Starting phenix.real_space_refine
on Wed Sep 17 06:46:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cfe_45543/09_2025/9cfe_45543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cfe_45543/09_2025/9cfe_45543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cfe_45543/09_2025/9cfe_45543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cfe_45543/09_2025/9cfe_45543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cfe_45543/09_2025/9cfe_45543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cfe_45543/09_2025/9cfe_45543.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.023
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: 5
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2064      2.51       5
     N     550      2.21       5
     O     624      1.98       5
     H    3130      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6382
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 1750
          Classifications: {'peptide': 115}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "B"
      Number of atoms: 1655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 1655
          Classifications: {'peptide': 108}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 2977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 2977
          Classifications: {'peptide': 193}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
  Time building chain proxies: 1.45, per 1000 atoms: 0.23
  Number of scatterers: 6382
  At special positions: 0
  Unit cell: (72.21, 62.25, 98.77, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     O     624      8.00
     N     550      7.00
     C    2064      6.00
     H    3130      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.02

  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: 0.35
  Conformation dependent library (CDL) restraints added in 278.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  756

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 7 sheets defined
      13.7% alpha, 32.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 86 through 90
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.604A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 343
    Processing helix  chain 'C' and resid 349 through 353
    Processing helix  chain 'C' and resid 364 through 370
      removed outlier: 3.865A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 387
      removed outlier: 3.530A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 438 through 443
    Processing helix  chain 'C' and resid 502 through 505
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 6.571A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   TYR A  33 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   MET A  34 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   VAL A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   TRP A  36 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12
      removed outlier: 6.571A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.465A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358
      removed outlier: 4.054A  pdb=" N   ASN C 394 " --> pdb=" O   GLU C 516 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454

    119 hydrogen bonds defined for protein.
    279 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: 1.47

  Time building geometry restraints manager: 0.56 seconds

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

  Histogram of bond lengths:
        0.93 -     1.11: 3126
        1.11 -     1.29: 530
        1.29 -     1.47: 1268
        1.47 -     1.65: 1524
        1.65 -     1.83: 16
  Bond restraints: 6464
  Sorted by residual:
  bond pdb=" N   TYR B  36 "
       pdb=" H   TYR B  36 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.77e+01
  bond pdb=" CZ  PHE C 374 "
       pdb=" HZ  PHE C 374 "
    ideal  model  delta    sigma   weight residual
    0.930  1.082 -0.152 2.00e-02 2.50e+03 5.76e+01
  bond pdb=" CD1 PHE B  99 "
       pdb=" HD1 PHE B  99 "
    ideal  model  delta    sigma   weight residual
    0.930  1.082 -0.152 2.00e-02 2.50e+03 5.75e+01
  bond pdb=" N   GLU B  17 "
       pdb=" H   GLU B  17 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" N   GLY A 106 "
       pdb=" H   GLY A 106 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.72e+01
  ... (remaining 6459 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 9521
        2.46 -     4.92: 1593
        4.92 -     7.38: 434
        7.38 -     9.83: 48
        9.83 -    12.29: 4
  Bond angle restraints: 11600
  Sorted by residual:
  angle pdb=" CA  PHE A  67 "
        pdb=" CB  PHE A  67 "
        pdb=" CG  PHE A  67 "
      ideal   model   delta    sigma   weight residual
     113.80  120.42   -6.62 1.00e+00 1.00e+00 4.39e+01
  angle pdb=" CA  PRO C 521 "
        pdb=" N   PRO C 521 "
        pdb=" CD  PRO C 521 "
      ideal   model   delta    sigma   weight residual
     112.00  102.92    9.08 1.40e+00 5.10e-01 4.20e+01
  angle pdb=" CA  ASN C 360 "
        pdb=" CB  ASN C 360 "
        pdb=" CG  ASN C 360 "
      ideal   model   delta    sigma   weight residual
