Starting phenix.real_space_refine
on Mon Jan 13 15:43:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xv9_38693/01_2025/8xv9_38693.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xv9_38693/01_2025/8xv9_38693.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xv9_38693/01_2025/8xv9_38693.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xv9_38693/01_2025/8xv9_38693.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xv9_38693/01_2025/8xv9_38693.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xv9_38693/01_2025/8xv9_38693.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
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    2127      2.51       5
     N     472      2.21       5
     O     531      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 3147
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3110
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 388, 3110
          Classifications: {'peptide': 388}
          Link IDs: {'PTRANS': 14, 'TRANS': 373}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'2TA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.57, per 1000 atoms: 0.82
  Number of scatterers: 3147
  At special positions: 0
  Unit cell: (67.41, 70.62, 77.04, 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     531      8.00
     N     472      7.00
     C    2127      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: 0.77
  Conformation dependent library (CDL) restraints added in 354.9 milliseconds
  

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  736

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      80.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 28
    Processing helix  chain 'A' and resid 34 through 40
      removed outlier: 3.765A  pdb=" N   TYR A  38 " --> pdb=" O   PHE A  34 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER A  40 " --> pdb=" O   ILE A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 55 through 65
      removed outlier: 3.915A  pdb=" N   TRP A  59 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   THR A  60 " --> pdb=" O   PHE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 77
      removed outlier: 3.705A  pdb=" N   ASP A  75 " --> pdb=" O   PHE A  71 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   VAL A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 99
      removed outlier: 3.833A  pdb=" N   ILE A  83 " --> pdb=" O   TYR A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 125
      removed outlier: 3.829A  pdb=" N   VAL A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ALA A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ALA A 125 " --> pdb=" O   VAL A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 130
      removed outlier: 3.586A  pdb=" N   SER A 129 " --> pdb=" O   TYR A 126 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL A 130 " --> pdb=" O   ILE A 127 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 126 through 130'
    Processing helix  chain 'A' and resid 132 through 135
    Processing helix  chain 'A' and resid 136 through 163
    Processing helix  chain 'A' and resid 168 through 189
      removed outlier: 4.087A  pdb=" N   PHE A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 307
      removed outlier: 5.277A  pdb=" N   GLN A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   ILE A 301 " --> pdb=" O   ASN A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 335
    Processing helix  chain 'A' and resid 343 through 346
    Processing helix  chain 'A' and resid 347 through 365
      removed outlier: 3.616A  pdb=" N   VAL A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 395
      removed outlier: 3.513A  pdb=" N   CYS A 372 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 426
      removed outlier: 3.848A  pdb=" N   ALA A 404 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 459
      removed outlier: 3.574A  pdb=" N   GLN A 438 " --> pdb=" O   PRO A 434 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE A 439 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR A 459 " --> pdb=" O   MET A 455 " (cutoff:3.500A)

    220 hydrogen bonds defined for protein.
