Starting phenix.real_space_refine
on Tue Aug  4 15:28:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w9c_65770/08_2026/9w9c_65770.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w9c_65770/08_2026/9w9c_65770.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w9c_65770/08_2026/9w9c_65770.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w9c_65770/08_2026/9w9c_65770.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w9c_65770/08_2026/9w9c_65770.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w9c_65770/08_2026/9w9c_65770.map"
  }
  resolution = 3.02
  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=  -0.001 sd=   0.052
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      34      5.16       5
     C    2885      2.51       5
     N     658      2.21       5
     O     719      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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4296
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4296
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 534, 4296
          Classifications: {'peptide': 534}
          Link IDs: {'PTRANS': 26, 'TRANS': 507}
          Chain breaks: 1
  Time building chain proxies: 1.18, per 1000 atoms: 0.27
  Number of scatterers: 4296
  At special positions: 0
  Unit cell: (77.891, 72.556, 84.293, 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      34     16.00
     O     719      8.00
     N     658      7.00
     C    2885      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 157 " - pdb=" SG  CYS A 166 " 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: 0.34
  Conformation dependent library (CDL) restraints added in 159.4 milliseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  990

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 1 sheets defined
      79.2% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 54
      removed outlier: 3.646A  pdb=" N   GLU A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 60
    Processing helix  chain 'A' and resid 60 through 69
      removed outlier: 4.031A  pdb=" N   TYR A  64 " --> pdb=" O   TRP A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 85
    Processing helix  chain 'A' and resid 85 through 101
    Processing helix  chain 'A' and resid 103 through 112
    Processing helix  chain 'A' and resid 116 through 147
      removed outlier: 3.748A  pdb=" N   LEU A 120 " --> pdb=" O   GLN A 116 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   ILE A 134 " --> pdb=" O   ASN A 130 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   ILE A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE A 136 " --> pdb=" O   TYR A 132 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU A 137 " --> pdb=" O   TYR A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 195
    Processing helix  chain 'A' and resid 210 through 230
      removed outlier: 4.164A  pdb=" N   LYS A 230 " --> pdb=" O   PHE A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 260
      removed outlier: 4.415A  pdb=" N   TYR A 240 " --> pdb=" O   GLY A 236 " (cutoff:3.500A)
      Proline residue:  A 246  - end of helix
    Processing helix  chain 'A' and resid 262 through 272
      removed outlier: 3.983A  pdb=" N   GLY A 266 " --> pdb=" O   GLY A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 279
      removed outlier: 3.612A  pdb=" N   LYS A 279 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 295
      removed outlier: 4.171A  pdb=" N   TRP A 284 " --> pdb=" O   ASP A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 308
      removed outlier: 3.665A  pdb=" N   TYR A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 349
    Processing helix  chain 'A' and resid 351 through 355
    Processing helix  chain 'A' and resid 362 through 373
      Proline residue:  A 368  - end of helix
      removed outlier: 3.614A  pdb=" N   MET A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 411
    Processing helix  chain 'A' and resid 411 through 416
      removed outlier: 3.752A  pdb=" N   ARG A 416 " --> pdb=" O   PRO A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 437
      removed outlier: 3.692A  pdb=" N   LEU A 423 " --> pdb=" O   GLY A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 455
      removed outlier: 3.981A  pdb=" N   ILE A 447 " --> pdb=" O   GLY A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 474
      removed outlier: 3.572A  pdb=" N   LEU A 462 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 490
    Processing helix  chain 'A' and resid 494 through 503
      removed outlier: 4.518A  pdb=" N   LYS A 498 " --> pdb=" O   TRP A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 519
    Processing helix  chain 'A' and resid 532 through 561
      removed outlier: 4.169A  pdb=" N   SER A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   MET A 547 " --> pdb=" O   ALA A 543 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   CYS A 549 " --> pdb=" O   SER A 545 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   VAL A 550 " --> pdb=" O   SER A 546 " (cutoff:3.500A)
      Proline residue:  A 551  - end of helix
    Processing helix  chain 'A' and resid 564 through 573
    Processing sheet with id=AA1, first strand: chain 'A' and resid 524 through 525

    287 hydrogen bonds defined for protein.