     112.60  118.79   -6.19 1.00e+00 1.00e+00 3.84e+01
  angle pdb=" CA  ILE A  12 "
        pdb=" CB  ILE A  12 "
        pdb=" CG1 ILE A  12 "
      ideal   model   delta    sigma   weight residual
     110.40  120.16   -9.76 1.70e+00 3.46e-01 3.29e+01
  angle pdb=" OD1 ASN C 360 "
        pdb=" CG  ASN C 360 "
        pdb=" ND2 ASN C 360 "
      ideal   model   delta    sigma   weight residual
     122.60  116.91    5.69 1.00e+00 1.00e+00 3.24e+01
  ... (remaining 11595 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.62: 2733
       15.62 -    31.24: 232
       31.24 -    46.86: 81
       46.86 -    62.48: 47
       62.48 -    78.10: 11
  Dihedral angle restraints: 3104
    sinusoidal: 1652
      harmonic: 1452
  Sorted by residual:
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.64   72.64     1      1.00e+01 1.00e-02 6.74e+01
  dihedral pdb=" C   PRO C 521 "
           pdb=" N   PRO C 521 "
           pdb=" CA  PRO C 521 "
           pdb=" CB  PRO C 521 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -139.31   18.61     0      2.50e+00 1.60e-01 5.54e+01
  dihedral pdb=" N   PRO C 521 "
           pdb=" C   PRO C 521 "
           pdb=" CA  PRO C 521 "
           pdb=" CB  PRO C 521 "
      ideal   model   delta  harmonic     sigma   weight residual
     115.10  133.13  -18.03     0      2.50e+00 1.60e-01 5.20e+01
  ... (remaining 3101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.176: 438
       0.176 -    0.351: 43
       0.351 -    0.526: 2
       0.526 -    0.702: 0
       0.702 -    0.877: 2
  Chirality restraints: 485
  Sorted by residual:
  chirality pdb=" CA  PRO C 521 "
            pdb=" N   PRO C 521 "
            pdb=" C   PRO C 521 "
            pdb=" CB  PRO C 521 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    1.84    0.88 2.00e-01 2.50e+01 1.92e+01
  chirality pdb=" CA  HIS C 519 "
            pdb=" N   HIS C 519 "
            pdb=" C   HIS C 519 "
            pdb=" CB  HIS C 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.80    0.71 2.00e-01 2.50e+01 1.26e+01
  chirality pdb=" CA  ASN C 501 "
            pdb=" N   ASN C 501 "
            pdb=" C   ASN C 501 "
            pdb=" CB  ASN C 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.51e+00
  ... (remaining 482 not shown)

  Planarity restraints: 983
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  47 "    0.321 2.00e-02 2.50e+03   1.22e-01 5.92e+02
        pdb=" CG  TRP A  47 "    0.059 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  47 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  47 "   -0.053 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  47 "   -0.112 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  47 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  47 "   -0.119 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  47 "    0.053 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  47 "   -0.065 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  47 "    0.062 2.00e-02 2.50e+03
        pdb=" HD1 TRP A  47 "    0.000 2.00e-02 2.50e+03
        pdb=" HE1 TRP A  47 "   -0.141 2.00e-02 2.50e+03
        pdb=" HE3 TRP A  47 "   -0.152 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A  47 "    0.120 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A  47 "   -0.056 2.00e-02 2.50e+03
        pdb=" HH2 TRP A  47 "    0.162 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  97 "    0.051 9.50e-02 1.11e+02   1.35e-01 4.01e+02
        pdb=" NE  ARG A  97 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  97 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  97 "   -0.054 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  97 "    0.040 2.00e-02 2.50e+03
        pdb="HH11 ARG A  97 "   -0.094 2.00e-02 2.50e+03
        pdb="HH12 ARG A  97 "    0.252 2.00e-02 2.50e+03
        pdb="HH21 ARG A  97 "    0.133 2.00e-02 2.50e+03
        pdb="HH22 ARG A  97 "   -0.256 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 403 "   -0.772 9.50e-02 1.11e+02   2.77e-01 3.02e+02
        pdb=" NE  ARG C 403 "   -0.067 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 403 "   -0.040 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 403 "   -0.131 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 403 "    0.058 2.00e-02 2.50e+03
        pdb="HH11 ARG C 403 "    0.218 2.00e-02 2.50e+03
        pdb="HH12 ARG C 403 "   -0.043 2.00e-02 2.50e+03
        pdb="HH21 ARG C 403 "    0.113 2.00e-02 2.50e+03
        pdb="HH22 ARG C 403 "   -0.074 2.00e-02 2.50e+03
  ... (remaining 980 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 434
        2.18 -     2.78: 10951
        2.78 -     3.39: 17813
        3.39 -     3.99: 24523
        3.99 -     4.60: 35321
  Nonbonded interactions: 89042
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 364 "
            pdb=" HG  SER C 366 "
     model   vdw
     1.570 2.450
  nonbonded pdb=" OD1 ASP A  72 "
            pdb=" HG  SER A  74 "
     model   vdw
     1.597 2.450
  nonbonded pdb=" HG  SER A  25 "
            pdb=" OE1 GLU A  26 "
