Starting phenix.real_space_refine
on Sat Apr  4 20:40:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xcb_66728/04_2026/9xcb_66728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xcb_66728/04_2026/9xcb_66728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xcb_66728/04_2026/9xcb_66728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xcb_66728/04_2026/9xcb_66728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xcb_66728/04_2026/9xcb_66728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xcb_66728/04_2026/9xcb_66728.cif"
  }
  resolution = 3.08
  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=   0.001
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      19      5.16       5
     C    2039      2.51       5
     N     494      2.21       5
     O     543      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3095
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3095
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 405, 3095
          Classifications: {'peptide': 405}
          Link IDs: {'PTRANS': 15, 'TRANS': 389}
          Chain breaks: 1
  Time building chain proxies: 0.83, per 1000 atoms: 0.27
  Number of scatterers: 3095
  At special positions: 0
  Unit cell: (71.4, 55.25, 72.25, 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      19     16.00
     O     543      8.00
     N     494      7.00
     C    2039      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 150.5 milliseconds
  

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  730

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      84.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 29
      removed outlier: 3.748A  pdb=" N   LYS A  29 " --> pdb=" O   TYR A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 42
      Proline residue:  A  36  - end of helix
      removed outlier: 3.774A  pdb=" N   GLU A  40 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 72
      removed outlier: 3.809A  pdb=" N   GLY A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   PHE A  51 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   PHE A  65 " --> pdb=" O   ALA A  61 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL A  66 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ASP A  72 " --> pdb=" O   GLY A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 96
      removed outlier: 4.180A  pdb=" N   TRP A  96 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 115
      removed outlier: 3.772A  pdb=" N   GLY A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 128
      removed outlier: 3.827A  pdb=" N   CYS A 121 " --> pdb=" O   GLY A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 163
      removed outlier: 3.705A  pdb=" N   SER A 144 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   MET A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASN A 146 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
      Proline residue:  A 153  - end of helix
      removed outlier: 3.863A  pdb=" N   ILE A 158 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU A 159 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 185
      removed outlier: 3.895A  pdb=" N   LEU A 185 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 222
    Processing helix  chain 'A' and resid 223 through 251
      removed outlier: 3.551A  pdb=" N   TRP A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 5.549A  pdb=" N   GLN A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   PHE A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 291
    Processing helix  chain 'A' and resid 300 through 321
    Processing helix  chain 'A' and resid 327 through 357
      removed outlier: 3.687A  pdb=" N   ILE A 331 " --> pdb=" O   PRO A 327 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY A 344 " --> pdb=" O   PHE A 340 " (cutoff:3.500A)
      Proline residue:  A 345  - end of helix
      removed outlier: 3.655A  pdb=" N   GLY A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ALA A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 380
      removed outlier: 3.858A  pdb=" N   SER A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   HIS A 366 " --> pdb=" O   CYS A 362 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   MET A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ASN A 374 " --> pdb=" O   GLY A 370 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL A 375 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 391
    Processing helix  chain 'A' and resid 392 through 414

    240 hydrogen bonds defined for protein.
    720 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: 0.46

