Starting phenix.real_space_refine
on Wed Sep 17 03:24:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xv5_38692/09_2025/8xv5_38692.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xv5_38692/09_2025/8xv5_38692.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xv5_38692/09_2025/8xv5_38692.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xv5_38692/09_2025/8xv5_38692.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xv5_38692/09_2025/8xv5_38692.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xv5_38692/09_2025/8xv5_38692.cif"
  }
  resolution = 3.7
  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=   0.016
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      16      5.16       5
     C    2108      2.51       5
     N     468      2.21       5
     O     530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3122
  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: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'PXM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.04, per 1000 atoms: 0.33
  Number of scatterers: 3122
  At special positions: 0
  Unit cell: (70.72, 61.36, 79.04, 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      16     16.00
     O     530      8.00
     N     468      7.00
     C    2108      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: 0.29
  Conformation dependent library (CDL) restraints added in 119.9 milliseconds
  
  Enol-peptide restraints added in 953.7 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:
      19 helices and 0 sheets defined
      82.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 27
    Processing helix  chain 'A' and resid 32 through 34
      No H-bonds generated for 'chain 'A' and resid 32 through 34'
    Processing helix  chain 'A' and resid 35 through 40
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 56 through 65
      removed outlier: 4.118A  pdb=" N   THR A  60 " --> pdb=" O   PHE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 75
      removed outlier: 3.618A  pdb=" N   VAL A  72 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 99
      removed outlier: 3.716A  pdb=" N   ILE A  83 " --> pdb=" O   TYR A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 125
      removed outlier: 3.637A  pdb=" N   MET A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLN A 107 " --> pdb=" O   VAL A 103 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   VAL A 108 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   VAL A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ALA A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 131
      removed outlier: 4.267A  pdb=" N   VAL A 130 " --> pdb=" O   TYR A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 163
      removed outlier: 3.578A  pdb=" N   SER A 140 " --> pdb=" O   TYR A 136 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   SER A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ALA A 158 " --> pdb=" O   GLY A 154 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 161 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 189
      removed outlier: 4.002A  pdb=" N   PHE A 189 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 273
    Processing helix  chain 'A' and resid 276 through 307
      removed outlier: 5.490A  pdb=" N   GLN A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
      removed outlier: 5.057A  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 340 through 345
    Processing helix  chain 'A' and resid 347 through 366
    Processing helix  chain 'A' and resid 368 through 395
      removed outlier: 3.625A  pdb=" N   CYS A 372 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 425
      removed outlier: 3.536A  pdb=" N   ALA A 404 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 459
      removed outlier: 3.830A  pdb=" N   PHE A 439 " --> pdb=" O   VAL A 435 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   LEU A 440 " --> pdb=" O   SER A 436 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    672 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: 0.47