     model   vdw
     1.604 2.450
  nonbonded pdb=" OE1 GLU B  90 "
            pdb=" HG  SER B  92 "
     model   vdw
     1.607 2.450
  nonbonded pdb="HG13 ILE A  12 "
            pdb=" H   GLN A  13 "
     model   vdw
     1.614 2.270
  ... (remaining 89037 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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 individual isotropic
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:             8.840
  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:             0.030
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.960
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6423
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      :  0.013   0.057   3338  Z= 0.790
  Angle     :  1.935   9.757   4540  Z= 1.272
  Chirality :  0.117   0.877    485
  Planarity :  0.018   0.245    592
  Dihedral  : 13.560  78.098   1196
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 0.16
  Ramachandran Plot:
    Outliers :  0.98 %
    Allowed  :  6.83 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  7.34 %
    Favored  : 90.68 %
  Cbeta Deviations :  1.06 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.68 (0.37), residues: 410
  helix: -4.09 (0.41), residues: 41
  sheet:  0.18 (0.48), residues: 110
  loop : -1.22 (0.34), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG B  91 
 TYR   0.204   0.024   TYR C 421 
 PHE   0.054   0.013   PHE C 342 
 TRP   0.196   0.028   TRP A  47 
 HIS   0.010   0.006   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.01322 ( 3334)
  covalent geometry    : angle       1.92934 ( 4532)
  SS BOND              : bond        0.01259 (    4)
  SS BOND              : angle       3.99635 (    8)
  hydrogen bonds       : bond        0.14160 (  115)
  hydrogen bonds       : angle       9.24095 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  347 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7474 (t80)
REVERT: C  393 THR cc_start: 0.6198 (OUTLIER) cc_final: 0.5809 (m)
  outliers start: 7
  outliers final: 4
  residues processed: 92
  average time/residue: 0.1995
  time to fit residues: 21.2760
Evaluate side-chains
  68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  521 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C 493 GLN
C 501 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.119600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.110840 restraints weight = 33433.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.4013 rms_B_bonded: 4.76
r_work: 0.3815 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   3338  Z= 0.166
  Angle     :  0.710   7.223   4540  Z= 0.379
  Chirality :  0.047   0.251    485
  Planarity :  0.007   0.107    592
  Dihedral  :  8.671  69.839    474
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.12 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 15.54 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.38), residues: 410
  helix: -3.44 (0.62), residues: 28
  sheet: -0.39 (0.43), residues: 140
  loop : -0.97 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  18 
 TYR   0.025   0.002   TYR C 369 
 PHE   0.008   0.001   PHE C 515 
 TRP   0.005   0.001   TRP C 436 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 3334)
  covalent geometry    : angle       0.70710 ( 4532)
  SS BOND              : bond        0.00557 (    4)
  SS BOND              : angle       1.58214 (    8)
  hydrogen bonds       : bond        0.04167 (  115)
  hydrogen bonds       : angle       7.08672 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  347 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.7918 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 70
  average time/residue: 0.1466
  time to fit residues: 12.6211
Evaluate side-chains
  63 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  361 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
C 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.119331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.110401 restraints weight = 33035.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 4.94
r_work: 0.3814 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.3766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3338  Z= 0.176
  Angle     :  0.647   6.390   4540  Z= 0.340
  Chirality :  0.045   0.239    485
  Planarity :  0.006   0.099    592
  Dihedral  :  7.922  75.599    468
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.12 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.69 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.39), residues: 410
  helix: -2.81 (0.72), residues: 28
  sheet: -0.62 (0.43), residues: 148
  loop : -0.90 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  18 
 TYR   0.021   0.001   TYR C 369 
 PHE   0.010   0.001   PHE A  67 
 TRP   0.006   0.001   TRP C 436 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 3334)
  covalent geometry    : angle       0.64477 ( 4532)
  SS BOND              : bond        0.00488 (    4)
  SS BOND              : angle       1.44729 (    8)
  hydrogen bonds       : bond        0.03435 (  115)
