Starting phenix.real_space_refine
on Tue Mar  3 12:05:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zha_14728/03_2026/7zha_14728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zha_14728/03_2026/7zha_14728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zha_14728/03_2026/7zha_14728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zha_14728/03_2026/7zha_14728.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zha_14728/03_2026/7zha_14728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zha_14728/03_2026/7zha_14728.cif"
  }
  resolution = 3.55
  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      22      5.16       5
     C    2543      2.51       5
     N     632      2.21       5
     O     639      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3836
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 487, 3811
          Classifications: {'peptide': 487}
          Link IDs: {'PTRANS': 23, 'TRANS': 463}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'JDW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.93, per 1000 atoms: 0.24
  Number of scatterers: 3836
  At special positions: 0
  Unit cell: (98.34, 64.02, 81.84, 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      22     16.00
     O     639      8.00
     N     632      7.00
     C    2543      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  51 " - pdb=" SG  CYS A 127 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  90 " - pdb=" SG  CYS A 148 " distance=2.03

  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: 0.30
  Conformation dependent library (CDL) restraints added in 124.1 milliseconds
  

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  882

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 1 sheets defined
      80.9% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 11
    Processing helix  chain 'A' and resid 15 through 42
      removed outlier: 4.722A  pdb=" N   VAL A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   VAL A  40 " --> pdb=" O   PHE A  36 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   PHE A  41 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 64
    Processing helix  chain 'A' and resid 66 through 75
    Processing helix  chain 'A' and resid 139 through 145
    Processing helix  chain 'A' and resid 147 through 150
    Processing helix  chain 'A' and resid 151 through 179
      removed outlier: 4.039A  pdb=" N   ASP A 155 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLN A 158 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   TYR A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 201
    Processing helix  chain 'A' and resid 204 through 234
      removed outlier: 3.976A  pdb=" N   PHE A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL A 234 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 264
      Proline residue:  A 258  - end of helix
      removed outlier: 3.856A  pdb=" N   ILE A 264 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 283
      Proline residue:  A 277  - end of helix
      removed outlier: 3.932A  pdb=" N   LEU A 280 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 288
    Processing helix  chain 'A' and resid 291 through 296
    Processing helix  chain 'A' and resid 301 through 313
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 344 through 373
      removed outlier: 3.942A  pdb=" N   MET A 370 " --> pdb=" O   GLN A 366 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ARG A 371 " --> pdb=" O   GLY A 367 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLY A 373 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 404
      removed outlier: 3.842A  pdb=" N   LEU A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 406 through 427
    Processing helix  chain 'A' and resid 431 through 436
      removed outlier: 4.339A  pdb=" N   THR A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 461
      removed outlier: 3.763A  pdb=" N   TYR A 461 " --> pdb=" O   ASN A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 495
      Proline residue:  A 485  - end of helix
      removed outlier: 3.914A  pdb=" N   VAL A 494 " --> pdb=" O   ARG A 490 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TRP A 495 " --> pdb=" O   LEU A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 514
      removed outlier: 3.831A  pdb=" N   ILE A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 517
      No H-bonds generated for 'chain 'A' and resid 515 through 517'
    Processing helix  chain 'A' and resid 527 through 535
      removed outlier: 4.406A  pdb=" N   ASP A 531 " --> pdb=" O   THR A 528 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL A 532 " --> pdb=" O   VAL A 529 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A 534 " --> pdb=" O   ASP A 531 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51

    270 hydrogen bonds defined for protein.
    792 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: 0.57