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 884
        1.34 -     1.46: 790
        1.46 -     1.58: 1516
        1.58 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 3218
  Sorted by residual:
  bond pdb=" C3  PXM A 501 "
       pdb=" O3  PXM A 501 "
    ideal  model  delta    sigma   weight residual
    1.340  1.397 -0.057 2.00e-02 2.50e+03 8.09e+00
  bond pdb=" C   PHE A  56 "
       pdb=" N   PRO A  57 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.018 1.19e-02 7.06e+03 2.36e+00
  bond pdb=" C2  PXM A 501 "
       pdb=" C2A PXM A 501 "
    ideal  model  delta    sigma   weight residual
    1.498  1.528 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" CB  PRO A  57 "
       pdb=" CG  PRO A  57 "
    ideal  model  delta    sigma   weight residual
    1.492  1.425  0.067 5.00e-02 4.00e+02 1.78e+00
  bond pdb=" CA  PHE A  56 "
       pdb=" C   PHE A  56 "
    ideal  model  delta    sigma   weight residual
    1.522  1.535 -0.014 1.26e-02 6.30e+03 1.15e+00
  ... (remaining 3213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 4205
        1.94 -     3.88: 151
        3.88 -     5.82: 29
        5.82 -     7.76: 8
        7.76 -     9.70: 3
  Bond angle restraints: 4396
  Sorted by residual:
  angle pdb=" CA  ILE A  36 "
        pdb=" C   ILE A  36 "
        pdb=" N   PRO A  37 "
      ideal   model   delta    sigma   weight residual
     118.88  123.91   -5.03 1.54e+00 4.22e-01 1.07e+01
  angle pdb=" CG1 ILE A  36 "
        pdb=" CB  ILE A  36 "
        pdb=" CG2 ILE A  36 "
      ideal   model   delta    sigma   weight residual
     110.70  101.83    8.87 3.00e+00 1.11e-01 8.75e+00
  angle pdb=" N   PHE A  56 "
        pdb=" CA  PHE A  56 "
        pdb=" C   PHE A  56 "
      ideal   model   delta    sigma   weight residual
     113.16  117.22   -4.06 1.42e+00 4.96e-01 8.16e+00
  angle pdb=" CA  LEU A 415 "
        pdb=" CB  LEU A 415 "
        pdb=" CG  LEU A 415 "
      ideal   model   delta    sigma   weight residual
     116.30  106.60    9.70 3.50e+00 8.16e-02 7.67e+00
  angle pdb=" CA  PRO A  37 "
        pdb=" N   PRO A  37 "
        pdb=" CD  PRO A  37 "
      ideal   model   delta    sigma   weight residual
     112.00  108.19    3.81 1.40e+00 5.10e-01 7.42e+00
  ... (remaining 4391 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.59: 1742
       16.59 -    33.17: 61
       33.17 -    49.76: 15
       49.76 -    66.35: 0
       66.35 -    82.93: 1
  Dihedral angle restraints: 1819
    sinusoidal: 667
      harmonic: 1152
  Sorted by residual:
  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 -157.58  -22.42     0      5.00e+00 4.00e-02 2.01e+01
  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  158.39   21.61     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  TYR A 142 "
           pdb=" C   TYR A 142 "
           pdb=" N   CYS A 143 "
           pdb=" CA  CYS A 143 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.22  -19.78     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 1816 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 297
       0.041 -    0.081: 150
       0.081 -    0.122: 40
       0.122 -    0.162: 11
       0.162 -    0.203: 4
  Chirality restraints: 502
  Sorted by residual:
  chirality pdb=" CA  TRP A  94 "
            pdb=" N   TRP A  94 "
            pdb=" C   TRP A  94 "
            pdb=" CB  TRP A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  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    2.31    0.20 2.00e-01 2.50e+01 9.87e-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    2.33    0.18 2.00e-01 2.50e+01 8.51e-01
  ... (remaining 499 not shown)

  Planarity restraints: 527
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  63 "    0.014 2.00e-02 2.50e+03   1.94e-02 7.56e+00
        pdb=" CG  TYR A  63 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  63 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  63 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  63 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  63 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A  63 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A  61 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   TYR A  61 "    0.043 2.00e-02 2.50e+03
        pdb=" O   TYR A  61 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   SER A  62 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 373 "    0.016 2.00e-02 2.50e+03   1.54e-02 4.74e+00
        pdb=" CG  TYR A 373 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 373 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 373 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 373 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 373 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 373 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 373 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 524 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 898
        2.80 -     3.33: 2953
        3.33 -     3.85: 5271
        3.85 -     4.38: 5926
        4.38 -     4.90: 10238
  Nonbonded interactions: 25286
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 144 "
            pdb=" OG1 THR A 147 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   LYS A 270 "
            pdb=" OG  SER A 274 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OE1 GLN A 294 "
            pdb=" OH  TYR A 442 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OH  TYR A 151 "
            pdb=" OE2 GLU A 320 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" OH  TYR A  61 "
            pdb=" OD2 ASP A 427 "
     model   vdw
     2.330 3.040
  ... (remaining 25281 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:             1.520
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.200
  Find NCS groups from input model:        0.010
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   3218  Z= 0.246
  Angle     :  0.901   9.695   4396  Z= 0.482
  Chirality :  0.053   0.203    502
  Planarity :  0.008   0.054    527
  Dihedral  :  9.695  82.934   1083
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.67 (0.33), residues: 384
  helix: -2.04 (0.22), residues: 295
  sheet:  None (None), residues: 0
  loop : -3.11 (0.60), residues: 89

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  29 
 TYR   0.046   0.003   TYR A  63 
 PHE   0.030   0.002   PHE A 439 
 TRP   0.024   0.003   TRP A  94 
 HIS   0.003   0.001   HIS A 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 ( 3218)
  covalent geometry    : angle       0.90128 ( 4396)
  hydrogen bonds       : bond        0.14025 (  224)
  hydrogen bonds       : angle       7.09459 (  672)

