Starting phenix.real_space_refine
on Thu Jul 18 18:59:56 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/07_2024/8xv5_38692.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/07_2024/8xv5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/07_2024/8xv5_38692.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/07_2024/8xv5_38692.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/07_2024/8xv5_38692.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xv5_38692/07_2024/8xv5_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
    Residue "A PHE  439": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  456": "NH1" <-> "NH2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 2.74, per 1000 atoms: 0.88
  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  - 3.50
        Amino acid           : False - 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: 3.66
  Conformation dependent library (CDL) restraints added in 985.1 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: 0.29
  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: 0.72

  Time building geometry restraints manager: 1.34 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:
       99.98 -   106.81: 86
      106.81 -   113.63: 1729
      113.63 -   120.45: 1385
      120.45 -   127.27: 1163
      127.27 -   134.09: 33
  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 2.440
  nonbonded pdb=" O   LYS A 270 "
            pdb=" OG  SER A 274 "
     model   vdw
     2.302 2.440
  nonbonded pdb=" OE1 GLN A 294 "
            pdb=" OH  TYR A 442 "
     model   vdw
     2.304 2.440
  nonbonded pdb=" OH  TYR A 151 "
            pdb=" OE2 GLU A 320 "
     model   vdw
     2.321 2.440
  nonbonded pdb=" OH  TYR A  61 "
            pdb=" OD2 ASP A 427 "
     model   vdw
     2.330 2.440
  ... (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:             0.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.750
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.550
-------------------------------------------------------------------------------
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= 0.349
  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 

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.249 
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: 0.0911
  time to fit residues: 14.7800
Evaluate side-chains
  101 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 28 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 9 optimal weight:    0.5980
   chunk 19 optimal weight:    0.2980
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7025
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3218  Z= 0.227
  Angle     :  0.595   5.836   4396  Z= 0.312
  Chirality :  0.041   0.156    502
  Planarity :  0.005   0.045    527
  Dihedral  :  5.873  69.829    426
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  :  7.21 %
    Favored  : 88.89 %
  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 (0.41), residues: 384
  helix: -0.05 (0.28), residues: 305
  sheet:  None (None), residues: 0
  loop : -2.28 (0.71), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  94 
 HIS   0.005   0.002   HIS A 364 
 PHE   0.013   0.001   PHE A  99 
 TYR   0.019   0.002   TYR A 445 
 ARG   0.002   0.000   ARG A  29 

*********************** 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 fitting.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7617 (tmm) cc_final: 0.7314 (tmm)
REVERT: A   61 TYR cc_start: 0.7130 (m-10) cc_final: 0.6777 (m-10)
REVERT: A   64 LEU cc_start: 0.8219 (tp) cc_final: 0.7922 (tt)
REVERT: A   71 PHE cc_start: 0.8415 (t80) cc_final: 0.8133 (t80)
REVERT: A  113 TYR cc_start: 0.7294 (t80) cc_final: 0.6998 (t80)
REVERT: A  133 PRO cc_start: 0.7845 (Cg_exo) cc_final: 0.7635 (Cg_endo)
REVERT: A  161 LEU cc_start: 0.7972 (tp) cc_final: 0.7604 (tt)
REVERT: A  167 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6999 (tmm)
REVERT: A  197 MET cc_start: 0.7029 (ttp) cc_final: 0.6574 (ttp)
REVERT: A  198 PHE cc_start: 0.6860 (m-80) cc_final: 0.6636 (m-80)
REVERT: A  362 LEU cc_start: 0.7350 (tp) cc_final: 0.7148 (tp)
REVERT: A  363 MET cc_start: 0.7273 (mtt) cc_final: 0.7066 (mtp)
REVERT: A  389 ILE cc_start: 0.8458 (mt) cc_final: 0.8106 (mm)
REVERT: A  399 ASN cc_start: 0.6895 (m-40) cc_final: 0.6566 (m-40)
REVERT: A  420 ILE cc_start: 0.8190 (mt) cc_final: 0.7889 (mm)
REVERT: A  428 GLN cc_start: 0.7160 (tt0) cc_final: 0.6899 (tt0)
REVERT: A  455 MET cc_start: 0.5743 (mmm) cc_final: 0.5327 (mmm)
  outliers start: 13
  outliers final: 7
  residues processed: 119
  average time/residue: 0.0991
  time to fit residues: 15.3566
Evaluate side-chains
  110 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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  273 TYR
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 28 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0370
   chunk 9 optimal weight:    0.4980
   chunk 34 optimal weight:    0.6980
   chunk 37 optimal weight:    0.1980
   chunk 30 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0470
   overall best weight:    0.2756