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1174
        1.34 -     1.46: 782
        1.46 -     1.58: 1947
        1.58 -     1.70: 0
        1.70 -     1.81: 30
  Bond restraints: 3933
  Sorted by residual:
  bond pdb=" C11 JDW A 601 "
       pdb=" N1  JDW A 601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.435 -0.098 2.00e-02 2.50e+03 2.41e+01
  bond pdb=" C13 JDW A 601 "
       pdb=" N2  JDW A 601 "
    ideal  model  delta    sigma   weight residual
    1.334  1.415 -0.081 2.00e-02 2.50e+03 1.64e+01
  bond pdb=" C3  JDW A 601 "
       pdb=" N1  JDW A 601 "
    ideal  model  delta    sigma   weight residual
    1.382  1.451 -0.069 2.00e-02 2.50e+03 1.17e+01
  bond pdb=" N   ASP A   5 "
       pdb=" CA  ASP A   5 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.16e-02 7.43e+03 6.76e+00
  bond pdb=" C7  JDW A 601 "
       pdb=" C8  JDW A 601 "
    ideal  model  delta    sigma   weight residual
    1.411  1.359  0.052 2.00e-02 2.50e+03 6.71e+00
  ... (remaining 3928 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 5103
        1.50 -     3.01: 194
        3.01 -     4.51: 39
        4.51 -     6.02: 9
        6.02 -     7.52: 8
  Bond angle restraints: 5353
  Sorted by residual:
  angle pdb=" CA  MET A 248 "
        pdb=" CB  MET A 248 "
        pdb=" CG  MET A 248 "
      ideal   model   delta    sigma   weight residual
     114.10  120.74   -6.64 2.00e+00 2.50e-01 1.10e+01
  angle pdb=" CA  ASP A   5 "
        pdb=" C   ASP A   5 "
        pdb=" O   ASP A   5 "
      ideal   model   delta    sigma   weight residual
     121.07  118.19    2.88 1.10e+00 8.26e-01 6.84e+00
  angle pdb=" C   TRP A 152 "
        pdb=" N   MET A 153 "
        pdb=" CA  MET A 153 "
      ideal   model   delta    sigma   weight residual
     121.18  116.03    5.15 1.98e+00 2.55e-01 6.77e+00
  angle pdb=" N   VAL A 529 "
        pdb=" CA  VAL A 529 "
        pdb=" C   VAL A 529 "
      ideal   model   delta    sigma   weight residual
     111.91  109.63    2.28 8.90e-01 1.26e+00 6.57e+00
  angle pdb=" CA  THR A 528 "
        pdb=" CB  THR A 528 "
        pdb=" CG2 THR A 528 "
      ideal   model   delta    sigma   weight residual
     110.50  114.77   -4.27 1.70e+00 3.46e-01 6.31e+00
  ... (remaining 5348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.84: 1997
       15.84 -    31.69: 203
       31.69 -    47.53: 57
       47.53 -    63.37: 9
       63.37 -    79.22: 5
  Dihedral angle restraints: 2271
    sinusoidal: 892
      harmonic: 1379
  Sorted by residual:
  dihedral pdb=" CB  CYS A  51 "
           pdb=" SG  CYS A  51 "
           pdb=" SG  CYS A 127 "
           pdb=" CB  CYS A 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   43.38   49.62     1      1.00e+01 1.00e-02 3.38e+01
  dihedral pdb=" CB  CYS A  90 "
           pdb=" SG  CYS A  90 "
           pdb=" SG  CYS A 148 "
           pdb=" CB  CYS A 148 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.09   39.09     1      1.00e+01 1.00e-02 2.15e+01
  dihedral pdb=" CA  ASN A 467 "
           pdb=" C   ASN A 467 "
           pdb=" N   PHE A 468 "
           pdb=" CA  PHE A 468 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.97  -18.03     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 2268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 534
       0.060 -    0.119: 75
       0.119 -    0.179: 9
       0.179 -    0.239: 0
       0.239 -    0.299: 1
  Chirality restraints: 619
  Sorted by residual:
  chirality pdb=" CG  LEU A 124 "
            pdb=" CB  LEU A 124 "
            pdb=" CD1 LEU A 124 "
            pdb=" CD2 LEU A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  MET A 153 "
            pdb=" N   MET A 153 "
            pdb=" C   MET A 153 "
            pdb=" CB  MET A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.06e-01
  chirality pdb=" CB  THR A 528 "
            pdb=" CA  THR A 528 "
            pdb=" OG1 THR A 528 "
            pdb=" CG2 THR A 528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.35e-01
  ... (remaining 616 not shown)

