Starting phenix.real_space_refine
on Sat Apr 26 18:42:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xv5_38692/04_2025/8xv5_38692.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xv5_38692/04_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_38692/04_2025/8xv5_38692.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xv5_38692/04_2025/8xv5_38692.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xv5_38692/04_2025/8xv5_38692.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xv5_38692/04_2025/8xv5_38692.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 2.63, per 1000 atoms: 0.84
  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: 0.82
  Conformation dependent library (CDL) restraints added in 891.8 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      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: 0.31
  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: 0.82

  Time building geometry restraints manager: 0.93 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:             0.810
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.530
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.370
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.67 (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
 TRP   0.024   0.003   TRP A  94 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.030   0.002   PHE A 439 
 TYR   0.046   0.003   TYR A  63 
 ARG   0.005   0.001   ARG A  29 

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

*********************** 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  : 0.311 
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: 0.0935
  time to fit residues: 15.2954
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  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0770
   chunk 9 optimal weight:    0.3980
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.122600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.109381 restraints weight = 5406.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.112606 restraints weight = 2581.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.114577 restraints weight = 1475.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3218  Z= 0.172
  Angle     :  0.610   6.125   4396  Z= 0.321
  Chirality :  0.041   0.161    502
  Planarity :  0.005   0.047    527
  Dihedral  :  6.099  72.272    426
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  :  6.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.41), residues: 384
  helix: -0.15 (0.28), residues: 306
  sheet:  None (None), residues: 0
  loop : -2.28 (0.72), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  94 
 HIS   0.006   0.002   HIS A 364 
 PHE   0.014   0.001   PHE A  99 
 TYR   0.018   0.002   TYR A 445 
 ARG   0.001   0.000   ARG A  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05073 (  224)
  hydrogen bonds       : angle       4.61677 (  672)
  covalent geometry    : bond        0.00368 ( 3218)
  covalent geometry    : angle       0.61047 ( 4396)

*********************** 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
  124 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7572 (tmm) cc_final: 0.7236 (tmm)
REVERT: A   64 LEU cc_start: 0.8272 (tp) cc_final: 0.7935 (tt)
REVERT: A  113 TYR cc_start: 0.7273 (t80) cc_final: 0.6969 (t80)
REVERT: A  127 ILE cc_start: 0.8329 (mt) cc_final: 0.8109 (mm)
REVERT: A  129 SER cc_start: 0.7618 (p) cc_final: 0.7393 (p)
REVERT: A  133 PRO cc_start: 0.7839 (Cg_exo) cc_final: 0.6862 (Cg_endo)
REVERT: A  145 SER cc_start: 0.8521 (m) cc_final: 0.8139 (t)
REVERT: A  161 LEU cc_start: 0.7963 (tp) cc_final: 0.7571 (tt)
REVERT: A  167 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6847 (tmm)
REVERT: A  198 PHE cc_start: 0.6804 (m-80) cc_final: 0.6499 (m-80)
REVERT: A  362 LEU cc_start: 0.7377 (tp) cc_final: 0.7168 (tp)
REVERT: A  363 MET cc_start: 0.7282 (mtt) cc_final: 0.7057 (mtp)
REVERT: A  389 ILE cc_start: 0.8437 (mt) cc_final: 0.8073 (mm)
REVERT: A  399 ASN cc_start: 0.6900 (m-40) cc_final: 0.6571 (m-40)
REVERT: A  416 VAL cc_start: 0.8075 (t) cc_final: 0.7873 (p)
REVERT: A  420 ILE cc_start: 0.8198 (mt) cc_final: 0.7911 (mm)
REVERT: A  455 MET cc_start: 0.5714 (mmm) cc_final: 0.5309 (mmm)
  outliers start: 13
  outliers final: 6
  residues processed: 119
  average time/residue: 0.1090
  time to fit residues: 16.9999
Evaluate side-chains
  111 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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 30 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 2 optimal weight:    0.0970
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.120821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.107300 restraints weight = 5232.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.110494 restraints weight = 2488.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.112534 restraints weight = 1430.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3218  Z= 0.174
  Angle     :  0.610   6.837   4396  Z= 0.316
  Chirality :  0.041   0.153    502
  Planarity :  0.004   0.039    527
  Dihedral  :  5.839  69.083    426
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 10.81 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.43), residues: 384
  helix:  0.61 (0.29), residues: 307
  sheet:  None (None), residues: 0
  loop : -2.14 (0.73), residues: 77