  hydrogen bonds       : angle       6.49483 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8277 (ptt90)
REVERT: A   46 GLU cc_start: 0.8270 (tt0) cc_final: 0.8028 (tt0)
REVERT: C  347 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.7856 (t80)
  outliers start: 8
  outliers final: 5
  residues processed: 68
  average time/residue: 0.1433
  time to fit residues: 12.0028
Evaluate side-chains
  62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  468 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.119466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.110601 restraints weight = 33767.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 4.82
r_work: 0.3824 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3338  Z= 0.169
  Angle     :  0.609   6.605   4540  Z= 0.318
  Chirality :  0.045   0.227    485
  Planarity :  0.007   0.095    592
  Dihedral  :  7.556  73.782    468
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.37 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.25 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.40), residues: 410
  helix: -2.43 (0.81), residues: 28
  sheet: -0.68 (0.42), residues: 148
  loop : -0.79 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  18 
 TYR   0.016   0.001   TYR C 369 
 PHE   0.018   0.001   PHE A  67 
 TRP   0.004   0.001   TRP C 436 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 3334)
  covalent geometry    : angle       0.60616 ( 4532)
  SS BOND              : bond        0.00512 (    4)
  SS BOND              : angle       1.44040 (    8)
  hydrogen bonds       : bond        0.03115 (  115)
  hydrogen bonds       : angle       6.24641 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8438 (ptt90)
REVERT: C  347 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.7687 (t80)
REVERT: C  519 HIS cc_start: 0.6546 (OUTLIER) cc_final: 0.5944 (m90)
  outliers start: 7
  outliers final: 4
  residues processed: 65
  average time/residue: 0.1621
  time to fit residues: 12.7624
Evaluate side-chains
  60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  519 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 33 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.120285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.111324 restraints weight = 33463.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 4.85
r_work: 0.3842 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.4473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   3338  Z= 0.136
  Angle     :  0.573   6.102   4540  Z= 0.299
  Chirality :  0.044   0.213    485
  Planarity :  0.006   0.091    592
  Dihedral  :  7.260  73.178    468
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.61 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 15.54 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.33 (0.40), residues: 410
  helix: -2.10 (0.84), residues: 28
  sheet: -0.73 (0.41), residues: 154
  loop : -0.73 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  96 
 TYR   0.014   0.001   TYR C 369 
 PHE   0.006   0.001   PHE C 486 
 TRP   0.004   0.001   TRP B  94 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3334)
  covalent geometry    : angle       0.57132 ( 4532)
  SS BOND              : bond        0.00435 (    4)
  SS BOND              : angle       1.23913 (    8)
  hydrogen bonds       : bond        0.02829 (  115)
  hydrogen bonds       : angle       6.02516 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8302 (ptt90)
REVERT: C  465 GLU cc_start: 0.8756 (tp30) cc_final: 0.8396 (tt0)
REVERT: C  493 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8166 (mm110)
REVERT: C  519 HIS cc_start: 0.6466 (OUTLIER) cc_final: 0.6062 (m90)
  outliers start: 11
  outliers final: 9
  residues processed: 65
  average time/residue: 0.1635
  time to fit residues: 12.9220
Evaluate side-chains
  64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  519 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
C 501 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.119127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.110133 restraints weight = 33473.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.4020 rms_B_bonded: 4.88
r_work: 0.3825 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3338  Z= 0.147
  Angle     :  0.573   6.277   4540  Z= 0.300
  Chirality :  0.044   0.215    485
  Planarity :  0.006   0.086    592
  Dihedral  :  7.146  72.801    468
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.61 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.95 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.25 (0.40), residues: 410
  helix: -2.05 (0.86), residues: 28
  sheet: -0.65 (0.41), residues: 154
  loop : -0.70 (0.41), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  18 
 TYR   0.011   0.001   TYR C 369 
 PHE   0.006   0.001   PHE C 338 
 TRP   0.004   0.001   TRP B  94 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3334)
  covalent geometry    : angle       0.57127 ( 4532)
  SS BOND              : bond        0.00464 (    4)