    654 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: 0.81

  Time building geometry restraints manager: 0.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 891
        1.35 -     1.47: 974
        1.47 -     1.59: 1351
        1.59 -     1.72: 0
        1.72 -     1.84: 30
  Bond restraints: 3246
  Sorted by residual:
  bond pdb=" CAQ 2TA A 501 "
       pdb=" CAR 2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.526  1.343  0.183 2.00e-02 2.50e+03 8.41e+01
  bond pdb=" CAT 2TA A 501 "
       pdb=" NAP 2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.456  1.285  0.171 2.00e-02 2.50e+03 7.34e+01
  bond pdb=" CAQ 2TA A 501 "
       pdb=" NAP 2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.454  1.583 -0.129 2.00e-02 2.50e+03 4.17e+01
  bond pdb=" NBE 2TA A 501 "
       pdb=" SBD 2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.639  1.757 -0.118 2.00e-02 2.50e+03 3.51e+01
  bond pdb=" C2  2TA A 501 "
       pdb=" NAF 2TA A 501 "
    ideal  model  delta    sigma   weight residual
    1.361  1.475 -0.114 2.00e-02 2.50e+03 3.26e+01
  ... (remaining 3241 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.38: 4380
        3.38 -     6.76: 41
        6.76 -    10.14: 14
       10.14 -    13.52: 1
       13.52 -    16.90: 1
  Bond angle restraints: 4437
  Sorted by residual:
  angle pdb=" C2  2TA A 501 "
        pdb=" NAF 2TA A 501 "
        pdb=" CAG 2TA A 501 "
      ideal   model   delta    sigma   weight residual
     131.32  114.42   16.90 3.00e+00 1.11e-01 3.17e+01
  angle pdb=" C4  2TA A 501 "
        pdb=" NAW 2TA A 501 "
        pdb=" CAX 2TA A 501 "
      ideal   model   delta    sigma   weight residual
     131.24  120.10   11.14 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" CA  ILE A  36 "
        pdb=" C   ILE A  36 "
        pdb=" N   PRO A  37 "
      ideal   model   delta    sigma   weight residual
     118.88  123.77   -4.89 1.54e+00 4.22e-01 1.01e+01
  angle pdb=" OBJ 2TA A 501 "
        pdb=" SBD 2TA A 501 "
        pdb=" OBK 2TA A 501 "
      ideal   model   delta    sigma   weight residual
     118.13  109.12    9.01 3.00e+00 1.11e-01 9.01e+00
  angle pdb=" N   TYR A  14 "
        pdb=" CA  TYR A  14 "
        pdb=" C   TYR A  14 "
      ideal   model   delta    sigma   weight residual
     109.81  115.94   -6.13 2.21e+00 2.05e-01 7.71e+00
  ... (remaining 4432 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.97: 1801
       28.97 -    57.95: 22
       57.95 -    86.92: 7
       86.92 -   115.90: 2
      115.90 -   144.87: 1
  Dihedral angle restraints: 1833
    sinusoidal: 681
      harmonic: 1152
  Sorted by residual:
  dihedral pdb=" CA  ARG A  78 "
           pdb=" C   ARG A  78 "
           pdb=" N   TYR A  79 "
           pdb=" CA  TYR A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.90   24.10     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CAG 2TA A 501 "
           pdb=" C2  2TA A 501 "
           pdb=" NAF 2TA A 501 "
           pdb=" N1  2TA A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.72 -145.59  144.87     1      3.00e+01 1.11e-03 1.94e+01
  dihedral pdb=" CA  VAL A 425 "
           pdb=" C   VAL A 425 "
           pdb=" N   VAL A 426 "
           pdb=" CA  VAL A 426 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.72  -21.28     0      5.00e+00 4.00e-02 1.81e+01
  ... (remaining 1830 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 292
       0.035 -    0.071: 148
       0.071 -    0.106: 45
       0.106 -    0.141: 13
       0.141 -    0.176: 4
  Chirality restraints: 502
  Sorted by residual:
  chirality pdb=" CA  PHE A  56 "
            pdb=" N   PHE A  56 "
            pdb=" C   PHE A  56 "
            pdb=" CB  PHE A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.72e-01
  chirality pdb=" CA  TYR A  14 "
            pdb=" N   TYR A  14 "
            pdb=" C   TYR A  14 "
            pdb=" CB  TYR A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CA  LYS A  80 "
            pdb=" N   LYS A  80 "
            pdb=" C   LYS A  80 "
            pdb=" CB  LYS A  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.15 2.00e-01 2.50e+01 5.28e-01
  ... (remaining 499 not shown)

  Planarity restraints: 529
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 373 "    0.018 2.00e-02 2.50e+03   1.64e-02 5.38e+00