  Planarity restraints: 660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 291 "   -0.050 5.00e-02 4.00e+02   7.57e-02 9.16e+00
        pdb=" N   PRO A 292 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 292 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 292 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 284 "    0.008 2.00e-02 2.50e+03   1.37e-02 3.77e+00
        pdb=" CG  TYR A 284 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 284 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 284 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 284 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 284 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 284 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 284 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  34 "   -0.010 2.00e-02 2.50e+03   1.19e-02 2.47e+00
        pdb=" CG  PHE A  34 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  34 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  34 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  34 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  34 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 657 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1337
        2.86 -     3.37: 4259
        3.37 -     3.88: 6345
        3.88 -     4.39: 6927
        4.39 -     4.90: 11467
  Nonbonded interactions: 30335
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 343 "
            pdb=" OG1 THR A 344 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" NH1 ARG A 407 "
            pdb=" O   LEU A 517 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" O   LEU A 154 "
            pdb=" OG1 THR A 157 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OG1 THR A  28 "
            pdb=" OH  TYR A 185 "
     model   vdw
     2.380 3.040
  nonbonded pdb=" NE2 GLN A  18 "
            pdb=" O   ILE A 233 "
     model   vdw
     2.395 3.120
  ... (remaining 30330 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.380
  Find NCS groups from input model:        0.020
  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:1.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098   3935  Z= 0.234
  Angle     :  0.734   7.522   5357  Z= 0.377
  Chirality :  0.044   0.299    619
  Planarity :  0.005   0.076    660
  Dihedral  : 14.090  79.215   1383
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 16.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  0.99 %
    Favored  : 98.51 %
  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:  1.39 (0.39), residues: 479
  helix:  1.52 (0.28), residues: 348
  sheet:  None (None), residues: 0
  loop : -0.62 (0.56), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  92 
 TYR   0.031   0.002   TYR A 284 
 PHE   0.028   0.002   PHE A  34 
 TRP   0.021   0.002   TRP A  65 
 HIS   0.002   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 3933)
  covalent geometry    : angle       0.73448 ( 5353)
  SS BOND              : bond        0.00032 (    2)
  SS BOND              : angle       0.61789 (    4)
  hydrogen bonds       : bond        0.12180 (  270)
  hydrogen bonds       : angle       5.17540 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 SER cc_start: 0.5832 (OUTLIER) cc_final: 0.4119 (p)
REVERT: A  281 PHE cc_start: 0.8611 (m-10) cc_final: 0.8375 (m-80)
REVERT: A  530 ASP cc_start: 0.8017 (m-30) cc_final: 0.7816 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 95
  average time/residue: 0.0527
  time to fit residues: 6.6264
Evaluate side-chains
  77 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0870
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0970
   chunk 32 optimal weight:    0.0670
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.2294

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

Flipped N/Q/H residues before XYZ refinement:
A 266 ASN
A 335 ASN
** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.182966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.161885 restraints weight = 6304.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.166784 restraints weight = 2935.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.169859 restraints weight = 1683.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.171734 restraints weight = 1125.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.173141 restraints weight = 856.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3935  Z= 0.137
  Angle     :  0.653   8.242   5357  Z= 0.329
  Chirality :  0.041   0.177    619
  Planarity :  0.005   0.051    660
  Dihedral  :  4.430  23.040    537
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 12.90 %
    Favored  : 83.87 %
  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 (0.39), residues: 479
  helix:  1.68 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.43 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  92 
 TYR   0.014   0.001   TYR A 284 
 PHE   0.016   0.002   PHE A  41 
 TRP   0.013   0.001   TRP A  71 
 HIS   0.006   0.003   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3933)
  covalent geometry    : angle       0.65248 ( 5353)
  SS BOND              : bond        0.00196 (    2)
  SS BOND              : angle       0.97659 (    4)
  hydrogen bonds       : bond        0.04586 (  270)
  hydrogen bonds       : angle       4.42351 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 TYR cc_start: 0.7616 (t80) cc_final: 0.7395 (t80)
REVERT: A  331 GLU cc_start: 0.7913 (tp30) cc_final: 0.7613 (tp30)
  outliers start: 13
  outliers final: 7
  residues processed: 87
  average time/residue: 0.0514
  time to fit residues: 6.0082
Evaluate side-chains
  78 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  438 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 16 optimal weight:    0.0040
   chunk 45 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 19 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** 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 = 0.4289 r_free = 0.4289 target = 0.180501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.159453 restraints weight = 6193.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.164112 restraints weight = 2857.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.167174 restraints weight = 1637.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.169039 restraints weight = 1094.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.170398 restraints weight = 830.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3935  Z= 0.144
  Angle     :  0.641   7.973   5357  Z= 0.324
  Chirality :  0.040   0.164    619
  Planarity :  0.005   0.040    660
  Dihedral  :  4.245  21.680    536
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.38 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 15.38 %
    Favored  : 80.65 %
  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:  1.84 (0.40), residues: 479
  helix:  1.81 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.48 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  87 
 TYR   0.014   0.002   TYR A 284 
 PHE   0.023   0.002   PHE A 356 
 TRP   0.025   0.001   TRP A  71 
 HIS   0.002   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3933)
  covalent geometry    : angle       0.64138 ( 5353)
  SS BOND              : bond        0.00178 (    2)
  SS BOND              : angle       0.36477 (    4)
  hydrogen bonds       : bond        0.04623 (  270)
  hydrogen bonds       : angle       4.42511 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  223 TRP cc_start: 0.8007 (t-100) cc_final: 0.7765 (t-100)
REVERT: A  513 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7341 (mm)
REVERT: A  515 MET cc_start: 0.8096 (tpp) cc_final: 0.7850 (tpp)
  outliers start: 16
  outliers final: 12
  residues processed: 84
  average time/residue: 0.0469
  time to fit residues: 5.3896
Evaluate side-chains
  80 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  513 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0970
   chunk 7 optimal weight:    5.9990
   chunk 27 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   chunk 24 optimal weight:    0.2980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.3378

