Starting phenix.real_space_refine
on Fri Aug 22 13:17:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xv9_38693/08_2025/8xv9_38693.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xv9_38693/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xv9_38693/08_2025/8xv9_38693.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xv9_38693/08_2025/8xv9_38693.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xv9_38693/08_2025/8xv9_38693.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xv9_38693/08_2025/8xv9_38693.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.017
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 0.91, per 1000 atoms: 0.29
  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: 0.19
  Conformation dependent library (CDL) restraints added in 78.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.11
  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: 0.61

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 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:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.700
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.120
-------------------------------------------------------------------------------
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= 0.409
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.001   0.000   ARG A  29 
 TYR   0.041   0.002   TYR A 373 
 PHE   0.017   0.002   PHE A 439 
 TRP   0.021   0.002   TRP A  59 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00808 ( 3246)
  covalent geometry    : angle       0.93620 ( 4437)
  hydrogen bonds       : bond        0.10817 (  220)
  hydrogen bonds       : angle       5.77522 (  654)

*********************** 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  : 0.114 
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: 0.7438 (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: 0.6563 (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: 0.7466 (mt)
REVERT: A  423 VAL cc_start: 0.7605 (t) cc_final: 0.7063 (m)
REVERT: A  440 LEU cc_start: 0.7185 (tp) cc_final: 0.6566 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0530
  time to fit residues: 6.7393
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  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0970
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.4378

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.158312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.143077 restraints weight = 5650.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.147176 restraints weight = 2997.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.149721 restraints weight = 1824.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.151524 restraints weight = 1237.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.152788 restraints weight = 901.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6232
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      :  0.003   0.032   3246  Z= 0.157
  Angle     :  0.633   6.172   4437  Z= 0.325
  Chirality :  0.042   0.156    502
  Planarity :  0.005   0.040    529
  Dihedral  : 13.542 154.061    440
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 11.11 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.41), residues: 384
  helix:  0.53 (0.29), residues: 284
  sheet:  None (None), residues: 0
  loop : -2.86 (0.58), residues: 100

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 138 
 TYR   0.031   0.002   TYR A 126 
 PHE   0.024   0.002   PHE A 439 
 TRP   0.013   0.002   TRP A  94 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3246)
  covalent geometry    : angle       0.63271 ( 4437)
  hydrogen bonds       : bond        0.04462 (  220)
  hydrogen bonds       : angle       4.00553 (  654)

*********************** 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
  94 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7536 (tp)
REVERT: A   86 GLN cc_start: 0.8597 (tt0) cc_final: 0.8260 (tt0)
REVERT: A  152 THR cc_start: 0.7766 (m) cc_final: 0.7090 (p)
REVERT: A  155 SER cc_start: 0.8691 (m) cc_final: 0.8489 (m)
REVERT: A  156 VAL cc_start: 0.7949 (t) cc_final: 0.7678 (p)
REVERT: A  167 MET cc_start: 0.6083 (mmm) cc_final: 0.5640 (ptp)
REVERT: A  363 MET cc_start: 0.6619 (tpt) cc_final: 0.5952 (ttm)
REVERT: A  369 ILE cc_start: 0.7833 (tp) cc_final: 0.7572 (tp)
REVERT: A  386 LEU cc_start: 0.7904 (mt) cc_final: 0.7530 (mm)
REVERT: A  389 ILE cc_start: 0.8103 (mt) cc_final: 0.7737 (mt)
REVERT: A  423 VAL cc_start: 0.7626 (t) cc_final: 0.7169 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 92
  average time/residue: 0.0435
  time to fit residues: 5.0787
Evaluate side-chains
  94 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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 21 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0060
   chunk 28 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A 364 HIS
** 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 = 0.3989 r_free = 0.3989 target = 0.154688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.139268 restraints weight = 5517.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.143260 restraints weight = 2964.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.146009 restraints weight = 1829.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.147563 restraints weight = 1233.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.148963 restraints weight = 920.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6318
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3246  Z= 0.197
  Angle     :  0.645   5.864   4437  Z= 0.339
  Chirality :  0.043   0.159    502
  Planarity :  0.005   0.043    529
  Dihedral  : 13.919 158.688    440
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 13.51 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.42), residues: 384
  helix:  1.00 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -2.74 (0.60), residues: 95