*********************** 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
  125 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A   48 SER cc_start: 0.7409 (m) cc_final: 0.7182 (t)
REVERT: A   52 THR cc_start: 0.7688 (m) cc_final: 0.7060 (p)
REVERT: A   61 TYR cc_start: 0.6986 (m-10) cc_final: 0.6722 (m-10)
REVERT: A   77 VAL cc_start: 0.7409 (m) cc_final: 0.7055 (p)
REVERT: A  103 VAL cc_start: 0.8060 (m) cc_final: 0.7683 (t)
REVERT: A  113 TYR cc_start: 0.7317 (t80) cc_final: 0.6984 (t80)
REVERT: A  127 ILE cc_start: 0.8370 (mt) cc_final: 0.8159 (mt)
REVERT: A  148 LEU cc_start: 0.8171 (mt) cc_final: 0.7943 (mm)
REVERT: A  197 MET cc_start: 0.7178 (ttp) cc_final: 0.6370 (ttp)
REVERT: A  198 PHE cc_start: 0.6933 (m-80) cc_final: 0.6537 (m-80)
REVERT: A  319 VAL cc_start: 0.7907 (t) cc_final: 0.7576 (t)
REVERT: A  325 PHE cc_start: 0.7773 (t80) cc_final: 0.7543 (t80)
REVERT: A  362 LEU cc_start: 0.7408 (tp) cc_final: 0.7182 (tp)
REVERT: A  373 TYR cc_start: 0.7509 (m-80) cc_final: 0.7296 (m-10)
REVERT: A  399 ASN cc_start: 0.6986 (m-40) cc_final: 0.6662 (m-40)
REVERT: A  455 MET cc_start: 0.5552 (mmm) cc_final: 0.5269 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0430
  time to fit residues: 7.1763
Evaluate side-chains
  101 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.1980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A 310 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.122694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.109528 restraints weight = 5403.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112770 restraints weight = 2564.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.114744 restraints weight = 1462.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.116048 restraints weight = 970.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.116765 restraints weight = 719.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3218  Z= 0.163
  Angle     :  0.597   5.896   4396  Z= 0.313
  Chirality :  0.040   0.156    502
  Planarity :  0.005   0.044    527
  Dihedral  :  5.983  71.156    426
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  :  7.21 %
    Favored  : 89.19 %
  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: -0.85 (0.41), residues: 384
  helix: -0.05 (0.28), residues: 306
  sheet:  None (None), residues: 0
  loop : -2.25 (0.72), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  29 
 TYR   0.018   0.002   TYR A 373 
 PHE   0.013   0.001   PHE A  99 
 TRP   0.020   0.001   TRP A  94 
 HIS   0.004   0.002   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3218)
  covalent geometry    : angle       0.59658 ( 4396)
  hydrogen bonds       : bond        0.04908 (  224)
  hydrogen bonds       : angle       4.51501 (  672)

*********************** 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
  123 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7612 (tmm) cc_final: 0.7193 (tmm)
REVERT: A   64 LEU cc_start: 0.8226 (tp) cc_final: 0.7919 (tt)
REVERT: A   89 SER cc_start: 0.8079 (m) cc_final: 0.7726 (p)
REVERT: A  113 TYR cc_start: 0.7261 (t80) cc_final: 0.6994 (t80)
REVERT: A  127 ILE cc_start: 0.8314 (mt) cc_final: 0.8077 (mm)
REVERT: A  129 SER cc_start: 0.7547 (p) cc_final: 0.7291 (p)
REVERT: A  133 PRO cc_start: 0.7826 (Cg_exo) cc_final: 0.6851 (Cg_endo)
REVERT: A  145 SER cc_start: 0.8478 (m) cc_final: 0.8124 (t)
REVERT: A  161 LEU cc_start: 0.7923 (tp) cc_final: 0.7576 (tt)
REVERT: A  167 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6887 (tmm)
REVERT: A  197 MET cc_start: 0.7037 (ttp) cc_final: 0.6641 (ttp)
REVERT: A  198 PHE cc_start: 0.6776 (m-80) cc_final: 0.6539 (m-80)
REVERT: A  363 MET cc_start: 0.7234 (mtt) cc_final: 0.6999 (mtp)
REVERT: A  389 ILE cc_start: 0.8436 (mt) cc_final: 0.8086 (mm)
REVERT: A  399 ASN cc_start: 0.6852 (m-40) cc_final: 0.6553 (m-40)
REVERT: A  420 ILE cc_start: 0.8194 (mt) cc_final: 0.7910 (mm)
REVERT: A  455 MET cc_start: 0.5705 (mmm) cc_final: 0.5301 (mmm)
  outliers start: 12
  outliers final: 6
  residues processed: 118
  average time/residue: 0.0420
  time to fit residues: 6.5779
Evaluate side-chains
  110 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  387 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 310 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.119949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106425 restraints weight = 5279.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.109537 restraints weight = 2531.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.111658 restraints weight = 1462.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.112937 restraints weight = 967.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113821 restraints weight = 725.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   3218  Z= 0.218
  Angle     :  0.630   6.152   4396  Z= 0.331
  Chirality :  0.043   0.161    502
  Planarity :  0.004   0.036    527
  Dihedral  :  5.906  68.759    426
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  :  9.61 %
    Favored  : 85.59 %
  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: -0.07 (0.42), residues: 384
  helix:  0.50 (0.29), residues: 308
  sheet:  None (None), residues: 0
  loop : -2.02 (0.73), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 138 
 TYR   0.029   0.002   TYR A 136 
 PHE   0.018   0.001   PHE A  99 
 TRP   0.018   0.002   TRP A  94 
 HIS   0.006   0.002   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 3218)
  covalent geometry    : angle       0.62955 ( 4396)
  hydrogen bonds       : bond        0.05031 (  224)
  hydrogen bonds       : angle       4.41639 (  672)