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

Flipped N/Q/H residues before XYZ refinement:
A  48 HIS
A 266 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.178853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.157831 restraints weight = 6209.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.162517 restraints weight = 2914.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.165623 restraints weight = 1680.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.167429 restraints weight = 1121.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.168815 restraints weight = 857.396|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3935  Z= 0.130
  Angle     :  0.629  12.616   5357  Z= 0.312
  Chirality :  0.039   0.135    619
  Planarity :  0.004   0.033    660
  Dihedral  :  4.107  18.709    536
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.59 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.35 %
    Favored  : 76.92 %
  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:  1.86 (0.40), residues: 479
  helix:  1.85 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.56 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  87 
 TYR   0.011   0.001   TYR A 284 
 PHE   0.017   0.002   PHE A 356 
 TRP   0.016   0.001   TRP A  71 
 HIS   0.003   0.001   HIS A  48 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3933)
  covalent geometry    : angle       0.62944 ( 5353)
  SS BOND              : bond        0.00109 (    2)
  SS BOND              : angle       0.58614 (    4)
  hydrogen bonds       : bond        0.04277 (  270)
  hydrogen bonds       : angle       4.30229 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.5239 (OUTLIER) cc_final: 0.4907 (m-10)
REVERT: A  131 TRP cc_start: 0.7925 (m100) cc_final: 0.7592 (m100)
REVERT: A  223 TRP cc_start: 0.7902 (t-100) cc_final: 0.7687 (t-100)
REVERT: A  513 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7318 (mm)
REVERT: A  515 MET cc_start: 0.8104 (tpp) cc_final: 0.7809 (tpp)
  outliers start: 15
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0512
  time to fit residues: 5.7430
Evaluate side-chains
  82 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  513 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 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 = 0.4203 r_free = 0.4203 target = 0.173068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.152056 restraints weight = 6311.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.156642 restraints weight = 2921.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.159507 restraints weight = 1683.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.161485 restraints weight = 1139.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.162727 restraints weight = 859.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3935  Z= 0.160
  Angle     :  0.657  10.937   5357  Z= 0.332
  Chirality :  0.040   0.146    619
  Planarity :  0.004   0.035    660
  Dihedral  :  4.175  19.407    536
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.80 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 18.61 %
    Favored  : 76.43 %
  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:  1.73 (0.40), residues: 479
  helix:  1.75 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.63 (0.60), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 406 
 TYR   0.012   0.002   TYR A 284 
 PHE   0.020   0.002   PHE A  41 
 TRP   0.019   0.001   TRP A  71 
 HIS   0.002   0.002   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 3933)
  covalent geometry    : angle       0.65675 ( 5353)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.54012 (    4)
  hydrogen bonds       : bond        0.04826 (  270)
  hydrogen bonds       : angle       4.51826 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.5505 (OUTLIER) cc_final: 0.5100 (m-10)
  outliers start: 20
  outliers final: 14
  residues processed: 76
  average time/residue: 0.0568
  time to fit residues: 5.7049
Evaluate side-chains
  76 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  436 THR
Chi-restraints excluded: chain A residue  438 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0050
   overall best weight:    0.6194