  Time building geometry restraints manager: 0.36 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: 928
        1.34 -     1.46: 709
        1.46 -     1.57: 1514
        1.57 -     1.69: 0
        1.69 -     1.81: 31
  Bond restraints: 3182
  Sorted by residual:
  bond pdb=" CG  LEU A 125 "
       pdb=" CD1 LEU A 125 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.87e-01
  bond pdb=" C   LEU A 274 "
       pdb=" O   LEU A 274 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.15e-02 7.56e+03 6.04e-01
  bond pdb=" CA  ILE A 417 "
       pdb=" CB  ILE A 417 "
    ideal  model  delta    sigma   weight residual
    1.534  1.543 -0.009 1.22e-02 6.72e+03 5.75e-01
  bond pdb=" CB  CYS A 176 "
       pdb=" SG  CYS A 176 "
    ideal  model  delta    sigma   weight residual
    1.808  1.784  0.024 3.30e-02 9.18e+02 5.49e-01
  bond pdb=" C   LEU A 305 "
       pdb=" N   PHE A 306 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.31e-02 5.83e+03 5.00e-01
  ... (remaining 3177 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 4245
        1.96 -     3.92: 70
        3.92 -     5.88: 13
        5.88 -     7.83: 2
        7.83 -     9.79: 1
  Bond angle restraints: 4331
  Sorted by residual:
  angle pdb=" N   ILE A 417 "
        pdb=" CA  ILE A 417 "
        pdb=" C   ILE A 417 "
      ideal   model   delta    sigma   weight residual
     108.84  113.12   -4.28 1.32e+00 5.74e-01 1.05e+01
  angle pdb=" N   TRP A 118 "
        pdb=" CA  TRP A 118 "
        pdb=" C   TRP A 118 "
      ideal   model   delta    sigma   weight residual
     109.81  116.09   -6.28 2.21e+00 2.05e-01 8.06e+00
  angle pdb=" CA  LEU A 293 "
        pdb=" CB  LEU A 293 "
        pdb=" CG  LEU A 293 "
      ideal   model   delta    sigma   weight residual
     116.30  126.09   -9.79 3.50e+00 8.16e-02 7.83e+00
  angle pdb=" C   MET A 421 "
        pdb=" N   GLY A 422 "
        pdb=" CA  GLY A 422 "
      ideal   model   delta    sigma   weight residual
     121.41  116.71    4.70 1.96e+00 2.60e-01 5.75e+00
  angle pdb=" N   MET A 421 "
        pdb=" CA  MET A 421 "
        pdb=" C   MET A 421 "
      ideal   model   delta    sigma   weight residual
     110.80  115.63   -4.83 2.13e+00 2.20e-01 5.13e+00
  ... (remaining 4326 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.53: 1513
       12.53 -    25.06: 201
       25.06 -    37.59: 70
       37.59 -    50.11: 16
       50.11 -    62.64: 3
  Dihedral angle restraints: 1803
    sinusoidal: 654
      harmonic: 1149
  Sorted by residual:
  dihedral pdb=" CA  SER A 294 "
           pdb=" C   SER A 294 "
           pdb=" N   ASN A 295 "
           pdb=" CA  ASN A 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.07   21.93     0      5.00e+00 4.00e-02 1.92e+01
  dihedral pdb=" CA  ILE A 417 "
           pdb=" C   ILE A 417 "
           pdb=" N   ARG A 418 "
           pdb=" CA  ARG A 418 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.55   17.45     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  ASN A 416 "
           pdb=" C   ASN A 416 "
           pdb=" N   ILE A 417 "
           pdb=" CA  ILE A 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.11  -16.89     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 1800 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 278
       0.027 -    0.054: 135
       0.054 -    0.080: 54
       0.080 -    0.107: 20
       0.107 -    0.134: 3
  Chirality restraints: 490
  Sorted by residual:
  chirality pdb=" CA  TRP A 118 "
            pdb=" N   TRP A 118 "
            pdb=" C   TRP A 118 "
            pdb=" CB  TRP A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  ILE A  42 "
            pdb=" N   ILE A  42 "
            pdb=" C   ILE A  42 "
            pdb=" CB  ILE A  42 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.94e-01
  chirality pdb=" CB  ILE A 417 "
            pdb=" CA  ILE A 417 "
            pdb=" CG1 ILE A 417 "
            pdb=" CG2 ILE A 417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.12 2.00e-01 2.50e+01 3.80e-01
  ... (remaining 487 not shown)