*********************** 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
  116 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7616 (tmm) cc_final: 0.7372 (tmm)
REVERT: A   64 LEU cc_start: 0.8266 (tp) cc_final: 0.8058 (tt)
REVERT: A   89 SER cc_start: 0.8119 (m) cc_final: 0.7755 (p)
REVERT: A  113 TYR cc_start: 0.7293 (t80) cc_final: 0.7068 (t80)
REVERT: A  124 TYR cc_start: 0.7121 (m-80) cc_final: 0.6442 (m-80)
REVERT: A  127 ILE cc_start: 0.8348 (mt) cc_final: 0.8119 (mm)
REVERT: A  129 SER cc_start: 0.7609 (p) cc_final: 0.7386 (p)
REVERT: A  145 SER cc_start: 0.8453 (m) cc_final: 0.8070 (t)
REVERT: A  161 LEU cc_start: 0.8087 (tp) cc_final: 0.7691 (tt)
REVERT: A  167 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6818 (tmm)
REVERT: A  197 MET cc_start: 0.7046 (ttp) cc_final: 0.6718 (ttp)
REVERT: A  198 PHE cc_start: 0.6769 (m-80) cc_final: 0.6520 (m-80)
REVERT: A  363 MET cc_start: 0.7241 (mtt) cc_final: 0.7037 (mtp)
REVERT: A  389 ILE cc_start: 0.8556 (mt) cc_final: 0.8142 (mm)
REVERT: A  399 ASN cc_start: 0.6885 (m-40) cc_final: 0.6577 (m-40)
REVERT: A  420 ILE cc_start: 0.8309 (mt) cc_final: 0.7971 (mm)
REVERT: A  455 MET cc_start: 0.5978 (mmm) cc_final: 0.5535 (mmm)
  outliers start: 16
  outliers final: 8
  residues processed: 109
  average time/residue: 0.0417
  time to fit residues: 6.0452
Evaluate side-chains
  109 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  387 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0970
   chunk 27 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0470
   chunk 35 optimal weight:    0.0870
   chunk 3 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.2454

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 310 GLN
A 393 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.122369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.108676 restraints weight = 5288.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.111827 restraints weight = 2534.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.113915 restraints weight = 1473.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.115091 restraints weight = 986.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.116051 restraints weight = 755.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3218  Z= 0.123
  Angle     :  0.549   6.051   4396  Z= 0.283
  Chirality :  0.039   0.136    502
  Planarity :  0.004   0.032    527
  Dihedral  :  5.780  70.385    426
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 11.71 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.64 (0.42), residues: 384
  helix:  1.05 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -2.02 (0.71), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 429 
 TYR   0.021   0.001   TYR A 373 
 PHE   0.009   0.001   PHE A 439 
 TRP   0.018   0.001   TRP A  94 
 HIS   0.004   0.002   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3218)
  covalent geometry    : angle       0.54943 ( 4396)
  hydrogen bonds       : bond        0.04302 (  224)
  hydrogen bonds       : angle       4.07278 (  672)