-------------------------------------------------------------------------------
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 = 0.4216 r_free = 0.4216 target = 0.174101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.153223 restraints weight = 6283.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.157822 restraints weight = 2926.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.160790 restraints weight = 1684.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.162606 restraints weight = 1125.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.163923 restraints weight = 857.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3935  Z= 0.145
  Angle     :  0.653  13.363   5357  Z= 0.328
  Chirality :  0.039   0.143    619
  Planarity :  0.004   0.036    660
  Dihedral  :  4.206  18.675    536
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.22 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 20.35 %
    Favored  : 75.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.68 (0.40), residues: 479
  helix:  1.74 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.71 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 128 
 TYR   0.019   0.002   TYR A 284 
 PHE   0.024   0.002   PHE A 356 
 TRP   0.016   0.001   TRP A  71 
 HIS   0.002   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3933)
  covalent geometry    : angle       0.65293 ( 5353)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       0.61220 (    4)
  hydrogen bonds       : bond        0.04590 (  270)
  hydrogen bonds       : angle       4.42163 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.5479 (OUTLIER) cc_final: 0.5069 (m-10)
REVERT: A  281 PHE cc_start: 0.8814 (m-10) cc_final: 0.8507 (m-80)
REVERT: A  284 TYR cc_start: 0.6543 (m-80) cc_final: 0.6132 (m-80)
  outliers start: 16
  outliers final: 11
  residues processed: 76
  average time/residue: 0.0527
  time to fit residues: 5.2574
Evaluate side-chains
  78 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  438 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0770
   chunk 19 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.4220 r_free = 0.4220 target = 0.174960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.154197 restraints weight = 6361.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.158804 restraints weight = 2917.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.161799 restraints weight = 1653.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.163610 restraints weight = 1099.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.164708 restraints weight = 831.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3935  Z= 0.144
  Angle     :  0.654  12.996   5357  Z= 0.329
  Chirality :  0.039   0.143    619
  Planarity :  0.004   0.036    660
  Dihedral  :  4.183  18.120    536
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.59 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 20.60 %
    Favored  : 74.69 %
  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:  1.73 (0.40), residues: 479
  helix:  1.83 (0.28), residues: 351
  sheet:  None (None), residues: 0
  loop : -0.77 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 128 
 TYR   0.018   0.002   TYR A 284 
 PHE   0.021   0.002   PHE A 356 
 TRP   0.014   0.001   TRP A  71 
 HIS   0.002   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3933)
  covalent geometry    : angle       0.65373 ( 5353)
  SS BOND              : bond        0.00173 (    2)
  SS BOND              : angle       0.59785 (    4)
  hydrogen bonds       : bond        0.04535 (  270)
  hydrogen bonds       : angle       4.40555 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.5408 (OUTLIER) cc_final: 0.5021 (m-10)
REVERT: A  281 PHE cc_start: 0.8787 (m-10) cc_final: 0.8336 (m-10)
REVERT: A  284 TYR cc_start: 0.6512 (m-80) cc_final: 0.6064 (m-80)
  outliers start: 19
  outliers final: 15
  residues processed: 81
  average time/residue: 0.0625
  time to fit residues: 6.4954
Evaluate side-chains
  81 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  438 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   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 414 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 = 0.4145 r_free = 0.4145 target = 0.167851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.146886 restraints weight = 6474.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.151350 restraints weight = 3048.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.154300 restraints weight = 1769.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.155900 restraints weight = 1194.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.157253 restraints weight = 925.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.3011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3935  Z= 0.187
  Angle     :  0.720  13.237   5357  Z= 0.364
  Chirality :  0.041   0.149    619
  Planarity :  0.005   0.036    660
  Dihedral  :  4.360  19.638    536
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.22 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 21.09 %
    Favored  : 73.95 %
  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:  1.53 (0.40), residues: 479
  helix:  1.67 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.91 (0.60), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 128 
 TYR   0.017   0.002   TYR A 284 
 PHE   0.022   0.002   PHE A 281 
 TRP   0.020   0.002   TRP A  71 
 HIS   0.003   0.002   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 3933)
  covalent geometry    : angle       0.71989 ( 5353)
  SS BOND              : bond        0.00252 (    2)
  SS BOND              : angle       0.63089 (    4)
  hydrogen bonds       : bond        0.05258 (  270)
  hydrogen bonds       : angle       4.69722 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.5622 (OUTLIER) cc_final: 0.5172 (m-10)
  outliers start: 20
  outliers final: 15
  residues processed: 84
  average time/residue: 0.0647
  time to fit residues: 6.8825
Evaluate side-chains
  82 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0670
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.172702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.152383 restraints weight = 6362.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.156830 restraints weight = 2936.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.159795 restraints weight = 1685.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.161651 restraints weight = 1115.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.162859 restraints weight = 837.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3935  Z= 0.152
  Angle     :  0.693  14.023   5357  Z= 0.345
  Chirality :  0.040   0.157    619
  Planarity :  0.004   0.037    660
  Dihedral  :  4.371  18.328    536
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.01 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 21.59 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.40), residues: 479
  helix:  1.80 (0.28), residues: 349
  sheet:  None (None), residues: 0
  loop : -0.87 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 128 
 TYR   0.016   0.002   TYR A 284 
 PHE   0.021   0.002   PHE A 281 
 TRP   0.016   0.001   TRP A  71 
 HIS   0.002   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3933)
  covalent geometry    : angle       0.69290 ( 5353)
  SS BOND              : bond        0.00180 (    2)
  SS BOND              : angle       0.73398 (    4)
  hydrogen bonds       : bond        0.04695 (  270)
  hydrogen bonds       : angle       4.54668 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.5477 (OUTLIER) cc_final: 0.5049 (m-10)
REVERT: A  223 TRP cc_start: 0.7782 (t-100) cc_final: 0.7565 (t-100)
  outliers start: 17
  outliers final: 14
  residues processed: 77
  average time/residue: 0.0672
  time to fit residues: 6.5433
Evaluate side-chains
  79 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0670
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 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 = 0.4193 r_free = 0.4193 target = 0.172268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.151674 restraints weight = 6418.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.156126 restraints weight = 2979.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.159014 restraints weight = 1720.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.160762 restraints weight = 1154.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.161850 restraints weight = 883.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3935  Z= 0.150
  Angle     :  0.699  14.717   5357  Z= 0.345
  Chirality :  0.040   0.150    619
  Planarity :  0.004   0.037    660
  Dihedral  :  4.320  17.938    536
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  4.59 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 21.34 %
    Favored  : 74.44 %
  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:  1.59 (0.40), residues: 479
  helix:  1.79 (0.28), residues: 349
  sheet:  None (None), residues: 0
  loop : -0.96 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 128 
 TYR   0.017   0.002   TYR A 284 
 PHE   0.017   0.002   PHE A 281 
 TRP   0.017   0.001   TRP A  71 
 HIS   0.002   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3933)
  covalent geometry    : angle       0.69880 ( 5353)
  SS BOND              : bond        0.00187 (    2)
  SS BOND              : angle       0.69269 (    4)
  hydrogen bonds       : bond        0.04660 (  270)
  hydrogen bonds       : angle       4.54857 (  792)