  Planarity restraints: 530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 306 "   -0.012 2.00e-02 2.50e+03   1.28e-02 2.87e+00
        pdb=" CG  PHE A 306 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 306 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 306 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 306 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 306 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 306 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 250 "    0.011 2.00e-02 2.50e+03   1.11e-02 2.14e+00
        pdb=" CG  PHE A 250 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 250 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 250 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 250 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 250 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 250 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 118 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO A 119 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 119 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 119 "    0.020 5.00e-02 4.00e+02
  ... (remaining 527 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 31
        2.64 -     3.21: 2911
        3.21 -     3.77: 4932
        3.77 -     4.34: 6455
        4.34 -     4.90: 10850
  Nonbonded interactions: 25179
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 140 "
            pdb=" OG1 THR A 143 "
     model   vdw
     2.080 3.040
  nonbonded pdb=" O   LEU A 141 "
            pdb=" OG  SER A 144 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   LEU A 317 "
            pdb=" OG1 THR A 321 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OG1 THR A 136 "
            pdb=" OD2 ASP A 285 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   SER A 164 "
            pdb=" OG1 THR A 168 "
     model   vdw
     2.287 3.040
  ... (remaining 25174 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 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:             2.010
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.210
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
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      :  0.003   0.029   3182  Z= 0.146
  Angle     :  0.615   9.792   4331  Z= 0.313
  Chirality :  0.038   0.134    490
  Planarity :  0.004   0.035    530
  Dihedral  : 13.423  62.642   1073
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.71 (0.43), residues: 401
  helix:  1.77 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -1.98 (0.73), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 300 
 TYR   0.020   0.001   TYR A  24 
 PHE   0.030   0.002   PHE A 306 
 TRP   0.008   0.001   TRP A 138 
 HIS   0.001   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3182)
  covalent geometry    : angle       0.61453 ( 4331)
  hydrogen bonds       : bond        0.06249 (  240)
  hydrogen bonds       : angle       4.04667 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7485 (mm-40)
REVERT: A  254 GLU cc_start: 0.5977 (mm-30) cc_final: 0.5527 (mm-30)
REVERT: A  286 ARG cc_start: 0.7384 (mtp180) cc_final: 0.6793 (mmp80)
REVERT: A  288 MET cc_start: 0.5459 (tpt) cc_final: 0.4335 (mtm)
REVERT: A  356 SER cc_start: 0.8493 (m) cc_final: 0.8043 (p)
REVERT: A  398 TRP cc_start: 0.7575 (t60) cc_final: 0.7170 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0660
  time to fit residues: 6.1919
Evaluate side-chains
  60 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
A 146 ASN
A 248 GLN
A 366 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.185365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.160509 restraints weight = 3522.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 2.09
r_work: 0.3750 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   3182  Z= 0.146
  Angle     :  0.632   7.649   4331  Z= 0.311
  Chirality :  0.039   0.152    490
  Planarity :  0.005   0.043    530
  Dihedral  :  4.159  21.669    431
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.99 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  8.26 %
    Favored  : 89.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.43), residues: 401
  helix:  1.88 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.64 (0.71), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 300 
 TYR   0.019   0.001   TYR A  24 
 PHE   0.027   0.001   PHE A 250 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.001   0.001   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 3182)
  covalent geometry    : angle       0.63230 ( 4331)
  hydrogen bonds       : bond        0.03947 (  240)
  hydrogen bonds       : angle       3.63732 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.106 
Fit side-chains
REVERT: A  254 GLU cc_start: 0.5898 (mm-30) cc_final: 0.5422 (mm-30)
REVERT: A  286 ARG cc_start: 0.7699 (mtp180) cc_final: 0.7043 (tpp-160)
REVERT: A  288 MET cc_start: 0.5414 (tpt) cc_final: 0.4434 (mtm)
REVERT: A  329 LEU cc_start: 0.8289 (tp) cc_final: 0.8016 (mt)
REVERT: A  356 SER cc_start: 0.8392 (m) cc_final: 0.8092 (p)
REVERT: A  398 TRP cc_start: 0.7552 (t60) cc_final: 0.7079 (t60)
  outliers start: 6
  outliers final: 2
  residues processed: 62
  average time/residue: 0.0561
  time to fit residues: 4.3891
Evaluate side-chains
  59 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 GLU
Chi-restraints excluded: chain A residue  413 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 3 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0570
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5298

-------------------------------------------------------------------------------
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 = 0.4138 r_free = 0.4138 target = 0.185948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.160901 restraints weight = 3558.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 2.08
r_work: 0.3760 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3182  Z= 0.127
  Angle     :  0.575   6.601   4331  Z= 0.289
  Chirality :  0.038   0.138    490
  Planarity :  0.005   0.043    530
  Dihedral  :  4.055  21.314    431
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.99 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 11.93 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.43), residues: 401
  helix:  2.06 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.56 (0.72), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 126 
 TYR   0.015   0.001   TYR A  24 
 PHE   0.016   0.001   PHE A 250 
 TRP   0.011   0.001   TRP A 165 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3182)
  covalent geometry    : angle       0.57464 ( 4331)
  hydrogen bonds       : bond        0.03698 (  240)
  hydrogen bonds       : angle       3.47748 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  254 GLU cc_start: 0.5877 (mm-30) cc_final: 0.5379 (mm-30)
REVERT: A  286 ARG cc_start: 0.7670 (mtp180) cc_final: 0.6986 (tpp-160)
REVERT: A  288 MET cc_start: 0.5347 (tpt) cc_final: 0.4274 (mtm)
REVERT: A  356 SER cc_start: 0.8252 (m) cc_final: 0.7868 (p)
REVERT: A  398 TRP cc_start: 0.7547 (t60) cc_final: 0.7054 (t60)
  outliers start: 4
  outliers final: 1
  residues processed: 58
  average time/residue: 0.0564
  time to fit residues: 4.1292
Evaluate side-chains
  56 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0060
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0030
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.4006