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 138 
 TYR   0.028   0.002   TYR A 445 
 PHE   0.017   0.002   PHE A 266 
 TRP   0.016   0.002   TRP A  12 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 3246)
  covalent geometry    : angle       0.64535 ( 4437)
  hydrogen bonds       : bond        0.04771 (  220)
  hydrogen bonds       : angle       3.88668 (  654)

*********************** 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
  99 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 TYR cc_start: 0.6707 (m-80) cc_final: 0.6335 (m-80)
REVERT: A  152 THR cc_start: 0.7896 (m) cc_final: 0.7201 (p)
REVERT: A  156 VAL cc_start: 0.7967 (t) cc_final: 0.7714 (p)
REVERT: A  386 LEU cc_start: 0.7866 (mt) cc_final: 0.7469 (tt)
REVERT: A  423 VAL cc_start: 0.7837 (t) cc_final: 0.7436 (m)
  outliers start: 9
  outliers final: 3
  residues processed: 93
  average time/residue: 0.0493
  time to fit residues: 5.9651
Evaluate side-chains
  88 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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 37 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0050
   chunk 14 optimal weight:    0.3980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.4794

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.155765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.140285 restraints weight = 5460.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.144447 restraints weight = 2998.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.147144 restraints weight = 1829.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.148968 restraints weight = 1230.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.150107 restraints weight = 885.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6306
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   3246  Z= 0.159
  Angle     :  0.621   6.281   4437  Z= 0.321
  Chirality :  0.041   0.140    502
  Planarity :  0.005   0.067    529
  Dihedral  : 13.870 157.802    440
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.42 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.42), residues: 384
  helix:  1.23 (0.29), residues: 294
  sheet:  None (None), residues: 0
  loop : -2.59 (0.62), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 138 
 TYR   0.027   0.002   TYR A 126 
 PHE   0.015   0.002   PHE A 439 
 TRP   0.011   0.001   TRP A  12 
 HIS   0.000   0.000   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3246)
  covalent geometry    : angle       0.62068 ( 4437)
  hydrogen bonds       : bond        0.04425 (  220)
  hydrogen bonds       : angle       3.81445 (  654)

*********************** 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: 9
    poor density    : 89
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 MET cc_start: 0.7972 (mmp) cc_final: 0.7501 (mpp)
REVERT: A   77 VAL cc_start: 0.8031 (m) cc_final: 0.7808 (t)
REVERT: A  128 TYR cc_start: 0.6750 (m-80) cc_final: 0.6382 (m-80)
REVERT: A  152 THR cc_start: 0.7904 (m) cc_final: 0.7258 (p)
REVERT: A  156 VAL cc_start: 0.7961 (t) cc_final: 0.7667 (p)
REVERT: A  366 THR cc_start: 0.8270 (p) cc_final: 0.8063 (p)
REVERT: A  386 LEU cc_start: 0.7846 (mt) cc_final: 0.7462 (tt)
REVERT: A  420 ILE cc_start: 0.7507 (mt) cc_final: 0.7289 (mt)
REVERT: A  421 MET cc_start: 0.7522 (ttm) cc_final: 0.7129 (ttp)
REVERT: A  423 VAL cc_start: 0.7916 (t) cc_final: 0.7446 (m)
REVERT: A  440 LEU cc_start: 0.7202 (tp) cc_final: 0.6754 (mt)
  outliers start: 9
  outliers final: 7
  residues processed: 93
  average time/residue: 0.0443
  time to fit residues: 5.5358
Evaluate side-chains
  96 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
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  129 SER
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 25 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 6 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   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 = 0.3977 r_free = 0.3977 target = 0.153256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.137915 restraints weight = 5489.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.141937 restraints weight = 2981.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.144612 restraints weight = 1830.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.146346 restraints weight = 1228.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.147551 restraints weight = 892.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6343
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3246  Z= 0.207
  Angle     :  0.672   6.408   4437  Z= 0.348
  Chirality :  0.043   0.158    502
  Planarity :  0.005   0.062    529
  Dihedral  : 13.559 158.926    440
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.72 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.59 (0.42), residues: 384
  helix:  1.21 (0.29), residues: 296
  sheet:  None (None), residues: 0
  loop : -2.47 (0.63), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 138 
 TYR   0.023   0.002   TYR A 126 
 PHE   0.018   0.002   PHE A 266 
 TRP   0.011   0.002   TRP A  94 
 HIS   0.002   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 3246)
  covalent geometry    : angle       0.67162 ( 4437)
  hydrogen bonds       : bond        0.04898 (  220)
  hydrogen bonds       : angle       3.94503 (  654)