        pdb=" CG  TYR A 373 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 373 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 373 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 373 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 373 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 373 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 373 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  29 "   -0.034 5.00e-02 4.00e+02   5.12e-02 4.19e+00
        pdb=" N   PRO A  30 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A  30 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  30 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  61 "   -0.010 2.00e-02 2.50e+03   1.96e-02 3.86e+00
        pdb=" C   TYR A  61 "    0.034 2.00e-02 2.50e+03
        pdb=" O   TYR A  61 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER A  62 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 526 not shown)

  Histogram of nonbonded interaction distances:
        2.40 -     2.90: 1181
        2.90 -     3.40: 3062
        3.40 -     3.90: 5208
        3.90 -     4.40: 5520
        4.40 -     4.90: 9624
  Nonbonded interactions: 24595
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  32 "
            pdb=" NAW 2TA A 501 "
     model   vdw
     2.402 3.120
  nonbonded pdb=" OD1 ASP A  75 "
            pdb=" OH  TYR A  79 "
     model   vdw
     2.412 3.040
  nonbonded pdb=" O   PHE A  22 "
            pdb=" OG  SER A  26 "
     model   vdw
     2.470 3.040
  nonbonded pdb=" OH  TYR A  61 "
            pdb=" OD2 ASP A 427 "
     model   vdw
     2.476 3.040
  nonbonded pdb=" O   LYS A 270 "
            pdb=" OG  SER A 274 "
     model   vdw
     2.485 3.040
  ... (remaining 24590 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:             0.750
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.940
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6114
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      :  0.008   0.183   3246  Z= 0.526
  Angle     :  0.936  16.896   4437  Z= 0.449
  Chirality :  0.047   0.176    502
  Planarity :  0.007   0.051    529
  Dihedral  : 12.311 144.871   1097
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.53 (0.31), residues: 384
  helix: -1.68 (0.22), residues: 279
  sheet:  None (None), residues: 0
  loop : -3.83 (0.44), residues: 105

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  59 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.017   0.002   PHE A 439 
 TYR   0.041   0.002   TYR A 373 
 ARG   0.001   0.000   ARG A  29 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 SER cc_start: 0.7605 (p) cc_final: 0.7084 (m)
REVERT: A   36 ILE cc_start: 0.7864 (tp) cc_final: 0.7439 (tp)
REVERT: A   77 VAL cc_start: 0.7653 (m) cc_final: 0.7315 (t)
REVERT: A  115 MET cc_start: 0.6896 (ttp) cc_final: 0.6562 (ttp)
REVERT: A  152 THR cc_start: 0.7629 (m) cc_final: 0.7115 (p)
REVERT: A  306 LYS cc_start: 0.6487 (mmtt) cc_final: 0.6262 (mmtt)
REVERT: A  364 HIS cc_start: 0.6529 (t70) cc_final: 0.6234 (t-90)
REVERT: A  369 ILE cc_start: 0.8050 (tp) cc_final: 0.7687 (tp)
REVERT: A  389 ILE cc_start: 0.7768 (mt) cc_final: 0.7465 (mt)
REVERT: A  423 VAL cc_start: 0.7605 (t) cc_final: 0.7056 (m)
REVERT: A  440 LEU cc_start: 0.7185 (tp) cc_final: 0.6565 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1207
  time to fit residues: 15.2528
Evaluate side-chains
  79 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 22 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 294 GLN
A 356 ASN
A 364 HIS
** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.156522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.140888 restraints weight = 5626.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.145076 restraints weight = 3003.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.147727 restraints weight = 1840.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6306
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3246  Z= 0.250
  Angle     :  0.661   6.252   4437  Z= 0.343
  Chirality :  0.043   0.157    502
  Planarity :  0.005   0.042    529
  Dihedral  : 13.701 155.494    440
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 11.71 %
    Favored  : 87.69 %
  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: -0.57 (0.41), residues: 384
  helix:  0.47 (0.29), residues: 284
  sheet:  None (None), residues: 0
  loop : -2.78 (0.60), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  94 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.026   0.002   PHE A 439 
 TYR   0.029   0.002   TYR A 126 
 ARG   0.001   0.000   ARG A 138 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7573 (tp)
REVERT: A   77 VAL cc_start: 0.7701 (m) cc_final: 0.7471 (t)