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

Flipped N/Q/H residues before XYZ refinement:
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 107 GLN
A 310 GLN
** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   3218  Z= 0.187
  Angle     :  0.569   6.843   4396  Z= 0.291
  Chirality :  0.039   0.140    502
  Planarity :  0.004   0.032    527
  Dihedral  :  5.559  69.159    426
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 13.51 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.34 (0.43), residues: 384
  helix:  0.88 (0.29), residues: 303
  sheet:  None (None), residues: 0
  loop : -2.14 (0.72), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  94 
 HIS   0.005   0.001   HIS A 364 
 PHE   0.014   0.001   PHE A  99 
 TYR   0.019   0.001   TYR A 373 
 ARG   0.001   0.000   ARG A  78 

*********************** 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 fitting.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7644 (tmm) cc_final: 0.7298 (tmm)
REVERT: A   61 TYR cc_start: 0.7099 (m-10) cc_final: 0.6688 (m-10)
REVERT: A   77 VAL cc_start: 0.7704 (m) cc_final: 0.7230 (p)
REVERT: A   89 SER cc_start: 0.7984 (m) cc_final: 0.7651 (p)
REVERT: A  113 TYR cc_start: 0.7258 (t80) cc_final: 0.6957 (t80)
REVERT: A  124 TYR cc_start: 0.7009 (m-80) cc_final: 0.6376 (m-80)
REVERT: A  133 PRO cc_start: 0.7868 (Cg_exo) cc_final: 0.6884 (Cg_endo)
REVERT: A  151 TYR cc_start: 0.7145 (t80) cc_final: 0.6881 (t80)
REVERT: A  161 LEU cc_start: 0.7803 (tp) cc_final: 0.7510 (tt)
REVERT: A  167 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6812 (tmm)
REVERT: A  197 MET cc_start: 0.6969 (ttp) cc_final: 0.6569 (ttp)
REVERT: A  198 PHE cc_start: 0.6770 (m-80) cc_final: 0.6535 (m-80)
REVERT: A  363 MET cc_start: 0.7273 (mtt) cc_final: 0.6993 (mtp)
REVERT: A  389 ILE cc_start: 0.8431 (mt) cc_final: 0.7989 (mm)
REVERT: A  399 ASN cc_start: 0.6847 (m-40) cc_final: 0.6493 (m-40)
REVERT: A  455 MET cc_start: 0.5977 (mmm) cc_final: 0.5488 (mmm)
  outliers start: 12
  outliers final: 7
  residues processed: 109
  average time/residue: 0.0892
  time to fit residues: 12.8763
Evaluate side-chains
  111 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 36 optimal weight:    0.1980
   chunk 18 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 310 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3218  Z= 0.278
  Angle     :  0.612   5.992   4396  Z= 0.319
  Chirality :  0.042   0.157    502
  Planarity :  0.004   0.029    527
  Dihedral  :  5.637  68.654    426
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 13.51 %
    Favored  : 82.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.42), residues: 384
  helix:  1.02 (0.29), residues: 303
  sheet:  None (None), residues: 0
  loop : -1.99 (0.68), residues: 81

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 170 
 TYR   0.027   0.002   TYR A 136 
 ARG   0.000   0.000   ARG A 138 