    846 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: 0.67

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1249
        1.35 -     1.46: 1248
        1.46 -     1.58: 1890
        1.58 -     1.70: 0
        1.70 -     1.81: 47
  Bond restraints: 4434
  Sorted by residual:
  bond pdb=" CB  VAL A 469 "
       pdb=" CG1 VAL A 469 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.48e+00
  bond pdb=" C   VAL A 550 "
       pdb=" N   PRO A 551 "
    ideal  model  delta    sigma   weight residual
    1.335  1.343 -0.008 1.28e-02 6.10e+03 4.36e-01
  bond pdb=" CB  GLU A  52 "
       pdb=" CG  GLU A  52 "
    ideal  model  delta    sigma   weight residual
    1.520  1.538 -0.018 3.00e-02 1.11e+03 3.74e-01
  bond pdb=" CA  PHE A 184 "
       pdb=" CB  PHE A 184 "
    ideal  model  delta    sigma   weight residual
    1.524  1.532 -0.009 1.41e-02 5.03e+03 3.72e-01
  bond pdb=" CB  VAL A 371 "
       pdb=" CG1 VAL A 371 "
    ideal  model  delta    sigma   weight residual
    1.521  1.501  0.020 3.30e-02 9.18e+02 3.71e-01
  ... (remaining 4429 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 5873
        1.13 -     2.26: 126
        2.26 -     3.38: 26
        3.38 -     4.51: 8
        4.51 -     5.64: 6
  Bond angle restraints: 6039
  Sorted by residual:
  angle pdb=" CA  CYS A 157 "
        pdb=" CB  CYS A 157 "
        pdb=" SG  CYS A 157 "
      ideal   model   delta    sigma   weight residual
     114.40  118.66   -4.26 2.30e+00 1.89e-01 3.44e+00
  angle pdb=" C   PRO A  63 "
        pdb=" N   TYR A  64 "
        pdb=" CA  TYR A  64 "
      ideal   model   delta    sigma   weight residual
     120.68  117.57    3.11 1.70e+00 3.46e-01 3.35e+00
  angle pdb=" C   ASP A 274 "
        pdb=" N   LEU A 275 "
        pdb=" CA  LEU A 275 "
      ideal   model   delta    sigma   weight residual
     121.54  124.93   -3.39 1.91e+00 2.74e-01 3.15e+00
  angle pdb=" N   LEU A 275 "
        pdb=" CA  LEU A 275 "
        pdb=" C   LEU A 275 "
      ideal   model   delta    sigma   weight residual
     110.80  114.46   -3.66 2.13e+00 2.20e-01 2.96e+00
  angle pdb=" CA  PHE A 184 "
        pdb=" C   PHE A 184 "
        pdb=" N   THR A 185 "
      ideal   model   delta    sigma   weight residual
     115.14  117.06   -1.92 1.22e+00 6.72e-01 2.48e+00
  ... (remaining 6034 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.36: 2303
       13.36 -    26.73: 178
       26.73 -    40.09: 34
       40.09 -    53.46: 8
       53.46 -    66.82: 2
  Dihedral angle restraints: 2525
    sinusoidal: 974
      harmonic: 1551
  Sorted by residual:
  dihedral pdb=" CB  CYS A 157 "
           pdb=" SG  CYS A 157 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -136.58   50.58     1      1.00e+01 1.00e-02 3.50e+01
  dihedral pdb=" CA  TYR A 525 "
           pdb=" C   TYR A 525 "
           pdb=" N   ASN A 526 "
           pdb=" CA  ASN A 526 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.94  -15.06     0      5.00e+00 4.00e-02 9.08e+00
  dihedral pdb=" N   ASN A 326 "
           pdb=" CA  ASN A 326 "
           pdb=" CB  ASN A 326 "
           pdb=" CG  ASN A 326 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.05   51.05     3      1.50e+01 4.44e-03 8.97e+00
  ... (remaining 2522 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 370
       0.025 -    0.050: 183
       0.050 -    0.075: 82
       0.075 -    0.100: 24
       0.100 -    0.125: 12
  Chirality restraints: 671
  Sorted by residual:
  chirality pdb=" CA  PRO A  63 "
            pdb=" N   PRO A  63 "
            pdb=" C   PRO A  63 "
            pdb=" CB  PRO A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 3.91e-01
  chirality pdb=" CA  PRO A  88 "
            pdb=" N   PRO A  88 "