*********************** 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
  116 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7635 (tmm) cc_final: 0.7278 (tmm)
REVERT: A   79 TYR cc_start: 0.6971 (m-80) cc_final: 0.6755 (m-80)
REVERT: A   89 SER cc_start: 0.7996 (m) cc_final: 0.7672 (p)
REVERT: A  113 TYR cc_start: 0.7225 (t80) cc_final: 0.6983 (t80)
REVERT: A  124 TYR cc_start: 0.7044 (m-80) cc_final: 0.6409 (m-80)
REVERT: A  127 ILE cc_start: 0.8352 (mt) cc_final: 0.8103 (mm)
REVERT: A  145 SER cc_start: 0.8275 (m) cc_final: 0.7894 (t)
REVERT: A  151 TYR cc_start: 0.7331 (t80) cc_final: 0.7128 (t80)
REVERT: A  159 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7609 (tp-100)
REVERT: A  161 LEU cc_start: 0.7865 (tp) cc_final: 0.7537 (tt)
REVERT: A  167 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6764 (tmm)
REVERT: A  198 PHE cc_start: 0.6703 (m-80) cc_final: 0.6424 (m-80)
REVERT: A  363 MET cc_start: 0.7222 (mtt) cc_final: 0.7008 (mtp)
REVERT: A  389 ILE cc_start: 0.8440 (mt) cc_final: 0.8005 (mm)
REVERT: A  399 ASN cc_start: 0.6838 (m-40) cc_final: 0.6515 (m-40)
REVERT: A  420 ILE cc_start: 0.8233 (mt) cc_final: 0.7899 (mm)
REVERT: A  455 MET cc_start: 0.5942 (mmm) cc_final: 0.5498 (mmm)
  outliers start: 13
  outliers final: 8
  residues processed: 109
  average time/residue: 0.0432
  time to fit residues: 6.2788
Evaluate side-chains
  106 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  146 VAL
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  387 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0970
   chunk 33 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
A 310 GLN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.121115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.107459 restraints weight = 5243.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.110622 restraints weight = 2486.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.112671 restraints weight = 1427.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.113988 restraints weight = 956.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.114678 restraints weight = 716.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3218  Z= 0.167
  Angle     :  0.583   6.061   4396  Z= 0.301
  Chirality :  0.041   0.150    502
  Planarity :  0.004   0.030    527
  Dihedral  :  5.751  69.844    426
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 14.11 %
    Favored  : 81.98 %
  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:  0.80 (0.42), residues: 384
  helix:  1.16 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.84 (0.70), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 456 
 TYR   0.019   0.002   TYR A 445 
 PHE   0.009   0.001   PHE A 439 
 TRP   0.011   0.001   TRP A  94 
 HIS   0.006   0.002   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3218)
  covalent geometry    : angle       0.58262 ( 4396)
  hydrogen bonds       : bond        0.04611 (  224)
  hydrogen bonds       : angle       4.11804 (  672)

*********************** 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
  110 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7610 (tmm) cc_final: 0.7230 (tmm)
REVERT: A   89 SER cc_start: 0.8021 (m) cc_final: 0.7805 (p)
REVERT: A  113 TYR cc_start: 0.7250 (t80) cc_final: 0.6997 (t80)
REVERT: A  124 TYR cc_start: 0.7087 (m-80) cc_final: 0.6452 (m-80)
REVERT: A  127 ILE cc_start: 0.8330 (mt) cc_final: 0.8101 (mm)
REVERT: A  145 SER cc_start: 0.8331 (m) cc_final: 0.7936 (t)
REVERT: A  159 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7605 (tp-100)
REVERT: A  167 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6906 (tmm)
REVERT: A  198 PHE cc_start: 0.6746 (m-80) cc_final: 0.6484 (m-80)
REVERT: A  363 MET cc_start: 0.7179 (mtt) cc_final: 0.6973 (mtp)
REVERT: A  389 ILE cc_start: 0.8487 (mt) cc_final: 0.8056 (mm)
REVERT: A  399 ASN cc_start: 0.6828 (m-40) cc_final: 0.6542 (m-40)
REVERT: A  420 ILE cc_start: 0.8381 (mt) cc_final: 0.8037 (mm)
REVERT: A  455 MET cc_start: 0.5981 (mmm) cc_final: 0.5504 (mmm)
  outliers start: 13
  outliers final: 9
  residues processed: 104
  average time/residue: 0.0442
  time to fit residues: 6.0609
Evaluate side-chains
  106 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  387 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 15 optimal weight:    0.0170
   chunk 32 optimal weight:    0.3980
   chunk 25 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 4 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0980
   chunk 24 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.3418