REVERT: A  152 THR cc_start: 0.7777 (m) cc_final: 0.7109 (p)
REVERT: A  156 VAL cc_start: 0.7966 (t) cc_final: 0.7694 (p)
REVERT: A  167 MET cc_start: 0.6194 (mmm) cc_final: 0.5744 (ptp)
REVERT: A  301 ILE cc_start: 0.7738 (mt) cc_final: 0.7530 (mt)
REVERT: A  366 THR cc_start: 0.8162 (p) cc_final: 0.7881 (p)
REVERT: A  369 ILE cc_start: 0.7829 (tp) cc_final: 0.7604 (tp)
REVERT: A  386 LEU cc_start: 0.7996 (mt) cc_final: 0.7775 (mm)
REVERT: A  423 VAL cc_start: 0.7710 (t) cc_final: 0.7260 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 93
  average time/residue: 0.1429
  time to fit residues: 16.4235
Evaluate side-chains
  88 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  272 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   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 364 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.153802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.138372 restraints weight = 5532.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.142420 restraints weight = 3009.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.145174 restraints weight = 1854.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6387
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3246  Z= 0.299
  Angle     :  0.669   5.797   4437  Z= 0.358
  Chirality :  0.044   0.150    502
  Planarity :  0.005   0.044    529
  Dihedral  : 14.058 159.078    440
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.81 %
    Favored  : 83.78 %
  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: -0.07 (0.42), residues: 384
  helix:  0.85 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -2.84 (0.59), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 341 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.020   0.002   PHE A 266 
 TYR   0.029   0.002   TYR A 445 
 ARG   0.003   0.001   ARG A 138 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 MET cc_start: 0.7921 (mmm) cc_final: 0.7432 (mpp)
REVERT: A  128 TYR cc_start: 0.6823 (m-80) cc_final: 0.6480 (m-80)
REVERT: A  152 THR cc_start: 0.8027 (m) cc_final: 0.7359 (p)
REVERT: A  156 VAL cc_start: 0.7998 (t) cc_final: 0.7726 (p)
REVERT: A  298 TYR cc_start: 0.7285 (m-10) cc_final: 0.6648 (m-10)
REVERT: A  363 MET cc_start: 0.6477 (tpt) cc_final: 0.6175 (mtt)
REVERT: A  364 HIS cc_start: 0.6776 (t-90) cc_final: 0.6497 (t-90)
REVERT: A  420 ILE cc_start: 0.7549 (mt) cc_final: 0.7347 (mt)
REVERT: A  421 MET cc_start: 0.7593 (ttp) cc_final: 0.7346 (ttp)
REVERT: A  423 VAL cc_start: 0.7923 (t) cc_final: 0.7501 (m)
REVERT: A  440 LEU cc_start: 0.7255 (tp) cc_final: 0.6672 (mt)
  outliers start: 8
  outliers final: 3
  residues processed: 100
  average time/residue: 0.1086
  time to fit residues: 13.9159
Evaluate side-chains
  94 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 CYS
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  415 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    0.4980
   chunk 30 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN
** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.154932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.139188 restraints weight = 5497.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.143268 restraints weight = 2979.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.146112 restraints weight = 1832.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6359
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3246  Z= 0.221
  Angle     :  0.656   6.573   4437  Z= 0.338
  Chirality :  0.042   0.152    502
  Planarity :  0.005   0.067    529
  Dihedral  : 13.950 159.030    440
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.22 %
    Favored  : 80.78 %
  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:  0.31 (0.42), residues: 384
  helix:  1.01 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -2.72 (0.64), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  94 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.014   0.002   PHE A 266 
 TYR   0.027   0.002   TYR A 126 
 ARG   0.002   0.000   ARG A 429 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 MET cc_start: 0.7922 (mmm) cc_final: 0.7613 (mmm)
REVERT: A  128 TYR cc_start: 0.6861 (m-80) cc_final: 0.6489 (m-80)
REVERT: A  152 THR cc_start: 0.7911 (m) cc_final: 0.7404 (p)
REVERT: A  366 THR cc_start: 0.8218 (p) cc_final: 0.7964 (p)
REVERT: A  420 ILE cc_start: 0.7500 (mt) cc_final: 0.7288 (mt)
REVERT: A  423 VAL cc_start: 0.7974 (t) cc_final: 0.7542 (m)
  outliers start: 10
  outliers final: 7
  residues processed: 92