            pdb=" C   PRO A  88 "
            pdb=" CB  PRO A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.48e-01
  chirality pdb=" CA  PRO A 153 "
            pdb=" N   PRO A 153 "
            pdb=" C   PRO A 153 "
            pdb=" CB  PRO A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.11 2.00e-01 2.50e+01 3.25e-01
  ... (remaining 668 not shown)

  Planarity restraints: 735
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 127 "   -0.007 2.00e-02 2.50e+03   1.34e-02 1.80e+00
        pdb=" C   SER A 127 "    0.023 2.00e-02 2.50e+03
        pdb=" O   SER A 127 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   TYR A 128 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 112 "   -0.021 5.00e-02 4.00e+02   3.26e-02 1.70e+00
        pdb=" N   PRO A 113 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 113 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 113 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 123 "   -0.006 2.00e-02 2.50e+03   1.21e-02 1.46e+00
        pdb=" C   VAL A 123 "    0.021 2.00e-02 2.50e+03
        pdb=" O   VAL A 123 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   VAL A 124 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 732 not shown)

  Histogram of nonbonded interaction distances:
        2.62 -     3.08: 3175
        3.08 -     3.53: 4851
        3.53 -     3.99: 6897
        3.99 -     4.44: 8930
        4.44 -     4.90: 13087
  Nonbonded interactions: 36940
  Sorted by model distance:
  nonbonded pdb=" N   SER A 457 "
            pdb=" O   SER A 457 "
     model   vdw
     2.625 2.496
  nonbonded pdb=" N   LYS A 417 "
            pdb=" O   LYS A 417 "
     model   vdw
     2.648 2.496
  nonbonded pdb=" O   THR A 100 "
            pdb=" OG  SER A 101 "
     model   vdw
     2.653 3.040
  nonbonded pdb=" O   GLU A 357 "
            pdb=" OG  SER A 358 "
     model   vdw
     2.655 3.040
  nonbonded pdb=" O   PHE A  81 "
            pdb=" N   GLY A  86 "
     model   vdw
     2.655 3.120
  ... (remaining 36935 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:             1.130
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.060
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
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   0.040   4435  Z= 0.136
  Angle     :  0.463   5.639   6041  Z= 0.242
  Chirality :  0.038   0.125    671
  Planarity :  0.004   0.033    735
  Dihedral  : 10.173  66.819   1532
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  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:  1.58 (0.38), residues: 530
  helix:  1.58 (0.27), residues: 388
  sheet:  None (None), residues: 0
  loop : -0.33 (0.56), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 194 
 TYR   0.014   0.001   TYR A  64 
 PHE   0.010   0.001   PHE A  90 
 TRP   0.007   0.001   TRP A 108 
 HIS   0.002   0.001   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.14 ( 4434)
  covalent geometry    : angle       0.46205 /  0.24 ( 6039)
  SS BOND              : bond        0.00152 /  0.08 (    1)
  SS BOND              : angle       1.60103 /  0.84 (    2)
  hydrogen bonds       : bond        0.11437 /  7.96 (  287)
  hydrogen bonds       : angle       6.07414 /  4.36 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 SER cc_start: 0.8434 (m) cc_final: 0.8163 (p)
REVERT: A  264 TYR cc_start: 0.8019 (t80) cc_final: 0.7730 (t80)
REVERT: A  274 ASP cc_start: 0.8123 (t0) cc_final: 0.7730 (t0)
REVERT: A  276 PHE cc_start: 0.8420 (m-10) cc_final: 0.8173 (m-80)
REVERT: A  279 LYS cc_start: 0.7390 (tttp) cc_final: 0.6632 (mmtt)
REVERT: A  354 GLU cc_start: 0.8855 (pt0) cc_final: 0.8621 (pt0)
REVERT: A  394 ASP cc_start: 0.8323 (m-30) cc_final: 0.7735 (m-30)
