 13.0470
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  : 0.356 
-------------------------------------------------------------------------------
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  304 ARG
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 17 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    0.2980
   chunk 20 optimal weight:    0.5980
   chunk 0 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.170399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.131958 restraints weight = 4460.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.135971 restraints weight = 2783.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.138379 restraints weight = 2080.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3286  Z= 0.203
  Angle     :  0.608   8.075   4458  Z= 0.307
  Chirality :  0.039   0.179    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.470  53.324    459
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.42), residues: 409
  helix:  1.83 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -0.43 (0.89), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 178 
 HIS   0.001   0.001   HIS A 260 
 PHE   0.014   0.001   PHE A 234 
 TYR   0.014   0.001   TYR A 426 
 ARG   0.004   0.000   ARG A 200 

*********************** 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
  80 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A  102 LYS cc_start: 0.7364 (mptt) cc_final: 0.6779 (mtmm)
REVERT: A  161 LEU cc_start: 0.8163 (mp) cc_final: 0.7797 (mp)
REVERT: A  407 SER cc_start: 0.8801 (t) cc_final: 0.8470 (p)
REVERT: A  413 LEU cc_start: 0.8926 (mm) cc_final: 0.8595 (tt)
REVERT: A  481 PHE cc_start: 0.8841 (t80) cc_final: 0.8592 (t80)
REVERT: A  530 ARG cc_start: 0.6988 (ttt-90) cc_final: 0.6610 (tmt-80)
  outliers start: 11
  outliers final: 11
  residues processed: 75
  average time/residue: 0.1279
  time to fit residues: 12.1408
Evaluate side-chains
  73 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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  304 ARG
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 15 optimal weight:    0.5980
   chunk 26 optimal weight:    6.9990
   chunk 36 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0370
   chunk 29 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.5258

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.170766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.132942 restraints weight = 4451.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.136941 restraints weight = 2755.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.139590 restraints weight = 2044.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2450

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= 0.194
  Angle     :  0.610   9.505   4458  Z= 0.306
  Chirality :  0.040   0.238    522
  Planarity :  0.004   0.038    542
  Dihedral  :  5.423  53.045    459
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.42), residues: 409
  helix:  1.86 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -0.49 (0.87), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.013   0.001   PHE A 234 
 TYR   0.012   0.001   TYR A 426 
 ARG   0.004   0.000   ARG A 200 

*********************** 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
  82 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 LYS cc_start: 0.7350 (mptt) cc_final: 0.6752 (mtmm)
REVERT: A  161 LEU cc_start: 0.8116 (mp) cc_final: 0.7763 (mp)
REVERT: A  407 SER cc_start: 0.8792 (t) cc_final: 0.8505 (p)
REVERT: A  413 LEU cc_start: 0.8903 (mm) cc_final: 0.8597 (tt)
REVERT: A  481 PHE cc_start: 0.8825 (t80) cc_final: 0.8570 (t80)
REVERT: A  530 ARG cc_start: 0.6908 (ttt-90) cc_final: 0.6561 (tmt-80)
  outliers start: 12
  outliers final: 11
  residues processed: 75
  average time/residue: 0.1501
  time to fit residues: 13.7216
Evaluate side-chains
  74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
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  304 ARG
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 34 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3950 r_free = 0.3950 target = 0.169391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.131964 restraints weight = 4440.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.135951 restraints weight = 2809.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.138423 restraints weight = 2102.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3286  Z= 0.214
  Angle     :  0.633   8.816   4458  Z= 0.317
  Chirality :  0.040   0.234    522
  Planarity :  0.004   0.039    542
  Dihedral  :  5.499  53.502    459
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 24.11 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.42), residues: 409
  helix:  1.83 (0.28), residues: 360
  sheet:  None (None), residues: 0
  loop : -0.48 (0.87), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 178 
 HIS   0.001   0.001   HIS A 341 
 PHE   0.014   0.001   PHE A 234 
 TYR   0.011   0.001   TYR A 426 
 ARG   0.004   0.000   ARG A 200 

*********************** 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
  76 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  102 LYS cc_start: 0.7353 (mptt) cc_final: 0.6692 (mtmm)
REVERT: A  161 LEU cc_start: 0.8166 (mp) cc_final: 0.7803 (mp)
REVERT: A  407 SER cc_start: 0.8772 (t) cc_final: 0.8517 (p)
REVERT: A  413 LEU cc_start: 0.8913 (mm) cc_final: 0.8595 (tt)
REVERT: A  481 PHE cc_start: 0.8820 (t80) cc_final: 0.8601 (t80)
REVERT: A  530 ARG cc_start: 0.6917 (ttt-90) cc_final: 0.6569 (tmt-80)
  outliers start: 12
  outliers final: 11
  residues processed: 70
  average time/residue: 0.1466
  time to fit residues: 12.7953
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  : 0.329 
-------------------------------------------------------------------------------
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  304 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 9 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3955 r_free = 0.3955 target = 0.169865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.131435 restraints weight = 4414.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.135457 restraints weight = 2823.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.138130 restraints weight = 2111.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3286  Z= 0.222
  Angle     :  0.651   8.744   4458  Z= 0.330
  Chirality :  0.041   0.236    522
  Planarity :  0.004   0.042    542
  Dihedral  :  5.565  54.235    459
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.70 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.42), residues: 409
  helix:  1.71 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -0.41 (0.87), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 341 
 PHE   0.013   0.001   PHE A 234 
 TYR   0.014   0.002   TYR A 116 
 ARG   0.009   0.001   ARG A 456 

********************** 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
  78 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 67
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  102 LYS cc_start: 0.7376 (mptt) cc_final: 0.6717 (mtmm)
REVERT: A  161 LEU cc_start: 0.8163 (mp) cc_final: 0.7797 (mp)
REVERT: A  407 SER cc_start: 0.8775 (t) cc_final: 0.8519 (p)
REVERT: A  413 LEU cc_start: 0.8897 (mm) cc_final: 0.8593 (tt)
REVERT: A  481 PHE cc_start: 0.8828 (t80) cc_final: 0.8573 (t80)
REVERT: A  530 ARG cc_start: 0.6917 (ttt-90) cc_final: 0.6566 (tmt-80)
  outliers start: 11
  outliers final: 11
  residues processed: 72
  average time/residue: 0.1506
  time to fit residues: 13.4503
Evaluate side-chains
  74 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
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  304 ARG
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3923 r_free = 0.3923 target = 0.167141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.130909 restraints weight = 4395.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.134979 restraints weight = 2702.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.137626 restraints weight = 1987.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.2481

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= 0.232
  Angle     :  0.649   9.069   4458  Z= 0.328
  Chirality :  0.041   0.235    522
  Planarity :  0.004   0.039    542
  Dihedral  :  5.594  54.446    459
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.42), residues: 409
  helix:  1.72 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -0.56 (0.86), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 178 
 HIS   0.002   0.001   HIS A 260 
 PHE   0.014   0.001   PHE A 234 
 TYR   0.014   0.001   TYR A 116 
 ARG   0.007   0.001   ARG A 456 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1361.65 seconds
wall clock time: 24 minutes 22.01 seconds (1462.01 seconds total)