*********************** 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
  107 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7638 (tmm) cc_final: 0.7219 (tmm)
REVERT: A   61 TYR cc_start: 0.7138 (m-10) cc_final: 0.6795 (m-10)
REVERT: A   75 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.6170 (m-30)
REVERT: A  113 TYR cc_start: 0.7308 (t80) cc_final: 0.7050 (t80)
REVERT: A  124 TYR cc_start: 0.7063 (m-80) cc_final: 0.6450 (m-80)
REVERT: A  145 SER cc_start: 0.8431 (m) cc_final: 0.7982 (t)
REVERT: A  151 TYR cc_start: 0.7112 (t80) cc_final: 0.6815 (t80)
REVERT: A  167 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6931 (tmm)
REVERT: A  173 ASN cc_start: 0.7332 (m-40) cc_final: 0.6940 (m110)
REVERT: A  197 MET cc_start: 0.6997 (ttp) cc_final: 0.6537 (ttp)
REVERT: A  198 PHE cc_start: 0.6858 (m-80) cc_final: 0.6561 (m-80)
REVERT: A  363 MET cc_start: 0.7224 (mtt) cc_final: 0.7013 (mtp)
REVERT: A  389 ILE cc_start: 0.8499 (mt) cc_final: 0.8095 (mm)
REVERT: A  399 ASN cc_start: 0.6899 (m-40) cc_final: 0.6556 (m-40)
REVERT: A  428 GLN cc_start: 0.7183 (tt0) cc_final: 0.6935 (tt0)
REVERT: A  455 MET cc_start: 0.6006 (mmm) cc_final: 0.5581 (mmm)
  outliers start: 13
  outliers final: 6
  residues processed: 100
  average time/residue: 0.0926
  time to fit residues: 12.0659
Evaluate side-chains
  104 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
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   75 ASP
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  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 15 optimal weight:    0.2980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0070
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.4398

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.3413

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= 0.224
  Angle     :  0.589   8.870   4396  Z= 0.300
  Chirality :  0.041   0.158    502
  Planarity :  0.003   0.023    527
  Dihedral  :  5.594  69.878    426
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 15.02 %
    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:  0.81 (0.42), residues: 384
  helix:  1.26 (0.29), residues: 304
  sheet:  None (None), residues: 0
  loop : -2.28 (0.64), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  94 
 HIS   0.004   0.001   HIS A 364 
 PHE   0.007   0.001   PHE A 439 
 TYR   0.021   0.002   TYR A 136 
 ARG   0.001   0.000   ARG A  29 

*********************** 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
  105 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7644 (tmm) cc_final: 0.7253 (tmm)
REVERT: A   61 TYR cc_start: 0.7129 (m-10) cc_final: 0.6735 (m-10)
REVERT: A   75 ASP cc_start: 0.6363 (OUTLIER) cc_final: 0.6130 (m-30)
REVERT: A  113 TYR cc_start: 0.7260 (t80) cc_final: 0.6966 (t80)
REVERT: A  124 TYR cc_start: 0.7055 (m-80) cc_final: 0.6425 (m-80)
REVERT: A  145 SER cc_start: 0.8387 (m) cc_final: 0.7934 (t)
REVERT: A  151 TYR cc_start: 0.7120 (t80) cc_final: 0.6846 (t80)
REVERT: A  167 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6995 (tpt)
REVERT: A  197 MET cc_start: 0.6968 (ttp) cc_final: 0.6519 (ttp)
REVERT: A  198 PHE cc_start: 0.6750 (m-80) cc_final: 0.6497 (m-80)
REVERT: A  363 MET cc_start: 0.7198 (mtt) cc_final: 0.6962 (mtp)
REVERT: A  389 ILE cc_start: 0.8492 (mt) cc_final: 0.8081 (mm)
REVERT: A  393 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7374 (mt0)
REVERT: A  399 ASN cc_start: 0.6890 (m-40) cc_final: 0.6555 (m-40)
REVERT: A  455 MET cc_start: 0.5995 (mmm) cc_final: 0.5608 (mmm)
  outliers start: 13
  outliers final: 8
  residues processed: 99
  average time/residue: 0.1004
  time to fit residues: 12.8845
Evaluate side-chains
  101 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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   75 ASP
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  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 9 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0980
   chunk 30 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0770
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0270
   chunk 19 optimal weight:    0.4980
   chunk 35 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.2196

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start:          0.3597

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= 0.164
  Angle     :  0.549   7.701   4396  Z= 0.279
  Chirality :  0.039   0.161    502
  Planarity :  0.003   0.025    527
  Dihedral  :  5.499  70.808    426
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 15.92 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.19 (0.43), residues: 384
  helix:  1.55 (0.29), residues: 304
  sheet:  None (None), residues: 0
  loop : -2.25 (0.66), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 364 
 PHE   0.009   0.001   PHE A 439 
 TYR   0.017   0.001   TYR A 445 
 ARG   0.003   0.000   ARG A 456 