REVERT: A  424 LEU cc_start: 0.9380 (tp) cc_final: 0.9177 (tp)
REVERT: A  468 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7935 (mt-10)
REVERT: A  486 GLU cc_start: 0.8026 (tt0) cc_final: 0.7688 (tt0)
REVERT: A  570 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7534 (mmp80)
REVERT: A  571 GLN cc_start: 0.8678 (tt0) cc_final: 0.8230 (tp40)
REVERT: A  576 ASP cc_start: 0.8533 (t0) cc_final: 0.8165 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0658
  time to fit residues: 11.5335
Evaluate side-chains
  104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 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 = 0.3560 r_free = 0.3560 target = 0.122786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.097868 restraints weight = 6095.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.27
r_work: 0.3087 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8411
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4435  Z= 0.155
  Angle     :  0.519   7.239   6041  Z= 0.266
  Chirality :  0.038   0.135    671
  Planarity :  0.004   0.029    735
  Dihedral  :  3.617  15.530    578
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.26 %
    Favored  : 88.25 %
  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:  1.75 (0.36), residues: 530
  helix:  1.72 (0.26), residues: 392
  sheet:  None (None), residues: 0
  loop : -0.40 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 194 
 TYR   0.016   0.001   TYR A  64 
 PHE   0.011   0.001   PHE A  74 
 TRP   0.007   0.001   TRP A 221 
 HIS   0.002   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.15 ( 4434)
  covalent geometry    : angle       0.51643 /  0.26 ( 6039)
  SS BOND              : bond        0.00195 /  0.10 (    1)
  SS BOND              : angle       2.67775 /  1.50 (    2)
  hydrogen bonds       : bond        0.03993 /  2.71 (  287)
  hydrogen bonds       : angle       4.65442 /  3.38 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 110
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7771 (mm-30)
REVERT: A  189 MET cc_start: 0.8799 (ttm) cc_final: 0.8438 (mtp)
REVERT: A  205 ASP cc_start: 0.8231 (t70) cc_final: 0.7963 (p0)
REVERT: A  208 SER cc_start: 0.8617 (m) cc_final: 0.8377 (p)
REVERT: A  264 TYR cc_start: 0.8191 (t80) cc_final: 0.7988 (t80)
REVERT: A  274 ASP cc_start: 0.8166 (t0) cc_final: 0.7882 (t0)
REVERT: A  282 GLN cc_start: 0.8219 (tp40) cc_final: 0.7860 (tp-100)
REVERT: A  394 ASP cc_start: 0.8405 (m-30) cc_final: 0.7869 (m-30)
REVERT: A  452 ASP cc_start: 0.9066 (t70) cc_final: 0.8838 (t0)
REVERT: A  453 TYR cc_start: 0.9284 (t80) cc_final: 0.8999 (t80)
REVERT: A  486 GLU cc_start: 0.8271 (tt0) cc_final: 0.7970 (tt0)
REVERT: A  571 GLN cc_start: 0.8712 (tt0) cc_final: 0.8242 (tp40)
REVERT: A  576 ASP cc_start: 0.8623 (t0) cc_final: 0.8257 (t0)
  outliers start: 7
  outliers final: 6
  residues processed: 113
  average time/residue: 0.0540
  time to fit residues: 8.3060
Evaluate side-chains
  106 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  521 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 7 optimal weight:    0.2980
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 44 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 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 = 0.3559 r_free = 0.3559 target = 0.122596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.097746 restraints weight = 6128.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.28
r_work: 0.3086 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4435  Z= 0.140
  Angle     :  0.502   5.835   6041  Z= 0.260
  Chirality :  0.038   0.122    671
  Planarity :  0.003   0.030    735
  Dihedral  :  3.596  15.403    578