-------------------------------------------------------------------------------
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 = 0.4151 r_free = 0.4151 target = 0.187576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.162767 restraints weight = 3510.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 2.06
r_work: 0.3778 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3182  Z= 0.112
  Angle     :  0.548   7.096   4331  Z= 0.275
  Chirality :  0.037   0.133    490
  Planarity :  0.005   0.044    530
  Dihedral  :  3.967  19.871    431
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.99 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 12.54 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.38 (0.43), residues: 401
  helix:  2.20 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.38 (0.73), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 126 
 TYR   0.012   0.001   TYR A  24 
 PHE   0.011   0.001   PHE A 250 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.001   0.000   HIS A 301 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 3182)
  covalent geometry    : angle       0.54822 ( 4331)
  hydrogen bonds       : bond        0.03492 (  240)
  hydrogen bonds       : angle       3.35041 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.7625 (OUTLIER) cc_final: 0.6292 (t-100)
REVERT: A  254 GLU cc_start: 0.5848 (mm-30) cc_final: 0.5328 (mm-30)
REVERT: A  286 ARG cc_start: 0.7675 (mtp180) cc_final: 0.6991 (tpp-160)
REVERT: A  288 MET cc_start: 0.5385 (tpt) cc_final: 0.3986 (mtp)
REVERT: A  356 SER cc_start: 0.8209 (m) cc_final: 0.7940 (p)
REVERT: A  398 TRP cc_start: 0.7536 (t60) cc_final: 0.7066 (t60)
  outliers start: 5
  outliers final: 3
  residues processed: 60
  average time/residue: 0.0401
  time to fit residues: 3.1207
Evaluate side-chains
  60 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  413 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0980
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.184576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.159325 restraints weight = 3516.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 2.09
r_work: 0.3737 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
moved from start:          0.1829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3182  Z= 0.138
  Angle     :  0.585   6.987   4331  Z= 0.293
  Chirality :  0.038   0.138    490
  Planarity :  0.005   0.044    530
  Dihedral  :  4.028  19.525    431
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.49 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 13.15 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.43), residues: 401
  helix:  2.04 (0.29), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.38 (0.74), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 126 
 TYR   0.016   0.001   TYR A  24 
 PHE   0.016   0.001   PHE A 250 
 TRP   0.008   0.001   TRP A 128 
 HIS   0.001   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3182)
  covalent geometry    : angle       0.58451 ( 4331)
  hydrogen bonds       : bond        0.03778 (  240)
  hydrogen bonds       : angle       3.47376 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 TRP cc_start: 0.7619 (OUTLIER) cc_final: 0.6291 (t-100)
REVERT: A  254 GLU cc_start: 0.5920 (mm-30) cc_final: 0.5339 (mm-30)
REVERT: A  286 ARG cc_start: 0.7698 (mtp180) cc_final: 0.6988 (tpp-160)
REVERT: A  356 SER cc_start: 0.8216 (m) cc_final: 0.7963 (p)
REVERT: A  398 TRP cc_start: 0.7564 (t60) cc_final: 0.7133 (t60)
  outliers start: 7
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0573
  time to fit residues: 4.4489
Evaluate side-chains
  61 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  413 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 GLN ** 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 = 0.4114 r_free = 0.4114 target = 0.183293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.158474 restraints weight = 3497.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3855 rms_B_bonded: 2.06
r_work: 0.3735 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3182  Z= 0.152
  Angle     :  0.618   8.999   4331  Z= 0.307
  Chirality :  0.039   0.141    490
  Planarity :  0.005   0.045    530
  Dihedral  :  4.178  19.236    431
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.49 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.46 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.43), residues: 401
  helix:  1.99 (0.28), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.36 (0.76), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 126 
 TYR   0.016   0.001   TYR A  24 
 PHE   0.020   0.001   PHE A 250 
 TRP   0.008   0.001   TRP A 118 
 HIS   0.002   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3182)
  covalent geometry    : angle       0.61758 ( 4331)
  hydrogen bonds       : bond        0.03873 (  240)
  hydrogen bonds       : angle       3.55327 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.6308 (t-100)
REVERT: A  126 ARG cc_start: 0.6794 (tpm170) cc_final: 0.6025 (tpt-90)
REVERT: A  254 GLU cc_start: 0.5939 (mm-30) cc_final: 0.5414 (mm-30)
REVERT: A  286 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7056 (tpp-160)
REVERT: A  288 MET cc_start: 0.5272 (tpt) cc_final: 0.4072 (mtm)
REVERT: A  356 SER cc_start: 0.8196 (m) cc_final: 0.7922 (p)
REVERT: A  398 TRP cc_start: 0.7542 (t60) cc_final: 0.7109 (t60)
  outliers start: 8
  outliers final: 5
  residues processed: 63
  average time/residue: 0.0677
  time to fit residues: 5.2069
Evaluate side-chains
  62 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  303 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    0.0270
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0060
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4854