  average time/residue: 0.0995
  time to fit residues: 12.0806
Evaluate side-chains
  93 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  272 CYS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  415 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.153347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.137987 restraints weight = 5508.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.141903 restraints weight = 2975.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.144578 restraints weight = 1844.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          0.4445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3246  Z= 0.284
  Angle     :  0.692   6.302   4437  Z= 0.358
  Chirality :  0.044   0.146    502
  Planarity :  0.005   0.061    529
  Dihedral  : 13.711 158.589    440
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.42 %
    Favored  : 78.98 %
  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:  0.43 (0.42), residues: 384
  helix:  1.07 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -2.52 (0.64), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  94 
 HIS   0.007   0.002   HIS A 364 
 PHE   0.018   0.002   PHE A 266 
 TYR   0.022   0.002   TYR A 126 
 ARG   0.002   0.000   ARG A 429 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 MET cc_start: 0.7991 (mmm) cc_final: 0.7577 (mmm)
REVERT: A   95 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6920 (mt)
REVERT: A  128 TYR cc_start: 0.6897 (m-80) cc_final: 0.6542 (m-80)
REVERT: A  152 THR cc_start: 0.7933 (m) cc_final: 0.7412 (p)
REVERT: A  167 MET cc_start: 0.6824 (mmm) cc_final: 0.6470 (ptp)
REVERT: A  316 ASN cc_start: 0.7252 (m-40) cc_final: 0.6981 (m110)
REVERT: A  384 MET cc_start: 0.6787 (tpp) cc_final: 0.6530 (mpp)
REVERT: A  386 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7302 (tt)
REVERT: A  391 VAL cc_start: 0.8555 (t) cc_final: 0.8296 (p)
REVERT: A  420 ILE cc_start: 0.7629 (mt) cc_final: 0.7409 (mt)
REVERT: A  423 VAL cc_start: 0.8014 (t) cc_final: 0.7575 (m)
  outliers start: 12
  outliers final: 9
  residues processed: 92
  average time/residue: 0.1019
  time to fit residues: 12.2861
Evaluate side-chains
  95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  272 CYS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  415 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 15 optimal weight:    0.0970
   chunk 37 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.153688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.138168 restraints weight = 5598.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.142172 restraints weight = 3000.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.144896 restraints weight = 1835.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.4649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   3246  Z= 0.256
  Angle     :  0.681   6.997   4437  Z= 0.347
  Chirality :  0.042   0.138    502
  Planarity :  0.005   0.054    529
  Dihedral  : 13.867 157.162    440
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 18.02 %
    Favored  : 77.78 %
  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:  0.68 (0.43), residues: 384
  helix:  1.20 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -2.28 (0.67), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  94 
 HIS   0.005   0.001   HIS A 364 
 PHE   0.019   0.002   PHE A 266 
 TYR   0.018   0.002   TYR A 445 
 ARG   0.002   0.000   ARG A 429 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 MET cc_start: 0.7994 (mmm) cc_final: 0.7544 (mmm)
REVERT: A   95 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6886 (mt)
REVERT: A  128 TYR cc_start: 0.6928 (m-80) cc_final: 0.6613 (m-80)
REVERT: A  152 THR cc_start: 0.8063 (m) cc_final: 0.7574 (p)
REVERT: A  167 MET cc_start: 0.6622 (mmm) cc_final: 0.5975 (ptp)
REVERT: A  363 MET cc_start: 0.6686 (mtt) cc_final: 0.6431 (ttm)
REVERT: A  386 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7313 (tt)
REVERT: A  391 VAL cc_start: 0.8542 (t) cc_final: 0.8307 (p)
REVERT: A  420 ILE cc_start: 0.7673 (mt) cc_final: 0.7391 (tp)
REVERT: A  423 VAL cc_start: 0.7989 (t) cc_final: 0.7582 (m)
  outliers start: 14
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0979
  time to fit residues: 12.6768
Evaluate side-chains
  95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  272 CYS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  415 LEU
Chi-restraints excluded: chain A residue  419 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 25 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0770