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 12.82 %
    Favored  : 83.76 %
  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 (0.36), residues: 530
  helix:  1.66 (0.25), residues: 392
  sheet:  None (None), residues: 0
  loop : -0.36 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 195 
 TYR   0.015   0.001   TYR A  64 
 PHE   0.013   0.001   PHE A  74 
 TRP   0.007   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 4434)
  covalent geometry    : angle       0.50131 /  0.26 ( 6039)
  SS BOND              : bond        0.00016 /  0.01 (    1)
  SS BOND              : angle       1.87982 /  1.02 (    2)
  hydrogen bonds       : bond        0.03845 /  2.60 (  287)
  hydrogen bonds       : angle       4.50450 /  3.26 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7589 (mm-30)
REVERT: A  189 MET cc_start: 0.8513 (ttm) cc_final: 0.8238 (mtp)
REVERT: A  205 ASP cc_start: 0.8067 (t70) cc_final: 0.7807 (p0)
REVERT: A  208 SER cc_start: 0.8609 (m) cc_final: 0.8273 (t)
REVERT: A  264 TYR cc_start: 0.8079 (t80) cc_final: 0.7840 (t80)
REVERT: A  274 ASP cc_start: 0.8174 (t0) cc_final: 0.7888 (t0)
REVERT: A  279 LYS cc_start: 0.7408 (tttp) cc_final: 0.6870 (mmtt)
REVERT: A  280 ASP cc_start: 0.8406 (m-30) cc_final: 0.8030 (p0)
REVERT: A  373 MET cc_start: 0.8472 (mmm) cc_final: 0.8176 (mmt)
REVERT: A  374 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7352 (mtp)
REVERT: A  394 ASP cc_start: 0.8241 (m-30) cc_final: 0.7685 (m-30)
REVERT: A  486 GLU cc_start: 0.8054 (tt0) cc_final: 0.7787 (tt0)
REVERT: A  571 GLN cc_start: 0.8626 (tt0) cc_final: 0.8225 (tp40)
REVERT: A  576 ASP cc_start: 0.8488 (t0) cc_final: 0.8157 (t0)
  outliers start: 16
  outliers final: 12
  residues processed: 120
  average time/residue: 0.0543
  time to fit residues: 8.8809
Evaluate side-chains
  117 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  548 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 21 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 7 optimal weight:    0.4980
   chunk 47 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 ASN
** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.123751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.099083 restraints weight = 6078.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.26
r_work: 0.3121 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4435  Z= 0.149
  Angle     :  0.508   6.027   6041  Z= 0.261
  Chirality :  0.038   0.124    671
  Planarity :  0.003   0.031    735
  Dihedral  :  3.640  15.402    578
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 14.53 %
    Favored  : 81.62 %
  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:  1.61 (0.36), residues: 530
  helix:  1.60 (0.25), residues: 392
  sheet:  None (None), residues: 0
  loop : -0.38 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 420 
 TYR   0.016   0.001   TYR A  64 
 PHE   0.013   0.001   PHE A  74 
 TRP   0.009   0.001   TRP A 229 
 HIS   0.001   0.000   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 ( 4434)
  covalent geometry    : angle       0.50686 /  0.26 ( 6039)
  SS BOND              : bond        0.00027 /  0.01 (    1)
  SS BOND              : angle       1.94479 /  1.04 (    2)
  hydrogen bonds       : bond        0.03848 /  2.60 (  287)
  hydrogen bonds       : angle       4.44385 /  3.20 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 MET cc_start: 0.8807 (ttm) cc_final: 0.8560 (mtp)
REVERT: A  199 ILE cc_start: 0.8647 (tp) cc_final: 0.8320 (tp)
REVERT: A  208 SER cc_start: 0.8658 (m) cc_final: 0.8329 (t)
REVERT: A  264 TYR cc_start: 0.8246 (t80) cc_final: 0.8001 (t80)
REVERT: A  274 ASP cc_start: 0.8246 (t0) cc_final: 0.7936 (t0)