*********************** 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
  108 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7669 (tmm) cc_final: 0.7280 (tmm)
REVERT: A   61 TYR cc_start: 0.7093 (m-10) cc_final: 0.6715 (m-10)
REVERT: A   75 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.6012 (m-30)
REVERT: A   89 SER cc_start: 0.7925 (m) cc_final: 0.7605 (p)
REVERT: A  124 TYR cc_start: 0.7023 (m-80) cc_final: 0.6375 (m-80)
REVERT: A  133 PRO cc_start: 0.7634 (Cg_exo) cc_final: 0.7391 (Cg_endo)
REVERT: A  145 SER cc_start: 0.8322 (m) cc_final: 0.7846 (t)
REVERT: A  167 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6946 (tpp)
REVERT: A  197 MET cc_start: 0.6914 (ttp) cc_final: 0.6467 (ttp)
REVERT: A  198 PHE cc_start: 0.6730 (m-80) cc_final: 0.6470 (m-80)
REVERT: A  363 MET cc_start: 0.7201 (mtt) cc_final: 0.6989 (mtp)
REVERT: A  389 ILE cc_start: 0.8406 (mt) cc_final: 0.7966 (mm)
REVERT: A  399 ASN cc_start: 0.6827 (m-40) cc_final: 0.6491 (m-40)
REVERT: A  455 MET cc_start: 0.5964 (mmm) cc_final: 0.5508 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 101
  average time/residue: 0.1006
  time to fit residues: 13.2576
Evaluate side-chains
  106 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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   75 ASP
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  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 20 optimal weight:    0.2980
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0070
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.4198

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 310 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.3642

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= 0.217
  Angle     :  0.582   7.089   4396  Z= 0.293
  Chirality :  0.041   0.175    502
  Planarity :  0.003   0.023    527
  Dihedral  :  5.479  69.898    426
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 16.52 %
    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 (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:  1.22 (0.43), residues: 384
  helix:  1.56 (0.29), residues: 304
  sheet:  None (None), residues: 0
  loop : -2.19 (0.66), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.013   0.001   PHE A 439 
 TYR   0.017   0.001   TYR A 445 
 ARG   0.001   0.000   ARG A 456 

*********************** 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 fitting.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 TYR cc_start: 0.7101 (m-10) cc_final: 0.6707 (m-10)
REVERT: A   75 ASP cc_start: 0.6308 (OUTLIER) cc_final: 0.6055 (m-30)
REVERT: A  113 TYR cc_start: 0.7247 (t80) cc_final: 0.6924 (t80)
REVERT: A  124 TYR cc_start: 0.7048 (m-80) cc_final: 0.6410 (m-80)
REVERT: A  133 PRO cc_start: 0.7658 (Cg_exo) cc_final: 0.7428 (Cg_endo)
REVERT: A  145 SER cc_start: 0.8366 (m) cc_final: 0.7896 (t)
REVERT: A  173 ASN cc_start: 0.7061 (m-40) cc_final: 0.6814 (m110)
REVERT: A  197 MET cc_start: 0.6951 (ttp) cc_final: 0.6484 (ttp)
REVERT: A  198 PHE cc_start: 0.6743 (m-80) cc_final: 0.6448 (m-80)
REVERT: A  363 MET cc_start: 0.7227 (mtt) cc_final: 0.7006 (mtp)
REVERT: A  389 ILE cc_start: 0.8447 (mt) cc_final: 0.8006 (mm)
REVERT: A  399 ASN cc_start: 0.6848 (m-40) cc_final: 0.6526 (m-40)
REVERT: A  455 MET cc_start: 0.6019 (mmm) cc_final: 0.5540 (mmm)
  outliers start: 13
  outliers final: 8
  residues processed: 101
  average time/residue: 0.1023
  time to fit residues: 13.4776
Evaluate side-chains
  102 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
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   75 ASP
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  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 18 optimal weight:    0.0670
   chunk 3 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0030
   chunk 32 optimal weight:    0.0010
   chunk 34 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.2734