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  94 
 HIS   0.005   0.002   HIS A 364 
 PHE   0.016   0.001   PHE A  99 
 TYR   0.027   0.002   TYR A 136 
 ARG   0.001   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04710 (  224)
  hydrogen bonds       : angle       4.30402 (  672)
  covalent geometry    : bond        0.00385 ( 3218)
  covalent geometry    : angle       0.61047 ( 4396)

*********************** 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: 14
    poor density    : 102
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7641 (tmm) cc_final: 0.7263 (tmm)
REVERT: A   64 LEU cc_start: 0.8277 (tp) cc_final: 0.8059 (tt)
REVERT: A   77 VAL cc_start: 0.7825 (m) cc_final: 0.7336 (p)
REVERT: A   89 SER cc_start: 0.8024 (m) cc_final: 0.7689 (p)
REVERT: A  113 TYR cc_start: 0.7256 (t80) cc_final: 0.7005 (t80)
REVERT: A  124 TYR cc_start: 0.7077 (m-80) cc_final: 0.6440 (m-80)
REVERT: A  127 ILE cc_start: 0.8312 (mt) cc_final: 0.8095 (mm)
REVERT: A  145 SER cc_start: 0.8419 (m) cc_final: 0.8035 (t)
REVERT: A  161 LEU cc_start: 0.8007 (tp) cc_final: 0.7652 (tt)
REVERT: A  167 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6801 (tmm)
REVERT: A  198 PHE cc_start: 0.6801 (m-80) cc_final: 0.6503 (m-80)
REVERT: A  363 MET cc_start: 0.7272 (mtt) cc_final: 0.7029 (mtp)
REVERT: A  389 ILE cc_start: 0.8491 (mt) cc_final: 0.8064 (mm)
REVERT: A  399 ASN cc_start: 0.6887 (m-40) cc_final: 0.6559 (m-40)
REVERT: A  420 ILE cc_start: 0.8284 (mt) cc_final: 0.7945 (mm)
REVERT: A  455 MET cc_start: 0.5964 (mmm) cc_final: 0.5493 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 109
  average time/residue: 0.1167
  time to fit residues: 16.6555
Evaluate side-chains
  111 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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  115 MET
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  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 11 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.3980
   chunk 20 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   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 310 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.120232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.106616 restraints weight = 5276.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109806 restraints weight = 2514.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.111824 restraints weight = 1445.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.3269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3218  Z= 0.190
  Angle     :  0.610   6.145   4396  Z= 0.317
  Chirality :  0.042   0.153    502
  Planarity :  0.004   0.035    527
  Dihedral  :  5.852  69.204    426
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 12.31 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.42), residues: 384
  helix:  0.90 (0.29), residues: 306
  sheet:  None (None), residues: 0
  loop : -2.16 (0.69), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  94 
 HIS   0.006   0.002   HIS A 364 
 PHE   0.008   0.001   PHE A 446 
 TYR   0.017   0.002   TYR A  63 
 ARG   0.001   0.000   ARG A 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04734 (  224)
  hydrogen bonds       : angle       4.23408 (  672)
  covalent geometry    : bond        0.00421 ( 3218)
  covalent geometry    : angle       0.60991 ( 4396)