*********************** 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
  98 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 MET cc_start: 0.8061 (mmp) cc_final: 0.7539 (mpp)
REVERT: A   36 ILE cc_start: 0.7879 (tp) cc_final: 0.7672 (tp)
REVERT: A   77 VAL cc_start: 0.8041 (m) cc_final: 0.7840 (t)
REVERT: A  128 TYR cc_start: 0.6861 (m-80) cc_final: 0.6520 (m-80)
REVERT: A  152 THR cc_start: 0.7923 (m) cc_final: 0.7375 (p)
REVERT: A  167 MET cc_start: 0.6705 (mmm) cc_final: 0.6424 (ptp)
REVERT: A  316 ASN cc_start: 0.7213 (m-40) cc_final: 0.6936 (m110)
REVERT: A  386 LEU cc_start: 0.7864 (mt) cc_final: 0.7419 (tt)
REVERT: A  420 ILE cc_start: 0.7635 (mt) cc_final: 0.7408 (mt)
REVERT: A  423 VAL cc_start: 0.8009 (t) cc_final: 0.7595 (m)
  outliers start: 8
  outliers final: 7
  residues processed: 94
  average time/residue: 0.0439
  time to fit residues: 5.5910
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  : 0.113 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    0.2980
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.154480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.139295 restraints weight = 5446.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.143331 restraints weight = 2969.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.145953 restraints weight = 1813.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.147589 restraints weight = 1221.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.148851 restraints weight = 897.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6332
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3246  Z= 0.181
  Angle     :  0.679   7.237   4437  Z= 0.342
  Chirality :  0.042   0.143    502
  Planarity :  0.005   0.055    529
  Dihedral  : 13.718 157.408    440
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.43), residues: 384
  helix:  1.22 (0.29), residues: 299
  sheet:  None (None), residues: 0
  loop : -2.18 (0.66), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 138 
 TYR   0.026   0.002   TYR A 376 
 PHE   0.018   0.002   PHE A 266 
 TRP   0.011   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3246)
  covalent geometry    : angle       0.67946 ( 4437)
  hydrogen bonds       : bond        0.04743 (  220)
  hydrogen bonds       : angle       3.98625 (  654)

*********************** 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: 10
    poor density    : 94
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 VAL cc_start: 0.7966 (m) cc_final: 0.7763 (t)
REVERT: A   86 GLN cc_start: 0.8637 (tt0) cc_final: 0.8404 (tt0)
REVERT: A  128 TYR cc_start: 0.6861 (m-80) cc_final: 0.6582 (m-80)
REVERT: A  139 VAL cc_start: 0.8424 (t) cc_final: 0.8204 (p)
REVERT: A  152 THR cc_start: 0.7929 (m) cc_final: 0.7444 (p)
REVERT: A  167 MET cc_start: 0.6860 (mmm) cc_final: 0.6376 (ptp)
REVERT: A  298 TYR cc_start: 0.6714 (m-10) cc_final: 0.5759 (m-10)
REVERT: A  363 MET cc_start: 0.6725 (mtt) cc_final: 0.6510 (ttm)
REVERT: A  386 LEU cc_start: 0.7864 (mt) cc_final: 0.7424 (tt)
REVERT: A  391 VAL cc_start: 0.8542 (t) cc_final: 0.8288 (p)
REVERT: A  423 VAL cc_start: 0.8023 (t) cc_final: 0.7610 (m)
  outliers start: 10
  outliers final: 8
  residues processed: 99
  average time/residue: 0.0436
  time to fit residues: 5.8507
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  : 0.117 
-------------------------------------------------------------------------------
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  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  407 PHE
Chi-restraints excluded: chain A residue  415 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   chunk 2 optimal weight:    0.2980
   chunk 7 optimal weight:    0.4980
   chunk 34 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.154773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.139363 restraints weight = 5528.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.143418 restraints weight = 2990.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.146120 restraints weight = 1827.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.147810 restraints weight = 1225.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.149033 restraints weight = 892.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6322
moved from start:          0.4564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3246  Z= 0.164
  Angle     :  0.670   6.890   4437  Z= 0.335
  Chirality :  0.041   0.134    502
  Planarity :  0.004   0.054    529
  Dihedral  : 13.716 155.527    440
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.82 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.43), residues: 384
  helix:  1.43 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -1.97 (0.70), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 138 
 TYR   0.026   0.002   TYR A 376 
 PHE   0.014   0.001   PHE A 266 
 TRP   0.011   0.001   TRP A  94 
 HIS   0.006   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3246)
  covalent geometry    : angle       0.66987 ( 4437)
  hydrogen bonds       : bond        0.04619 (  220)
  hydrogen bonds       : angle       3.87131 (  654)