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.3756

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= 0.178
  Angle     :  0.585   9.260   4396  Z= 0.291
  Chirality :  0.040   0.184    502
  Planarity :  0.003   0.023    527
  Dihedral  :  5.551  71.604    426
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.42 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.43), residues: 384
  helix:  1.70 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -2.27 (0.65), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.014   0.001   PHE A 439 
 TYR   0.017   0.001   TYR A 445 
 ARG   0.001   0.000   ARG A  29 

*********************** 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
  109 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7633 (tmm) cc_final: 0.7253 (tmm)
REVERT: A   61 TYR cc_start: 0.7071 (m-10) cc_final: 0.6656 (m-10)
REVERT: A   75 ASP cc_start: 0.6233 (OUTLIER) cc_final: 0.5999 (m-30)
REVERT: A   89 SER cc_start: 0.8042 (m) cc_final: 0.7754 (p)
REVERT: A  124 TYR cc_start: 0.7038 (m-80) cc_final: 0.6400 (m-80)
REVERT: A  145 SER cc_start: 0.8276 (m) cc_final: 0.7861 (t)
REVERT: A  161 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7581 (tp)
REVERT: A  197 MET cc_start: 0.6920 (ttp) cc_final: 0.6475 (ttp)
REVERT: A  198 PHE cc_start: 0.6714 (m-80) cc_final: 0.6435 (m-80)
REVERT: A  359 SER cc_start: 0.7078 (m) cc_final: 0.6723 (p)
REVERT: A  363 MET cc_start: 0.7205 (mtt) cc_final: 0.6941 (mtp)
REVERT: A  389 ILE cc_start: 0.8412 (mt) cc_final: 0.7963 (mm)
REVERT: A  399 ASN cc_start: 0.6817 (m-40) cc_final: 0.6475 (m-40)
REVERT: A  439 PHE cc_start: 0.7984 (m-80) cc_final: 0.7755 (m-10)
REVERT: A  455 MET cc_start: 0.6055 (mmm) cc_final: 0.5609 (mmm)
  outliers start: 12
  outliers final: 9
  residues processed: 103
  average time/residue: 0.1095
  time to fit residues: 14.9605
Evaluate side-chains
  113 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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   75 ASP
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  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 30 optimal weight:    0.3980
   chunk 32 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0980
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    0.2980
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0970
   overall best weight:    0.2178

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

Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
A 310 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.3860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   3218  Z= 0.162
  Angle     :  0.587  10.714   4396  Z= 0.287
  Chirality :  0.040   0.181    502
  Planarity :  0.003   0.023    527
  Dihedral  :  5.510  71.927    426
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 17.12 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.43), residues: 384
  helix:  1.74 (0.29), residues: 302
  sheet:  None (None), residues: 0
  loop : -2.08 (0.66), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 364 
 PHE   0.014   0.001   PHE A 439 
 TYR   0.017   0.001   TYR A 445 
 ARG   0.001   0.000   ARG A  29 

*********************** 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
  114 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7631 (tmm) cc_final: 0.7255 (tmm)
REVERT: A   61 TYR cc_start: 0.7051 (m-10) cc_final: 0.6657 (m-10)
REVERT: A   75 ASP cc_start: 0.6180 (OUTLIER) cc_final: 0.5947 (m-30)
REVERT: A   86 GLN cc_start: 0.7728 (tt0) cc_final: 0.7511 (tt0)
REVERT: A   89 SER cc_start: 0.8085 (m) cc_final: 0.7814 (p)
REVERT: A  124 TYR cc_start: 0.7040 (m-80) cc_final: 0.6380 (m-80)
REVERT: A  145 SER cc_start: 0.8264 (m) cc_final: 0.7841 (t)
REVERT: A  161 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7436 (tp)
REVERT: A  197 MET cc_start: 0.6904 (ttp) cc_final: 0.6470 (ttp)
REVERT: A  198 PHE cc_start: 0.6714 (m-80) cc_final: 0.6425 (m-80)
REVERT: A  359 SER cc_start: 0.7046 (m) cc_final: 0.6705 (p)
REVERT: A  363 MET cc_start: 0.7196 (mtt) cc_final: 0.6933 (mtp)
REVERT: A  389 ILE cc_start: 0.8375 (mt) cc_final: 0.7922 (mm)
REVERT: A  399 ASN cc_start: 0.6845 (m-40) cc_final: 0.6532 (m-40)
REVERT: A  439 PHE cc_start: 0.7897 (m-80) cc_final: 0.7685 (m-10)
REVERT: A  455 MET cc_start: 0.6050 (mmm) cc_final: 0.5643 (mmm)
  outliers start: 13
  outliers final: 10
  residues processed: 107
  average time/residue: 0.1002
  time to fit residues: 14.1229
Evaluate side-chains
  110 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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   75 ASP
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  156 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  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 23 optimal weight:    0.0970
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0670
   chunk 31 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.4716