*********************** 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
  113 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   89 SER cc_start: 0.8107 (m) cc_final: 0.7778 (p)
REVERT: A  124 TYR cc_start: 0.7109 (m-80) cc_final: 0.6417 (m-80)
REVERT: A  127 ILE cc_start: 0.8343 (mt) cc_final: 0.8112 (mm)
REVERT: A  145 SER cc_start: 0.8369 (m) cc_final: 0.8005 (t)
REVERT: A  151 TYR cc_start: 0.7301 (t80) cc_final: 0.7054 (t80)
REVERT: A  159 GLN cc_start: 0.8109 (tp-100) cc_final: 0.7726 (tp-100)
REVERT: A  161 LEU cc_start: 0.8091 (tp) cc_final: 0.7863 (tt)
REVERT: A  167 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6913 (tmm)
REVERT: A  198 PHE cc_start: 0.6796 (m-80) cc_final: 0.6493 (m-80)
REVERT: A  292 PHE cc_start: 0.7640 (t80) cc_final: 0.7183 (t80)
REVERT: A  363 MET cc_start: 0.7284 (mtt) cc_final: 0.7066 (mtp)
REVERT: A  389 ILE cc_start: 0.8517 (mt) cc_final: 0.8111 (mm)
REVERT: A  399 ASN cc_start: 0.6901 (m-40) cc_final: 0.6575 (m-40)
REVERT: A  420 ILE cc_start: 0.8297 (mt) cc_final: 0.7966 (mm)
REVERT: A  455 MET cc_start: 0.5973 (mmm) cc_final: 0.5553 (mmm)
  outliers start: 14
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1025
  time to fit residues: 14.1300
Evaluate side-chains
  104 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
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  167 MET
Chi-restraints excluded: chain A residue  187 SER
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 11 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3542 r_free = 0.3542 target = 0.119011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.105411 restraints weight = 5245.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.108545 restraints weight = 2502.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.110592 restraints weight = 1437.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   3218  Z= 0.235
  Angle     :  0.640   6.131   4396  Z= 0.335
  Chirality :  0.044   0.158    502
  Planarity :  0.004   0.037    527
  Dihedral  :  5.871  65.028    426
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 14.11 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.42), residues: 384
  helix:  0.87 (0.28), residues: 308
  sheet:  None (None), residues: 0
  loop : -2.03 (0.68), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  94 
 HIS   0.005   0.002   HIS A 364 
 PHE   0.009   0.001   PHE A 170 
 TYR   0.017   0.002   TYR A 136 
 ARG   0.003   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04999 (  224)
  hydrogen bonds       : angle       4.32238 (  672)
  covalent geometry    : bond        0.00518 ( 3218)
  covalent geometry    : angle       0.63977 ( 4396)

*********************** 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
  114 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7658 (tmm) cc_final: 0.7413 (tmm)
REVERT: A   71 PHE cc_start: 0.8467 (t80) cc_final: 0.8189 (t80)
REVERT: A   89 SER cc_start: 0.8090 (m) cc_final: 0.7840 (p)
REVERT: A  124 TYR cc_start: 0.7123 (m-80) cc_final: 0.6445 (m-80)
REVERT: A  127 ILE cc_start: 0.8342 (mt) cc_final: 0.8113 (mm)
REVERT: A  145 SER cc_start: 0.8404 (m) cc_final: 0.8031 (t)
REVERT: A  159 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7725 (tp-100)
REVERT: A  161 LEU cc_start: 0.8156 (tp) cc_final: 0.7871 (tt)
REVERT: A  167 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7006 (tmm)
REVERT: A  198 PHE cc_start: 0.6784 (m-80) cc_final: 0.6528 (m-80)
REVERT: A  389 ILE cc_start: 0.8556 (mt) cc_final: 0.8175 (mm)
REVERT: A  393 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7394 (mt0)
REVERT: A  399 ASN cc_start: 0.6929 (m-40) cc_final: 0.6674 (m-40)
REVERT: A  420 ILE cc_start: 0.8373 (mt) cc_final: 0.8093 (mm)
REVERT: A  455 MET cc_start: 0.5961 (mmm) cc_final: 0.5682 (mmm)
  outliers start: 17
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1039
  time to fit residues: 14.1963
Evaluate side-chains
  106 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
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  116 VAL
Chi-restraints excluded: chain A residue  146 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  314 ILE
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 31 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0980
   chunk 14 optimal weight:    0.5980
   chunk 16 optimal weight:    0.1980
   chunk 1 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.121147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.107544 restraints weight = 5330.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.110787 restraints weight = 2520.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.112874 restraints weight = 1443.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3218  Z= 0.148
  Angle     :  0.572   6.047   4396  Z= 0.294
  Chirality :  0.040   0.140    502
  Planarity :  0.004   0.033    527
  Dihedral  :  5.807  65.585    426
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.62 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.42), residues: 384
  helix:  1.29 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.88 (0.68), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  94 
 HIS   0.005   0.001   HIS A 364 
 PHE   0.010   0.001   PHE A 439 
 TYR   0.016   0.001   TYR A 383 
 ARG   0.003   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04399 (  224)
  hydrogen bonds       : angle       4.06917 (  672)
  covalent geometry    : bond        0.00327 ( 3218)
  covalent geometry    : angle       0.57183 ( 4396)