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

Flipped N/Q/H residues before XYZ refinement:
A 310 GLN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.121867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.107922 restraints weight = 5235.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.111108 restraints weight = 2527.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.113198 restraints weight = 1469.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.114500 restraints weight = 988.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.115177 restraints weight = 746.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3218  Z= 0.137
  Angle     :  0.575   9.699   4396  Z= 0.290
  Chirality :  0.040   0.149    502
  Planarity :  0.004   0.029    527
  Dihedral  :  5.702  70.263    426
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.32 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.09 (0.42), residues: 384
  helix:  1.36 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.74 (0.69), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 456 
 TYR   0.015   0.001   TYR A 383 
 PHE   0.007   0.001   PHE A 439 
 TRP   0.013   0.001   TRP A  94 
 HIS   0.004   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3218)
  covalent geometry    : angle       0.57458 ( 4396)
  hydrogen bonds       : bond        0.04306 (  224)
  hydrogen bonds       : angle       3.99360 (  672)

*********************** 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
  109 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7610 (tmm) cc_final: 0.7189 (tmm)
REVERT: A   51 ILE cc_start: 0.8517 (mt) cc_final: 0.8255 (tt)
REVERT: A  124 TYR cc_start: 0.7094 (m-80) cc_final: 0.6432 (m-80)
REVERT: A  127 ILE cc_start: 0.8335 (mt) cc_final: 0.8086 (mm)
REVERT: A  145 SER cc_start: 0.8265 (m) cc_final: 0.7873 (t)
REVERT: A  159 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7475 (tp-100)
REVERT: A  167 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6650 (tpp)
REVERT: A  198 PHE cc_start: 0.6682 (m-80) cc_final: 0.6438 (m-80)
REVERT: A  363 MET cc_start: 0.7241 (mtt) cc_final: 0.7024 (mtp)
REVERT: A  389 ILE cc_start: 0.8425 (mt) cc_final: 0.7969 (mm)
REVERT: A  399 ASN cc_start: 0.6843 (m-40) cc_final: 0.6524 (m-40)
REVERT: A  420 ILE cc_start: 0.8320 (mt) cc_final: 0.7997 (mm)
REVERT: A  421 MET cc_start: 0.7292 (ttp) cc_final: 0.7083 (ttp)
REVERT: A  455 MET cc_start: 0.6000 (mmm) cc_final: 0.5524 (mmm)
  outliers start: 11
  outliers final: 8
  residues processed: 103
  average time/residue: 0.0404
  time to fit residues: 5.5100
Evaluate side-chains
  106 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  387 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0020
   chunk 35 optimal weight:    0.3980
   chunk 14 optimal weight:    0.7980
   chunk 23 optimal weight:    0.1980
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 310 GLN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.122084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.109203 restraints weight = 5334.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.112270 restraints weight = 2512.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.114266 restraints weight = 1425.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.115462 restraints weight = 930.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.116306 restraints weight = 687.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.3797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3218  Z= 0.141
  Angle     :  0.585   8.330   4396  Z= 0.296
  Chirality :  0.041   0.149    502
  Planarity :  0.004   0.028    527
  Dihedral  :  5.695  70.332    426
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.22 %
    Favored  : 80.18 %
  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:  1.14 (0.42), residues: 384
  helix:  1.37 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.58 (0.71), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 456 
 TYR   0.014   0.001   TYR A 383 
 PHE   0.008   0.001   PHE A  90 
 TRP   0.014   0.001   TRP A  94 
 HIS   0.004   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3218)
  covalent geometry    : angle       0.58513 ( 4396)
  hydrogen bonds       : bond        0.04321 (  224)
  hydrogen bonds       : angle       3.96113 (  672)

*********************** 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
  107 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A   51 ILE cc_start: 0.8573 (mt) cc_final: 0.8336 (tt)
REVERT: A  124 TYR cc_start: 0.7082 (m-80) cc_final: 0.6438 (m-80)
REVERT: A  127 ILE cc_start: 0.8349 (mt) cc_final: 0.8092 (mm)
REVERT: A  145 SER cc_start: 0.8249 (m) cc_final: 0.7892 (t)
REVERT: A  167 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6892 (tpt)
REVERT: A  198 PHE cc_start: 0.6667 (m-80) cc_final: 0.6423 (m-80)
REVERT: A  363 MET cc_start: 0.7204 (mtt) cc_final: 0.7002 (mtp)
REVERT: A  389 ILE cc_start: 0.8443 (mt) cc_final: 0.7992 (mm)
REVERT: A  399 ASN cc_start: 0.6806 (m-40) cc_final: 0.6502 (m-40)
REVERT: A  420 ILE cc_start: 0.8330 (mt) cc_final: 0.8009 (mm)
REVERT: A  455 MET cc_start: 0.5965 (mmm) cc_final: 0.5628 (mmm)
  outliers start: 12
  outliers final: 8
  residues processed: 101
  average time/residue: 0.0393
  time to fit residues: 5.3729
Evaluate side-chains
  105 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  387 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 19 optimal weight:    0.1980
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0770
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 37 optimal weight:    0.1980
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   overall best weight:    0.2338