*********************** 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
  102 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  128 TYR cc_start: 0.6863 (m-80) cc_final: 0.6575 (m-80)
REVERT: A  139 VAL cc_start: 0.8409 (t) cc_final: 0.8199 (p)
REVERT: A  152 THR cc_start: 0.7969 (m) cc_final: 0.7479 (p)
REVERT: A  298 TYR cc_start: 0.6725 (m-10) cc_final: 0.5861 (m-10)
REVERT: A  363 MET cc_start: 0.6678 (mtt) cc_final: 0.6369 (ttm)
REVERT: A  386 LEU cc_start: 0.7900 (mt) cc_final: 0.7471 (tt)
REVERT: A  391 VAL cc_start: 0.8551 (t) cc_final: 0.8301 (p)
REVERT: A  423 VAL cc_start: 0.7956 (t) cc_final: 0.7578 (m)
  outliers start: 10
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0425
  time to fit residues: 5.5770
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  : 0.115 
-------------------------------------------------------------------------------
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  319 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0670
   chunk 19 optimal weight:    0.0970
   chunk 15 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.4116

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN
** A 364 HIS ** 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 = 0.4004 r_free = 0.4004 target = 0.155573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.139676 restraints weight = 5482.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.143964 restraints weight = 2972.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.146690 restraints weight = 1816.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.148594 restraints weight = 1225.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.149807 restraints weight = 879.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6304
moved from start:          0.4632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3246  Z= 0.152
  Angle     :  0.680   6.956   4437  Z= 0.341
  Chirality :  0.041   0.148    502
  Planarity :  0.004   0.043    529
  Dihedral  : 13.529 152.879    440
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 20.72 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.43), residues: 384
  helix:  1.60 (0.30), residues: 298
  sheet:  None (None), residues: 0
  loop : -1.97 (0.68), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 138 
 TYR   0.023   0.002   TYR A 376 
 PHE   0.013   0.001   PHE A 266 
 TRP   0.010   0.001   TRP A  94 
 HIS   0.009   0.002   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3246)
  covalent geometry    : angle       0.67961 ( 4437)
  hydrogen bonds       : bond        0.04528 (  220)
  hydrogen bonds       : angle       3.81343 (  654)

*********************** 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
  102 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.069 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 TYR cc_start: 0.6836 (m-80) cc_final: 0.6602 (m-80)
REVERT: A  139 VAL cc_start: 0.8397 (t) cc_final: 0.8186 (p)
REVERT: A  152 THR cc_start: 0.7972 (m) cc_final: 0.7482 (p)
REVERT: A  298 TYR cc_start: 0.6660 (m-10) cc_final: 0.5817 (m-10)
REVERT: A  363 MET cc_start: 0.6643 (mtt) cc_final: 0.6434 (ttm)
REVERT: A  366 THR cc_start: 0.8268 (p) cc_final: 0.8058 (p)
REVERT: A  386 LEU cc_start: 0.7835 (mt) cc_final: 0.7407 (tt)
REVERT: A  423 VAL cc_start: 0.7967 (t) cc_final: 0.7564 (m)
  outliers start: 10
  outliers final: 9
  residues processed: 95
  average time/residue: 0.0453
  time to fit residues: 5.7497
Evaluate side-chains
  97 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
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  129 SER
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  272 CYS
Chi-restraints excluded: chain A residue  319 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 22 optimal weight:    0.2980
   chunk 10 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   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 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.154515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.138734 restraints weight = 5517.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.142940 restraints weight = 2974.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145709 restraints weight = 1821.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.147478 restraints weight = 1218.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.148775 restraints weight = 884.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6332
moved from start:          0.4855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3246  Z= 0.181
  Angle     :  0.710   7.306   4437  Z= 0.357
  Chirality :  0.042   0.144    502
  Planarity :  0.005   0.042    529
  Dihedral  : 13.450 151.270    440
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.62 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.43), residues: 384
  helix:  1.45 (0.29), residues: 301
  sheet:  None (None), residues: 0
  loop : -1.93 (0.70), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.026   0.002   TYR A 376 
 PHE   0.016   0.002   PHE A 266 
 TRP   0.012   0.001   TRP A  94 
 HIS   0.010   0.002   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 3246)
  covalent geometry    : angle       0.70999 ( 4437)
  hydrogen bonds       : bond        0.04800 (  220)
  hydrogen bonds       : angle       3.92708 (  654)