-------------------------------------------------------------------------------
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 = 0.4147 r_free = 0.4147 target = 0.186933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.161869 restraints weight = 3542.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 2.09
r_work: 0.3768 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3182  Z= 0.119
  Angle     :  0.585   8.708   4331  Z= 0.291
  Chirality :  0.037   0.132    490
  Planarity :  0.005   0.044    530
  Dihedral  :  4.116  19.638    431
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.24 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.68 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.40 (0.43), residues: 401
  helix:  2.20 (0.28), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.30 (0.76), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 126 
 TYR   0.012   0.001   TYR A  24 
 PHE   0.012   0.001   PHE A 250 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.001   0.001   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3182)
  covalent geometry    : angle       0.58516 ( 4331)
  hydrogen bonds       : bond        0.03515 (  240)
  hydrogen bonds       : angle       3.42539 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.7557 (OUTLIER) cc_final: 0.6247 (t-100)
REVERT: A  254 GLU cc_start: 0.5918 (mm-30) cc_final: 0.5395 (mm-30)
REVERT: A  286 ARG cc_start: 0.7628 (mtp180) cc_final: 0.6727 (mtp85)
REVERT: A  288 MET cc_start: 0.5117 (tpt) cc_final: 0.3918 (mtt)
REVERT: A  356 SER cc_start: 0.8127 (m) cc_final: 0.7892 (p)
REVERT: A  398 TRP cc_start: 0.7547 (t60) cc_final: 0.7098 (t60)
  outliers start: 5
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0555
  time to fit residues: 4.1281
Evaluate side-chains
  62 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  303 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0050
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0770
   chunk 14 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.3952

-------------------------------------------------------------------------------
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 = 0.4154 r_free = 0.4154 target = 0.187583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.162625 restraints weight = 3594.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 2.09
r_work: 0.3783 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3182  Z= 0.116
  Angle     :  0.589   8.771   4331  Z= 0.292
  Chirality :  0.037   0.130    490
  Planarity :  0.005   0.044    530
  Dihedral  :  4.053  18.971    431
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.49 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 14.68 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.43), residues: 401
  helix:  2.29 (0.28), residues: 327
  sheet:  None (None), residues: 0
  loop : -1.30 (0.75), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 418 
 TYR   0.011   0.001   TYR A  24 
 PHE   0.009   0.001   PHE A 250 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.001   0.000   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 3182)
  covalent geometry    : angle       0.58860 ( 4331)
  hydrogen bonds       : bond        0.03393 (  240)
  hydrogen bonds       : angle       3.35678 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: A  107 TRP cc_start: 0.7563 (OUTLIER) cc_final: 0.6157 (t-100)
REVERT: A  126 ARG cc_start: 0.6781 (tpm170) cc_final: 0.5967 (tpt-90)
REVERT: A  254 GLU cc_start: 0.5904 (mm-30) cc_final: 0.5400 (mm-30)
REVERT: A  286 ARG cc_start: 0.7561 (mtp180) cc_final: 0.6903 (tpp-160)
REVERT: A  288 MET cc_start: 0.5106 (tpt) cc_final: 0.3940 (mtp)
REVERT: A  398 TRP cc_start: 0.7567 (t60) cc_final: 0.7102 (t60)
  outliers start: 5
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0591
  time to fit residues: 4.3303
Evaluate side-chains
  60 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  413 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0050
   overall best weight:    0.3394