*********************** 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
  107 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7735 (tmm) cc_final: 0.7399 (tmm)
REVERT: A   89 SER cc_start: 0.8030 (m) cc_final: 0.7779 (p)
REVERT: A  124 TYR cc_start: 0.7088 (m-80) cc_final: 0.6450 (m-80)
REVERT: A  127 ILE cc_start: 0.8363 (mt) cc_final: 0.8143 (mm)
REVERT: A  145 SER cc_start: 0.8313 (m) cc_final: 0.7950 (t)
REVERT: A  159 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7603 (tp-100)
REVERT: A  167 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6938 (tmm)
REVERT: A  185 LEU cc_start: 0.7826 (tp) cc_final: 0.7600 (tp)
REVERT: A  198 PHE cc_start: 0.6709 (m-80) cc_final: 0.6465 (m-80)
REVERT: A  389 ILE cc_start: 0.8495 (mt) cc_final: 0.8066 (mm)
REVERT: A  393 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7378 (mt0)
REVERT: A  399 ASN cc_start: 0.6890 (m-40) cc_final: 0.6612 (m-40)
REVERT: A  420 ILE cc_start: 0.8358 (mt) cc_final: 0.8021 (mm)
REVERT: A  455 MET cc_start: 0.6025 (mmm) cc_final: 0.5714 (mmm)
  outliers start: 11
  outliers final: 7
  residues processed: 101
  average time/residue: 0.1125
  time to fit residues: 14.7261
Evaluate side-chains
  102 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  314 ILE
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 33 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0470
   chunk 34 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0970
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 23 optimal weight:    0.1980
   chunk 19 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.2876

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.121768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.108427 restraints weight = 5257.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.111571 restraints weight = 2500.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.113620 restraints weight = 1438.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.3772

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= 0.127
  Angle     :  0.575   9.901   4396  Z= 0.290
  Chirality :  0.040   0.141    502
  Planarity :  0.004   0.030    527
  Dihedral  :  5.788  65.143    426
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 16.82 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.43), residues: 384
  helix:  1.47 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.82 (0.68), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.008   0.001   PHE A 439 
 TYR   0.024   0.001   TYR A 445 
 ARG   0.003   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04211 (  224)
  hydrogen bonds       : angle       3.95248 (  672)
  covalent geometry    : bond        0.00276 ( 3218)
  covalent geometry    : angle       0.57525 ( 4396)

*********************** 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
  109 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   17 VAL cc_start: 0.7577 (OUTLIER) cc_final: 0.7356 (p)
REVERT: A   28 MET cc_start: 0.7727 (tmm) cc_final: 0.7421 (tmm)
REVERT: A   51 ILE cc_start: 0.8590 (mt) cc_final: 0.8347 (tt)
REVERT: A   89 SER cc_start: 0.7953 (m) cc_final: 0.7729 (p)
REVERT: A  124 TYR cc_start: 0.7079 (m-80) cc_final: 0.6436 (m-80)
REVERT: A  127 ILE cc_start: 0.8359 (mt) cc_final: 0.8122 (mm)
REVERT: A  145 SER cc_start: 0.8266 (m) cc_final: 0.7887 (t)
REVERT: A  185 LEU cc_start: 0.7805 (tp) cc_final: 0.7579 (tp)
REVERT: A  198 PHE cc_start: 0.6724 (m-80) cc_final: 0.6483 (m-80)
REVERT: A  359 SER cc_start: 0.7186 (m) cc_final: 0.6906 (p)
REVERT: A  389 ILE cc_start: 0.8448 (mt) cc_final: 0.8008 (mm)
REVERT: A  393 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7374 (mt0)
REVERT: A  399 ASN cc_start: 0.6854 (m-40) cc_final: 0.6572 (m-40)
REVERT: A  420 ILE cc_start: 0.8346 (mt) cc_final: 0.8039 (mm)
REVERT: A  455 MET cc_start: 0.5998 (mmm) cc_final: 0.5721 (mmm)
  outliers start: 13
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0996
  time to fit residues: 13.6064
Evaluate side-chains
  105 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 ILE
Chi-restraints excluded: chain A residue   17 VAL
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  310 GLN
Chi-restraints excluded: chain A residue  314 ILE
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 31 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0010
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.6786