*********************** 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
  99 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 TYR cc_start: 0.6920 (m-80) cc_final: 0.6686 (m-80)
REVERT: A  139 VAL cc_start: 0.8402 (t) cc_final: 0.8190 (p)
REVERT: A  152 THR cc_start: 0.8121 (m) cc_final: 0.7631 (p)
REVERT: A  298 TYR cc_start: 0.6780 (m-10) cc_final: 0.5957 (m-10)
REVERT: A  386 LEU cc_start: 0.7730 (mt) cc_final: 0.7323 (tt)
REVERT: A  423 VAL cc_start: 0.8010 (t) cc_final: 0.7611 (m)
  outliers start: 9
  outliers final: 8
  residues processed: 93
  average time/residue: 0.0416
  time to fit residues: 5.1637
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  : 0.082 
-------------------------------------------------------------------------------
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  319 VAL
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 27 optimal weight:    0.0050
   chunk 36 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0000
   chunk 13 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    0.1980
   chunk 24 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.3198

-------------------------------------------------------------------------------
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 = 0.4012 r_free = 0.4012 target = 0.156226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.140439 restraints weight = 5400.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.144666 restraints weight = 2922.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.147430 restraints weight = 1785.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.149215 restraints weight = 1198.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.150571 restraints weight = 874.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6284
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3246  Z= 0.140
  Angle     :  0.680   7.373   4437  Z= 0.338
  Chirality :  0.041   0.136    502
  Planarity :  0.004   0.041    529
  Dihedral  : 13.317 148.584    440
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.42 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.44), residues: 384
  helix:  1.69 (0.30), residues: 300
  sheet:  None (None), residues: 0
  loop : -1.74 (0.70), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 138 
 TYR   0.022   0.002   TYR A 376 
 PHE   0.020   0.001   PHE A 198 
 TRP   0.009   0.001   TRP A  94 
 HIS   0.011   0.003   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3246)
  covalent geometry    : angle       0.68001 ( 4437)
  hydrogen bonds       : bond        0.04454 (  220)
  hydrogen bonds       : angle       3.82763 (  654)

********************** 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
  96 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 TYR cc_start: 0.6895 (m-80) cc_final: 0.6677 (m-80)
REVERT: A  139 VAL cc_start: 0.8366 (t) cc_final: 0.8158 (p)
REVERT: A  152 THR cc_start: 0.7998 (m) cc_final: 0.7516 (p)
REVERT: A  386 LEU cc_start: 0.7715 (mt) cc_final: 0.7307 (tt)
REVERT: A  423 VAL cc_start: 0.7974 (t) cc_final: 0.7565 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 93
  average time/residue: 0.0424
  time to fit residues: 5.3345
Evaluate side-chains
  94 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
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  347 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 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   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 316 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.154647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.138805 restraints weight = 5433.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.142938 restraints weight = 2953.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.145709 restraints weight = 1813.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.147519 restraints weight = 1214.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.148760 restraints weight = 878.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6330
moved from start:          0.4982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3246  Z= 0.184
  Angle     :  0.716   8.290   4437  Z= 0.360
  Chirality :  0.043   0.139    502
  Planarity :  0.004   0.040    529
  Dihedral  : 13.377 149.009    440
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 24.02 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.44), residues: 384
  helix:  1.55 (0.30), residues: 299
  sheet:  None (None), residues: 0
  loop : -1.80 (0.70), residues: 85

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  78 
 TYR   0.024   0.002   TYR A 376 
 PHE   0.017   0.002   PHE A 266 
 TRP   0.011   0.001   TRP A  94 
 HIS   0.010   0.003   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 3246)
  covalent geometry    : angle       0.71609 ( 4437)
  hydrogen bonds       : bond        0.04765 (  220)
  hydrogen bonds       : angle       3.93938 (  654)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 757.61 seconds
wall clock time: 13 minutes 50.48 seconds (830.48 seconds total)