REVERT: A  279 LYS cc_start: 0.7466 (tttp) cc_final: 0.6877 (mmtt)
REVERT: A  280 ASP cc_start: 0.8601 (m-30) cc_final: 0.8125 (p0)
REVERT: A  373 MET cc_start: 0.8613 (mmm) cc_final: 0.8277 (mmt)
REVERT: A  394 ASP cc_start: 0.8380 (m-30) cc_final: 0.7853 (m-30)
REVERT: A  486 GLU cc_start: 0.8238 (tt0) cc_final: 0.7978 (tt0)
REVERT: A  571 GLN cc_start: 0.8710 (tt0) cc_final: 0.8198 (tp40)
REVERT: A  576 ASP cc_start: 0.8617 (t0) cc_final: 0.8251 (t0)
  outliers start: 18
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0562
  time to fit residues: 8.7880
Evaluate side-chains
  115 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ASP
Chi-restraints excluded: chain A residue  487 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0070
   overall best weight:    0.6398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 158 ASN
** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.124615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.099999 restraints weight = 6107.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 2.28
r_work: 0.3119 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.2034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4435  Z= 0.140
  Angle     :  0.504   6.560   6041  Z= 0.258
  Chirality :  0.038   0.124    671
  Planarity :  0.003   0.030    735
  Dihedral  :  3.645  15.444    578
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.81 %
    Favored  : 80.56 %
  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:  1.61 (0.36), residues: 530
  helix:  1.59 (0.25), residues: 392
  sheet:  None (None), residues: 0
  loop : -0.35 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 194 
 TYR   0.016   0.001   TYR A  64 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.007   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 ( 4434)
  covalent geometry    : angle       0.50335 /  0.26 ( 6039)
  SS BOND              : bond        0.00010 /  0.01 (    1)
  SS BOND              : angle       1.37343 /  0.74 (    2)
  hydrogen bonds       : bond        0.03761 /  2.54 (  287)
  hydrogen bonds       : angle       4.38241 /  3.14 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 MET cc_start: 0.8798 (ttm) cc_final: 0.8544 (mtp)
REVERT: A  199 ILE cc_start: 0.8564 (tp) cc_final: 0.8198 (tp)
REVERT: A  205 ASP cc_start: 0.8231 (t70) cc_final: 0.7934 (p0)
REVERT: A  208 SER cc_start: 0.8603 (m) cc_final: 0.8263 (t)
REVERT: A  264 TYR cc_start: 0.8236 (t80) cc_final: 0.7980 (t80)
REVERT: A  274 ASP cc_start: 0.8220 (t0) cc_final: 0.7912 (t0)
REVERT: A  279 LYS cc_start: 0.7444 (tttp) cc_final: 0.6911 (mmtt)
REVERT: A  280 ASP cc_start: 0.8605 (m-30) cc_final: 0.8130 (p0)
REVERT: A  373 MET cc_start: 0.8607 (mmm) cc_final: 0.8271 (mmt)
REVERT: A  394 ASP cc_start: 0.8380 (m-30) cc_final: 0.7856 (m-30)
REVERT: A  486 GLU cc_start: 0.8220 (tt0) cc_final: 0.7960 (tt0)
REVERT: A  571 GLN cc_start: 0.8763 (tt0) cc_final: 0.8296 (tp40)
REVERT: A  576 ASP cc_start: 0.8632 (t0) cc_final: 0.8240 (t0)
  outliers start: 17
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0432
  time to fit residues: 6.8081
Evaluate side-chains
  118 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 43 optimal weight:    0.4980
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0470
   chunk 48 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.5078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.100560 restraints weight = 6218.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.30
r_work: 0.3125 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4435  Z= 0.125
  Angle     :  0.502   6.893   6041  Z= 0.257
  Chirality :  0.038   0.125    671
  Planarity :  0.003   0.030    735
  Dihedral  :  3.626  15.053    578