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3218  Z= 0.236
  Angle     :  0.624   9.021   4396  Z= 0.310
  Chirality :  0.043   0.191    502
  Planarity :  0.003   0.024    527
  Dihedral  :  5.631  71.330    426
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 11.81
  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:  1.26 (0.43), residues: 384
  helix:  1.58 (0.29), residues: 305
  sheet:  None (None), residues: 0
  loop : -2.18 (0.67), residues: 79

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  94 
 HIS   0.002   0.001   HIS A 200 
 PHE   0.012   0.001   PHE A 439 
 TYR   0.017   0.001   TYR A 445 
 ARG   0.001   0.000   ARG A  29 

********************** 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
  111 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   28 MET cc_start: 0.7626 (tmm) cc_final: 0.7420 (tmm)
REVERT: A   61 TYR cc_start: 0.7064 (m-10) cc_final: 0.6659 (m-10)
REVERT: A   75 ASP cc_start: 0.6291 (OUTLIER) cc_final: 0.6019 (m-30)
REVERT: A   89 SER cc_start: 0.8079 (m) cc_final: 0.7780 (p)
REVERT: A  113 TYR cc_start: 0.7244 (t80) cc_final: 0.6946 (t80)
REVERT: A  124 TYR cc_start: 0.7040 (m-80) cc_final: 0.6415 (m-80)
REVERT: A  145 SER cc_start: 0.8390 (m) cc_final: 0.7952 (t)
REVERT: A  161 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7629 (tp)
REVERT: A  197 MET cc_start: 0.6965 (ttp) cc_final: 0.6483 (ttp)
REVERT: A  198 PHE cc_start: 0.6825 (m-80) cc_final: 0.6502 (m-80)
REVERT: A  359 SER cc_start: 0.7213 (m) cc_final: 0.6840 (p)
REVERT: A  363 MET cc_start: 0.7228 (mtt) cc_final: 0.6948 (mtp)
REVERT: A  389 ILE cc_start: 0.8435 (mt) cc_final: 0.7978 (mm)
REVERT: A  399 ASN cc_start: 0.6834 (m-40) cc_final: 0.6514 (m-40)
REVERT: A  439 PHE cc_start: 0.7982 (m-80) cc_final: 0.7771 (m-10)
REVERT: A  455 MET cc_start: 0.6055 (mmm) cc_final: 0.5675 (mmm)
  outliers start: 12
  outliers final: 10
  residues processed: 105
  average time/residue: 0.0831
  time to fit residues: 11.5289
Evaluate side-chains
  109 residues out of total 333 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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   75 ASP
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  156 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  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 26 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3527 r_free = 0.3527 target = 0.118374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.105218 restraints weight = 5307.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.108305 restraints weight = 2509.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.110329 restraints weight = 1433.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   3218  Z= 0.314
  Angle     :  0.679   8.794   4396  Z= 0.341
  Chirality :  0.045   0.192    502
  Planarity :  0.004   0.025    527
  Dihedral  :  5.774  70.789    426
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.52 %
    Favored  : 77.48 %
  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:  0.88 (0.42), residues: 384
  helix:  1.27 (0.29), residues: 306
  sheet:  None (None), residues: 0
  loop : -2.14 (0.68), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  94 
 HIS   0.003   0.001   HIS A 200 
 PHE   0.013   0.001   PHE A 439 
 TYR   0.017   0.002   TYR A  63 
 ARG   0.002   0.000   ARG A  29 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1138.12 seconds
wall clock time: 22 minutes 38.56 seconds (1358.56 seconds total)