   chunk 27 optimal weight:    0.2980
   chunk 24 optimal weight:    0.7980
   chunk 11 optimal weight:    0.0570
   chunk 0 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.3056

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.155973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.140855 restraints weight = 5399.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.144869 restraints weight = 2933.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.147460 restraints weight = 1790.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6340
moved from start:          0.4621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   3246  Z= 0.180
  Angle     :  0.643   7.199   4437  Z= 0.319
  Chirality :  0.040   0.129    502
  Planarity :  0.004   0.050    529
  Dihedral  : 13.862 160.063    440
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.72 %
    Favored  : 76.58 %
  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:  1.27 (0.43), residues: 384
  helix:  1.62 (0.30), residues: 298
  sheet:  None (None), residues: 0
  loop : -1.97 (0.68), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  94 
 HIS   0.005   0.001   HIS A 364 
 PHE   0.011   0.001   PHE A 325 
 TYR   0.022   0.002   TYR A 445 
 ARG   0.001   0.000   ARG A 429 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 MET cc_start: 0.7942 (mmm) cc_final: 0.7600 (mmm)
REVERT: A  128 TYR cc_start: 0.6917 (m-80) cc_final: 0.6544 (m-80)
REVERT: A  152 THR cc_start: 0.7982 (m) cc_final: 0.7477 (p)
REVERT: A  386 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7314 (tt)
REVERT: A  391 VAL cc_start: 0.8477 (t) cc_final: 0.8254 (p)
REVERT: A  401 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7623 (mt-10)
REVERT: A  423 VAL cc_start: 0.7947 (t) cc_final: 0.7530 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 96
  average time/residue: 0.1011
  time to fit residues: 12.5839
Evaluate side-chains
  97 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 PHE
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  272 CYS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  415 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 27 optimal weight:    0.0470
   chunk 23 optimal weight:    0.0000
   chunk 8 optimal weight:    0.4980
   chunk 2 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0870
   chunk 32 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.2460

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.157521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.141884 restraints weight = 5404.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.146053 restraints weight = 2943.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.148829 restraints weight = 1794.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6318
moved from start:          0.4694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3246  Z= 0.169
  Angle     :  0.639   7.476   4437  Z= 0.317
  Chirality :  0.039   0.128    502
  Planarity :  0.004   0.039    529
  Dihedral  : 13.477 158.172    440
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.92 %
    Favored  : 75.38 %
  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:  1.51 (0.44), residues: 384
  helix:  1.77 (0.30), residues: 299
  sheet:  None (None), residues: 0
  loop : -1.82 (0.70), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  94 
 HIS   0.007   0.002   HIS A 364 
 PHE   0.012   0.001   PHE A 325 
 TYR   0.021   0.001   TYR A 445 
 ARG   0.001   0.000   ARG A 138 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 TYR cc_start: 0.6911 (m-80) cc_final: 0.6579 (m-80)
REVERT: A  139 VAL cc_start: 0.8450 (t) cc_final: 0.8220 (p)
REVERT: A  152 THR cc_start: 0.7969 (m) cc_final: 0.7463 (p)
REVERT: A  386 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7286 (tt)
REVERT: A  391 VAL cc_start: 0.8475 (t) cc_final: 0.8245 (p)
REVERT: A  423 VAL cc_start: 0.7930 (t) cc_final: 0.7511 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1018
  time to fit residues: 12.8828
Evaluate side-chains
  98 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  129 SER
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  415 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0470
   chunk 22 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.155303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.139972 restraints weight = 5522.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.143924 restraints weight = 3003.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146536 restraints weight = 1845.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6348