  SS BOND              : angle       1.24836 (    8)
  hydrogen bonds       : bond        0.02756 (  115)
  hydrogen bonds       : angle       5.94332 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8247 (ptt90)
REVERT: C  493 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8227 (mm110)
REVERT: C  519 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.5962 (m90)
  outliers start: 11
  outliers final: 8
  residues processed: 67
  average time/residue: 0.1479
  time to fit residues: 12.2116
Evaluate side-chains
  67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  519 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 39 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.9782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.118706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.109253 restraints weight = 33070.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 5.12
r_work: 0.3808 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.4868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3338  Z= 0.152
  Angle     :  0.567   6.113   4540  Z= 0.297
  Chirality :  0.044   0.214    485
  Planarity :  0.006   0.082    592
  Dihedral  :  6.942  72.624    466
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.85 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.80 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.14 (0.41), residues: 410
  helix: -2.59 (0.87), residues: 22
  sheet: -0.66 (0.41), residues: 154
  loop : -0.54 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.010   0.001   TYR C 369 
 PHE   0.008   0.001   PHE C 338 
 TRP   0.004   0.001   TRP B  94 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3334)
  covalent geometry    : angle       0.56475 ( 4532)
  SS BOND              : bond        0.00458 (    4)
  SS BOND              : angle       1.26004 (    8)
  hydrogen bonds       : bond        0.02763 (  115)
  hydrogen bonds       : angle       5.90500 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8136 (ptt90)
REVERT: A   46 GLU cc_start: 0.8357 (tt0) cc_final: 0.8014 (tt0)
REVERT: C  465 GLU cc_start: 0.8767 (tp30) cc_final: 0.8441 (tt0)
REVERT: C  493 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8243 (mm110)
REVERT: C  519 HIS cc_start: 0.6611 (OUTLIER) cc_final: 0.5993 (m90)
  outliers start: 10
  outliers final: 6
  residues processed: 64
  average time/residue: 0.1551
  time to fit residues: 12.1425
Evaluate side-chains
  62 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  519 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 11 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0980
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.119434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.110444 restraints weight = 33109.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.4020 rms_B_bonded: 4.87
r_work: 0.3829 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.5007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   3338  Z= 0.108
  Angle     :  0.543   4.765   4540  Z= 0.282
  Chirality :  0.044   0.199    485
  Planarity :  0.005   0.077    592
  Dihedral  :  6.322  70.696    464
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.37 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 16.95 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.09 (0.41), residues: 410
  helix: -2.00 (0.87), residues: 28
  sheet: -0.62 (0.41), residues: 154
  loop : -0.51 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  38 
 TYR   0.010   0.001   TYR C 369 
 PHE   0.013   0.001   PHE C 347 
 TRP   0.005   0.001   TRP A  47 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3334)
  covalent geometry    : angle       0.54151 ( 4532)
  SS BOND              : bond        0.00233 (    4)
  SS BOND              : angle       1.02332 (    8)
  hydrogen bonds       : bond        0.02655 (  115)
  hydrogen bonds       : angle       5.82268 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8151 (ptt90)
REVERT: A   46 GLU cc_start: 0.8327 (tt0) cc_final: 0.8007 (tt0)
REVERT: B   96 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7996 (ttp-170)
REVERT: C  465 GLU cc_start: 0.8733 (tp30) cc_final: 0.8394 (tt0)
REVERT: C  493 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8333 (mm110)
REVERT: C  519 HIS cc_start: 0.6363 (OUTLIER) cc_final: 0.6012 (m90)
  outliers start: 11
  outliers final: 8
  residues processed: 67
  average time/residue: 0.1474
  time to fit residues: 12.0770
Evaluate side-chains
  68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue   18 LEU
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain C residue  347 PHE
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  519 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0020
   chunk 21 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.4988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.119792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.110718 restraints weight = 33510.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.4025 rms_B_bonded: 4.93