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

Flipped N/Q/H residues before XYZ refinement:
A 310 GLN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.123349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109570 restraints weight = 5432.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.112723 restraints weight = 2615.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.114806 restraints weight = 1509.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.116095 restraints weight = 1008.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.116965 restraints weight = 758.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3218  Z= 0.119
  Angle     :  0.572   8.739   4396  Z= 0.287
  Chirality :  0.040   0.143    502
  Planarity :  0.004   0.032    527
  Dihedral  :  5.638  71.215    426
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 16.82 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.38 (0.42), residues: 384
  helix:  1.58 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.57 (0.70), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 456 
 TYR   0.014   0.001   TYR A 383 
 PHE   0.011   0.001   PHE A  90 
 TRP   0.013   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 3218)
  covalent geometry    : angle       0.57210 ( 4396)
  hydrogen bonds       : bond        0.04021 (  224)
  hydrogen bonds       : angle       3.82933 (  672)

*********************** 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
  110 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.119 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7605 (tmm) cc_final: 0.7281 (tmm)
REVERT: A   51 ILE cc_start: 0.8564 (mt) cc_final: 0.8334 (tt)
REVERT: A  124 TYR cc_start: 0.7085 (m-80) cc_final: 0.6437 (m-80)
REVERT: A  127 ILE cc_start: 0.8381 (mt) cc_final: 0.8132 (mm)
REVERT: A  145 SER cc_start: 0.8127 (m) cc_final: 0.7763 (t)
REVERT: A  167 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6836 (tpt)
REVERT: A  198 PHE cc_start: 0.6651 (m-80) cc_final: 0.6407 (m-80)
REVERT: A  363 MET cc_start: 0.7187 (mtt) cc_final: 0.6965 (mtp)
REVERT: A  389 ILE cc_start: 0.8365 (mt) cc_final: 0.7900 (mm)
REVERT: A  399 ASN cc_start: 0.6833 (m-40) cc_final: 0.6524 (m-40)
REVERT: A  420 ILE cc_start: 0.8298 (mt) cc_final: 0.7970 (mm)
REVERT: A  455 MET cc_start: 0.5934 (mmm) cc_final: 0.5732 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 102
  average time/residue: 0.0417
  time to fit residues: 5.7222
Evaluate side-chains
  107 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  387 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0870
   chunk 10 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 310 GLN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.120887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.107429 restraints weight = 5382.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.110506 restraints weight = 2581.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.112571 restraints weight = 1492.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.113854 restraints weight = 992.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.114699 restraints weight = 738.773|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   3218  Z= 0.178
  Angle     :  0.623   9.132   4396  Z= 0.315
  Chirality :  0.043   0.157    502
  Planarity :  0.004   0.030    527
  Dihedral  :  5.703  70.408    426
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.72 %
    Favored  : 78.68 %
  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:  1.03 (0.42), residues: 384
  helix:  1.29 (0.29), residues: 306
  sheet:  None (None), residues: 0
  loop : -1.66 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 456 
 TYR   0.029   0.002   TYR A 126 
 PHE   0.014   0.001   PHE A 439 
 TRP   0.011   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 3218)
  covalent geometry    : angle       0.62269 ( 4396)
  hydrogen bonds       : bond        0.04533 (  224)
  hydrogen bonds       : angle       4.06287 (  672)