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 TRP cc_start: 0.5444 (OUTLIER) cc_final: 0.5055 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 76
  average time/residue: 0.0483
  time to fit residues: 4.8243
Evaluate side-chains
  78 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 VAL
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   65 TRP
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  241 ILE
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  267 TRP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  363 VAL
Chi-restraints excluded: chain A residue  398 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    0.3980
   chunk 6 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 414 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 = 0.4202 r_free = 0.4202 target = 0.173007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.152597 restraints weight = 6375.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.157101 restraints weight = 2971.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.159868 restraints weight = 1705.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.161867 restraints weight = 1147.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.163004 restraints weight = 854.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.4059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3935  Z= 0.156
  Angle     :  0.715  14.671   5357  Z= 0.356
  Chirality :  0.040   0.150    619
  Planarity :  0.004   0.037    660
  Dihedral  :  4.403  17.861    536
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.22 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 21.84 %
    Favored  : 74.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.40), residues: 479
  helix:  1.76 (0.28), residues: 349
  sheet:  None (None), residues: 0
  loop : -1.00 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 128 
 TYR   0.044   0.002   TYR A 284 
 PHE   0.030   0.002   PHE A  34 
 TRP   0.023   0.002   TRP A 223 
 HIS   0.002   0.001   HIS A 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3933)
  covalent geometry    : angle       0.71547 ( 5353)
  SS BOND              : bond        0.00180 (    2)
  SS BOND              : angle       0.66457 (    4)
  hydrogen bonds       : bond        0.04738 (  270)
  hydrogen bonds       : angle       4.60305 (  792)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 911.49 seconds
wall clock time: 16 minutes 21.80 seconds (981.80 seconds total)