r_work: 0.3841 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.5142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3338  Z= 0.105
  Angle     :  0.526   4.811   4540  Z= 0.272
  Chirality :  0.043   0.134    485
  Planarity :  0.005   0.054    592
  Dihedral  :  6.240  71.217    464
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.37 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.08 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.01 (0.41), residues: 410
  helix: -1.93 (0.87), residues: 28
  sheet: -0.54 (0.42), residues: 144
  loop : -0.50 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  38 
 TYR   0.009   0.001   TYR C 369 
 PHE   0.014   0.001   PHE C 338 
 TRP   0.005   0.001   TRP A  47 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 3334)
  covalent geometry    : angle       0.52479 ( 4532)
  SS BOND              : bond        0.00358 (    4)
  SS BOND              : angle       0.99079 (    8)
  hydrogen bonds       : bond        0.02625 (  115)
  hydrogen bonds       : angle       5.71210 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8195 (ptt90)
REVERT: A   46 GLU cc_start: 0.8396 (tt0) cc_final: 0.8078 (tt0)
REVERT: C  465 GLU cc_start: 0.8717 (tp30) cc_final: 0.8364 (tt0)
REVERT: C  493 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8316 (mm110)
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.1412
  time to fit residues: 11.7907
Evaluate side-chains
  64 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  468 ILE
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  519 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 2 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.119222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.110154 restraints weight = 32778.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 4.89
r_work: 0.3828 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.5251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3338  Z= 0.138
  Angle     :  0.549   5.259   4540  Z= 0.285
  Chirality :  0.044   0.138    485
  Planarity :  0.005   0.052    592
  Dihedral  :  6.263  72.272    464
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.10 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 18.64 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.42), residues: 410
  helix: -1.95 (0.88), residues: 28
  sheet: -0.55 (0.43), residues: 144
  loop : -0.47 (0.43), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  38 
 TYR   0.008   0.001   TYR C 369 
 PHE   0.017   0.001   PHE C 338 
 TRP   0.004   0.001   TRP A  47 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3334)
  covalent geometry    : angle       0.54710 ( 4532)
  SS BOND              : bond        0.00390 (    4)
  SS BOND              : angle       1.14318 (    8)
  hydrogen bonds       : bond        0.02669 (  115)
  hydrogen bonds       : angle       5.68337 (  279)

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

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

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  820 Ramachandran restraints generated.
    410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8231 (ptt90)
REVERT: A   46 GLU cc_start: 0.8393 (tt0) cc_final: 0.8079 (tt0)
  outliers start: 6
  outliers final: 5
  residues processed: 59
  average time/residue: 0.1623
  time to fit residues: 11.5723
Evaluate side-chains
  60 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain C residue  361 CYS
Chi-restraints excluded: chain C residue  370 ASN
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  519 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.1980
   chunk 30 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
C 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.119685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.110501 restraints weight = 32998.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.4017 rms_B_bonded: 3.26
r_work: 0.3910 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.5336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3338  Z= 0.111
  Angle     :  0.538   5.239   4540  Z= 0.277
  Chirality :  0.043   0.135    485
  Planarity :  0.005   0.059    592
  Dihedral  :  6.088  70.889    464
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.37 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.36 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.42), residues: 410
  helix: -2.04 (0.84), residues: 28
  sheet: -0.29 (0.44), residues: 132
  loop : -0.44 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  38 
 TYR   0.007   0.001   TYR C 369 
 PHE   0.018   0.001   PHE C 338 
 TRP   0.005   0.001   TRP A  47 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3334)
  covalent geometry    : angle       0.53678 ( 4532)
  SS BOND              : bond        0.00359 (    4)
  SS BOND              : angle       0.97353 (    8)
  hydrogen bonds       : bond        0.02635 (  115)
  hydrogen bonds       : angle       5.61494 (  279)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2947.90 seconds
wall clock time: 50 minutes 42.03 seconds (3042.03 seconds total)