*********************** 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
  107 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7640 (tmm) cc_final: 0.7164 (tmm)
REVERT: A   51 ILE cc_start: 0.8579 (mt) cc_final: 0.8332 (tt)
REVERT: A  124 TYR cc_start: 0.7101 (m-80) cc_final: 0.6458 (m-80)
REVERT: A  127 ILE cc_start: 0.8338 (mt) cc_final: 0.8129 (mm)
REVERT: A  145 SER cc_start: 0.8278 (m) cc_final: 0.7912 (t)
REVERT: A  198 PHE cc_start: 0.6731 (m-80) cc_final: 0.6434 (m-80)
REVERT: A  363 MET cc_start: 0.7199 (mtt) cc_final: 0.6979 (mtp)
REVERT: A  389 ILE cc_start: 0.8456 (mt) cc_final: 0.7996 (mm)
REVERT: A  399 ASN cc_start: 0.6813 (m-40) cc_final: 0.6563 (m-40)
REVERT: A  420 ILE cc_start: 0.8350 (mt) cc_final: 0.8026 (mm)
REVERT: A  455 MET cc_start: 0.5965 (mmm) cc_final: 0.5718 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0386
  time to fit residues: 5.3057
Evaluate side-chains
  110 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  387 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 23 optimal weight:    0.1980
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 310 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.121631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108251 restraints weight = 5312.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.111369 restraints weight = 2555.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.113369 restraints weight = 1476.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.114632 restraints weight = 984.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.115341 restraints weight = 738.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
moved from start:          0.4001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3218  Z= 0.154
  Angle     :  0.632  10.199   4396  Z= 0.313
  Chirality :  0.043   0.186    502
  Planarity :  0.004   0.029    527
  Dihedral  :  5.828  72.108    426
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.02 %
    Favored  : 78.68 %
  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:  1.13 (0.42), residues: 384
  helix:  1.39 (0.28), residues: 303
  sheet:  None (None), residues: 0
  loop : -1.63 (0.69), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 456 
 TYR   0.027   0.002   TYR A 126 
 PHE   0.013   0.001   PHE A 439 
 TRP   0.011   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3218)
  covalent geometry    : angle       0.63239 ( 4396)
  hydrogen bonds       : bond        0.04320 (  224)
  hydrogen bonds       : angle       3.99756 (  672)

********************** 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
  116 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7652 (tmm) cc_final: 0.7344 (tmm)
REVERT: A   51 ILE cc_start: 0.8586 (mt) cc_final: 0.8327 (tt)
REVERT: A  124 TYR cc_start: 0.7102 (m-80) cc_final: 0.6445 (m-80)
REVERT: A  127 ILE cc_start: 0.8335 (mt) cc_final: 0.8125 (mm)
REVERT: A  145 SER cc_start: 0.8236 (m) cc_final: 0.7910 (t)
REVERT: A  161 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7553 (tp)
REVERT: A  198 PHE cc_start: 0.6688 (m-80) cc_final: 0.6426 (m-80)
REVERT: A  389 ILE cc_start: 0.8424 (mt) cc_final: 0.7959 (mm)
REVERT: A  399 ASN cc_start: 0.6812 (m-40) cc_final: 0.6507 (m-40)
REVERT: A  419 THR cc_start: 0.7951 (m) cc_final: 0.7498 (p)
REVERT: A  420 ILE cc_start: 0.8352 (mt) cc_final: 0.7953 (mm)
REVERT: A  455 MET cc_start: 0.5966 (mmm) cc_final: 0.5764 (mmm)
  outliers start: 11
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0372
  time to fit residues: 5.5298
Evaluate side-chains
  107 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  387 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 16 optimal weight:    0.1980
   chunk 6 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 2 optimal weight:    0.2980
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0870
   chunk 34 optimal weight:    0.6980
   chunk 8 optimal weight:    0.1980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.2758

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

Flipped N/Q/H residues before XYZ refinement:
A 310 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.122705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.109148 restraints weight = 5359.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.112371 restraints weight = 2570.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.114453 restraints weight = 1482.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.115631 restraints weight = 985.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.116567 restraints weight = 752.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6992
moved from start:          0.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3218  Z= 0.131
  Angle     :  0.612   9.539   4396  Z= 0.305
  Chirality :  0.042   0.162    502
  Planarity :  0.004   0.030    527
  Dihedral  :  5.788  72.538    426
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.12 %
    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:  1.25 (0.42), residues: 384
  helix:  1.47 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -1.55 (0.69), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 456 
 TYR   0.025   0.001   TYR A 126 
 PHE   0.014   0.001   PHE A 439 
 TRP   0.010   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3218)
  covalent geometry    : angle       0.61227 ( 4396)
  hydrogen bonds       : bond        0.04117 (  224)
  hydrogen bonds       : angle       3.97475 (  672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 746.29 seconds
wall clock time: 13 minutes 32.08 seconds (812.08 seconds total)