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.119705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.106092 restraints weight = 5220.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.109229 restraints weight = 2509.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.111288 restraints weight = 1454.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   3218  Z= 0.215
  Angle     :  0.638   9.134   4396  Z= 0.328
  Chirality :  0.043   0.150    502
  Planarity :  0.004   0.033    527
  Dihedral  :  6.060  66.304    426
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 18.02 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.42), residues: 384
  helix:  1.20 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.81 (0.67), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.008   0.001   PHE A 170 
 TYR   0.022   0.002   TYR A 445 
 ARG   0.004   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04826 (  224)
  hydrogen bonds       : angle       4.22426 (  672)
  covalent geometry    : bond        0.00477 ( 3218)
  covalent geometry    : angle       0.63770 ( 4396)

*********************** 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
  108 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   89 SER cc_start: 0.8100 (m) cc_final: 0.7825 (p)
REVERT: A  124 TYR cc_start: 0.7114 (m-80) cc_final: 0.6497 (m-80)
REVERT: A  127 ILE cc_start: 0.8376 (mt) cc_final: 0.8137 (mm)
REVERT: A  145 SER cc_start: 0.8371 (m) cc_final: 0.8030 (t)
REVERT: A  159 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7563 (tp-100)
REVERT: A  185 LEU cc_start: 0.7846 (tp) cc_final: 0.7617 (tp)
REVERT: A  198 PHE cc_start: 0.6816 (m-80) cc_final: 0.6524 (m-80)
REVERT: A  389 ILE cc_start: 0.8509 (mt) cc_final: 0.8068 (mm)
REVERT: A  399 ASN cc_start: 0.6892 (m-40) cc_final: 0.6620 (m-40)
REVERT: A  420 ILE cc_start: 0.8414 (mt) cc_final: 0.8161 (mm)
REVERT: A  455 MET cc_start: 0.6053 (mmm) cc_final: 0.5793 (mmm)
  outliers start: 13
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0975
  time to fit residues: 13.1466
Evaluate side-chains
  108 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 SER
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  146 VAL
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  314 ILE
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 11 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0370
   chunk 21 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.5658

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.120474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.106874 restraints weight = 5211.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.110056 restraints weight = 2504.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.112130 restraints weight = 1444.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.3824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3218  Z= 0.188
  Angle     :  0.627   9.134   4396  Z= 0.321
  Chirality :  0.042   0.148    502
  Planarity :  0.004   0.034    527
  Dihedral  :  6.130  66.996    426
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.32 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.42), residues: 384
  helix:  1.24 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.73 (0.68), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.008   0.001   PHE A 439 
 TYR   0.022   0.002   TYR A 445 
 ARG   0.004   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04681 (  224)
  hydrogen bonds       : angle       4.18465 (  672)
  covalent geometry    : bond        0.00418 ( 3218)
  covalent geometry    : angle       0.62660 ( 4396)

*********************** 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  : 0.361 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7617 (tmm) cc_final: 0.7408 (tmm)
REVERT: A   51 ILE cc_start: 0.8555 (mt) cc_final: 0.8286 (tt)
REVERT: A   89 SER cc_start: 0.8063 (m) cc_final: 0.7795 (p)
REVERT: A  124 TYR cc_start: 0.7110 (m-80) cc_final: 0.6490 (m-80)
REVERT: A  127 ILE cc_start: 0.8384 (mt) cc_final: 0.8145 (mm)
REVERT: A  145 SER cc_start: 0.8361 (m) cc_final: 0.8014 (t)
REVERT: A  159 GLN cc_start: 0.8008 (tp-100) cc_final: 0.7545 (tp-100)
REVERT: A  185 LEU cc_start: 0.7849 (tp) cc_final: 0.7623 (tp)
REVERT: A  198 PHE cc_start: 0.6790 (m-80) cc_final: 0.6525 (m-80)
REVERT: A  389 ILE cc_start: 0.8498 (mt) cc_final: 0.8055 (mm)
REVERT: A  399 ASN cc_start: 0.6889 (m-40) cc_final: 0.6631 (m-40)
REVERT: A  420 ILE cc_start: 0.8405 (mt) cc_final: 0.8147 (mm)
REVERT: A  455 MET cc_start: 0.6046 (mmm) cc_final: 0.5787 (mmm)
  outliers start: 12
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1085
  time to fit residues: 14.2228
Evaluate side-chains
  105 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
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  187 SER
Chi-restraints excluded: chain A residue  273 TYR
Chi-restraints excluded: chain A residue  310 GLN
Chi-restraints excluded: chain A residue  314 ILE
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 20 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.119685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.106443 restraints weight = 5086.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.109549 restraints weight = 2477.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.111389 restraints weight = 1436.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.3845