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.188538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.163828 restraints weight = 3596.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 2.07
r_work: 0.3798 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3182  Z= 0.110
  Angle     :  0.594   8.706   4331  Z= 0.291
  Chirality :  0.036   0.129    490
  Planarity :  0.005   0.044    530
  Dihedral  :  4.040  19.175    431
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.99 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.68 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.43), residues: 401
  helix:  2.37 (0.28), residues: 326
  sheet:  None (None), residues: 0
  loop : -1.29 (0.74), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 126 
 TYR   0.010   0.001   TYR A  24 
 PHE   0.007   0.001   PHE A  94 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.001   0.000   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3182)
  covalent geometry    : angle       0.59366 ( 4331)
  hydrogen bonds       : bond        0.03286 (  240)
  hydrogen bonds       : angle       3.33389 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.7558 (OUTLIER) cc_final: 0.6114 (t-100)
REVERT: A  126 ARG cc_start: 0.6898 (tpm170) cc_final: 0.6143 (tpt-90)
REVERT: A  254 GLU cc_start: 0.5891 (mm-30) cc_final: 0.5394 (mm-30)
REVERT: A  286 ARG cc_start: 0.7565 (mtp180) cc_final: 0.6914 (tpp-160)
REVERT: A  288 MET cc_start: 0.5001 (tpt) cc_final: 0.3837 (mtt)
REVERT: A  398 TRP cc_start: 0.7563 (t60) cc_final: 0.7107 (t60)
  outliers start: 7
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0587
  time to fit residues: 4.3019
Evaluate side-chains
  62 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  413 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0370
   chunk 18 optimal weight:    5.9990
   chunk 30 optimal weight:    0.2980
   chunk 27 optimal weight:    3.9990
   chunk 3 optimal weight:    0.2980
   chunk 11 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.4258

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.188330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.163523 restraints weight = 3467.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 2.07
r_work: 0.3792 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3182  Z= 0.116
  Angle     :  0.605   9.196   4331  Z= 0.294
  Chirality :  0.037   0.137    490
  Planarity :  0.005   0.045    530
  Dihedral  :  4.075  18.884    431
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  4.99 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.68 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.43), residues: 401
  helix:  2.32 (0.28), residues: 326
  sheet:  None (None), residues: 0
  loop : -1.24 (0.75), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 126 
 TYR   0.011   0.001   TYR A  24 
 PHE   0.008   0.001   PHE A  94 
 TRP   0.009   0.001   TRP A 165 
 HIS   0.001   0.000   HIS A 366 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 3182)
  covalent geometry    : angle       0.60490 ( 4331)
  hydrogen bonds       : bond        0.03350 (  240)
  hydrogen bonds       : angle       3.34851 (  720)

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

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

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  802 Ramachandran restraints generated.
    401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  107 TRP cc_start: 0.7574 (OUTLIER) cc_final: 0.6094 (t-100)
REVERT: A  126 ARG cc_start: 0.6839 (tpm170) cc_final: 0.6108 (tpt-90)
REVERT: A  254 GLU cc_start: 0.5855 (mm-30) cc_final: 0.5365 (mm-30)
REVERT: A  286 ARG cc_start: 0.7538 (mtp180) cc_final: 0.6920 (tpp-160)
REVERT: A  288 MET cc_start: 0.5043 (tpt) cc_final: 0.3926 (mtp)
REVERT: A  398 TRP cc_start: 0.7573 (t60) cc_final: 0.7104 (t60)
  outliers start: 7
  outliers final: 6
  residues processed: 59
  average time/residue: 0.0599
  time to fit residues: 4.4159
Evaluate side-chains
  62 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 MET
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  107 TRP
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  413 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.4102 r_free = 0.4102 target = 0.182629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.157628 restraints weight = 3567.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 2.09
r_work: 0.3727 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3182  Z= 0.159
  Angle     :  0.670   8.931   4331  Z= 0.329
  Chirality :  0.039   0.148    490
  Planarity :  0.005   0.046    530
  Dihedral  :  4.301  20.471    431
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.24 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.98 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.42), residues: 401
  helix:  2.01 (0.28), residues: 326
  sheet:  None (None), residues: 0
  loop : -1.40 (0.74), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  28 
 TYR   0.016   0.002   TYR A  24 
 PHE   0.015   0.001   PHE A 250 
 TRP   0.010   0.001   TRP A 128 
 HIS   0.002   0.001   HIS A 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3182)
  covalent geometry    : angle       0.66957 ( 4331)
  hydrogen bonds       : bond        0.03961 (  240)
  hydrogen bonds       : angle       3.58388 (  720)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 853.14 seconds
wall clock time: 15 minutes 18.33 seconds (918.33 seconds total)