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3246  Z= 0.217
  Angle     :  0.680   7.604   4437  Z= 0.340
  Chirality :  0.042   0.132    502
  Planarity :  0.004   0.039    529
  Dihedral  : 13.453 157.397    440
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 22.52 %
    Favored  : 74.77 %
  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:  1.35 (0.44), residues: 384
  helix:  1.60 (0.30), residues: 300
  sheet:  None (None), residues: 0
  loop : -1.70 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  94 
 HIS   0.007   0.002   HIS A 364 
 PHE   0.014   0.001   PHE A 266 
 TYR   0.018   0.002   TYR A 445 
 ARG   0.002   0.000   ARG A 144 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 TYR cc_start: 0.6958 (m-80) cc_final: 0.6641 (m-80)
REVERT: A  152 THR cc_start: 0.7985 (m) cc_final: 0.7477 (p)
REVERT: A  386 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7282 (tt)
REVERT: A  423 VAL cc_start: 0.7985 (t) cc_final: 0.7580 (m)
  outliers start: 9
  outliers final: 7
  residues processed: 94
  average time/residue: 0.1042
  time to fit residues: 12.7742
Evaluate side-chains
  97 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  115 MET
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  195 LYS
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  415 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 9 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.153522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.137946 restraints weight = 5377.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.141864 restraints weight = 2915.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.144472 restraints weight = 1809.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6399
moved from start:          0.5075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3246  Z= 0.283
  Angle     :  0.731   9.596   4437  Z= 0.369
  Chirality :  0.044   0.209    502
  Planarity :  0.004   0.040    529
  Dihedral  : 13.564 154.661    440
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 22.52 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.90 (0.43), residues: 384
  helix:  1.25 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.79 (0.72), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  94 
 HIS   0.007   0.002   HIS A 364 
 PHE   0.021   0.002   PHE A 266 
 TYR   0.020   0.002   TYR A 459 
 ARG   0.004   0.001   ARG A 144 

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ILE cc_start: 0.7968 (tp) cc_final: 0.7759 (tp)
REVERT: A  128 TYR cc_start: 0.7128 (m-80) cc_final: 0.6801 (m-80)
REVERT: A  152 THR cc_start: 0.8145 (m) cc_final: 0.7916 (t)
REVERT: A  301 ILE cc_start: 0.7584 (mm) cc_final: 0.7367 (mt)
REVERT: A  386 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7332 (tt)
REVERT: A  423 VAL cc_start: 0.8014 (t) cc_final: 0.7603 (m)
  outliers start: 8
  outliers final: 6
  residues processed: 93
  average time/residue: 0.1045
  time to fit residues: 12.6748
Evaluate side-chains
  100 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  115 MET
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  407 PHE
Chi-restraints excluded: chain A residue  415 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0570
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.154844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.139050 restraints weight = 5488.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.143075 restraints weight = 2983.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.145836 restraints weight = 1840.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6372
moved from start:          0.5071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3246  Z= 0.228
  Angle     :  0.705   9.297   4437  Z= 0.350
  Chirality :  0.044   0.298    502
  Planarity :  0.004   0.035    529
  Dihedral  : 13.471 155.132    440
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.72 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.43), residues: 384
  helix:  1.41 (0.29), residues: 300
  sheet:  None (None), residues: 0
  loop : -1.72 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  94 
 HIS   0.007   0.002   HIS A 364 
 PHE   0.017   0.002   PHE A 325 
 TYR   0.032   0.002   TYR A 298 
 ARG   0.002   0.000   ARG A 144 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1316.77 seconds
wall clock time: 24 minutes 10.85 seconds (1450.85 seconds total)