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= 0.211
  Angle     :  0.645   9.016   4396  Z= 0.331
  Chirality :  0.043   0.152    502
  Planarity :  0.004   0.035    527
  Dihedral  :  6.282  68.292    426
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.32 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.42), residues: 384
  helix:  1.16 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -1.73 (0.68), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.008   0.001   PHE A 453 
 TYR   0.022   0.002   TYR A 445 
 ARG   0.005   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04827 (  224)
  hydrogen bonds       : angle       4.24670 (  672)
  covalent geometry    : bond        0.00470 ( 3218)
  covalent geometry    : angle       0.64495 ( 4396)

********************** 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
  108 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A   28 MET cc_start: 0.7627 (tmm) cc_final: 0.7393 (tmm)
REVERT: A   40 SER cc_start: 0.7119 (m) cc_final: 0.6724 (t)
REVERT: A   89 SER cc_start: 0.8095 (m) cc_final: 0.7820 (p)
REVERT: A  124 TYR cc_start: 0.7113 (m-80) cc_final: 0.6496 (m-80)
REVERT: A  127 ILE cc_start: 0.8379 (mt) cc_final: 0.8137 (mm)
REVERT: A  145 SER cc_start: 0.8380 (m) cc_final: 0.8054 (t)
REVERT: A  159 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7559 (tp-100)
REVERT: A  185 LEU cc_start: 0.7849 (tp) cc_final: 0.7618 (tp)
REVERT: A  198 PHE cc_start: 0.6803 (m-80) cc_final: 0.6526 (m-80)
REVERT: A  389 ILE cc_start: 0.8510 (mt) cc_final: 0.8075 (mm)
REVERT: A  399 ASN cc_start: 0.6882 (m-40) cc_final: 0.6627 (m-40)
REVERT: A  420 ILE cc_start: 0.8429 (mt) cc_final: 0.8176 (mm)
REVERT: A  455 MET cc_start: 0.6099 (mmm) cc_final: 0.5824 (mmm)
  outliers start: 12
  outliers final: 12
  residues processed: 104
  average time/residue: 0.1034
  time to fit residues: 14.1293
Evaluate side-chains
  108 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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   26 SER
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  156 VAL
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  314 ILE
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 18 optimal weight:    0.0980
   chunk 36 optimal weight:    0.0980
   chunk 22 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0980
   chunk 29 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    0.3980
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   overall best weight:    0.2180

-------------------------------------------------------------------------------
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 = 0.3599 r_free = 0.3599 target = 0.122837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.109293 restraints weight = 5249.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.112574 restraints weight = 2500.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.114657 restraints weight = 1434.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.3940

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= 0.123
  Angle     :  0.587   9.885   4396  Z= 0.295
  Chirality :  0.040   0.148    502
  Planarity :  0.004   0.030    527
  Dihedral  :  6.129  67.481    426
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.32 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.43), residues: 384
  helix:  1.57 (0.29), residues: 303
  sheet:  None (None), residues: 0
  loop : -1.64 (0.71), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.009   0.001   PHE A 439 
 TYR   0.020   0.001   TYR A 445 
 ARG   0.004   0.000   ARG A 456 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04167 (  224)
  hydrogen bonds       : angle       3.98051 (  672)
  covalent geometry    : bond        0.00263 ( 3218)
  covalent geometry    : angle       0.58665 ( 4396)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1530.75 seconds
wall clock time: 27 minutes 5.87 seconds (1625.87 seconds total)