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 15.38 %
    Favored  : 80.34 %
  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 (0.36), residues: 530
  helix:  1.62 (0.25), residues: 392
  sheet:  None (None), residues: 0
  loop : -0.36 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 416 
 TYR   0.016   0.001   TYR A 132 
 PHE   0.011   0.001   PHE A  90 
 TRP   0.007   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 4434)
  covalent geometry    : angle       0.50159 /  0.26 ( 6039)
  SS BOND              : bond        0.00021 /  0.01 (    1)
  SS BOND              : angle       1.37085 /  0.73 (    2)
  hydrogen bonds       : bond        0.03663 /  2.48 (  287)
  hydrogen bonds       : angle       4.35178 /  3.12 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 MET cc_start: 0.8510 (ttm) cc_final: 0.8253 (mtp)
REVERT: A  199 ILE cc_start: 0.8423 (tp) cc_final: 0.8082 (tp)
REVERT: A  205 ASP cc_start: 0.8099 (t70) cc_final: 0.7876 (p0)
REVERT: A  208 SER cc_start: 0.8553 (m) cc_final: 0.8207 (t)
REVERT: A  264 TYR cc_start: 0.8082 (t80) cc_final: 0.7758 (t80)
REVERT: A  274 ASP cc_start: 0.7961 (t0) cc_final: 0.7727 (t0)
REVERT: A  280 ASP cc_start: 0.8418 (m-30) cc_final: 0.8040 (p0)
REVERT: A  373 MET cc_start: 0.8443 (mmm) cc_final: 0.8110 (mmt)
REVERT: A  394 ASP cc_start: 0.8214 (m-30) cc_final: 0.7675 (m-30)
REVERT: A  486 GLU cc_start: 0.7989 (tt0) cc_final: 0.7759 (tt0)
REVERT: A  571 GLN cc_start: 0.8613 (tt0) cc_final: 0.8238 (tp40)
REVERT: A  576 ASP cc_start: 0.8521 (t0) cc_final: 0.8165 (t0)
  outliers start: 20
  outliers final: 17
  residues processed: 118
  average time/residue: 0.0356
  time to fit residues: 5.7505
Evaluate side-chains
  120 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0570
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5898

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.124544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.099852 restraints weight = 6159.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.31
r_work: 0.3117 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.2163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4435  Z= 0.135
  Angle     :  0.520   7.696   6041  Z= 0.262
  Chirality :  0.038   0.127    671
  Planarity :  0.003   0.030    735
  Dihedral  :  3.632  15.069    578
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 15.81 %
    Favored  : 80.34 %
  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:  1.60 (0.36), residues: 530
  helix:  1.61 (0.25), residues: 393
  sheet:  None (None), residues: 0
  loop : -0.44 (0.55), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 416 
 TYR   0.016   0.001   TYR A  64 
 PHE   0.011   0.001   PHE A  74 
 TRP   0.008   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 4434)
  covalent geometry    : angle       0.51947 /  0.26 ( 6039)
  SS BOND              : bond        0.00038 /  0.02 (    1)
  SS BOND              : angle       1.36018 /  0.73 (    2)
  hydrogen bonds       : bond        0.03703 /  2.50 (  287)
  hydrogen bonds       : angle       4.36202 /  3.12 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 MET cc_start: 0.8511 (ttm) cc_final: 0.8257 (mtp)
REVERT: A  199 ILE cc_start: 0.8405 (tp) cc_final: 0.8061 (tp)
REVERT: A  205 ASP cc_start: 0.8070 (t70) cc_final: 0.7834 (p0)
REVERT: A  208 SER cc_start: 0.8537 (m) cc_final: 0.8194 (t)
REVERT: A  264 TYR cc_start: 0.8106 (t80) cc_final: 0.7830 (t80)
REVERT: A  274 ASP cc_start: 0.8004 (t0) cc_final: 0.7761 (t0)
REVERT: A  279 LYS cc_start: 0.7431 (tttp) cc_final: 0.6893 (mmtt)
REVERT: A  280 ASP cc_start: 0.8402 (m-30) cc_final: 0.8051 (p0)
REVERT: A  373 MET cc_start: 0.8452 (mmm) cc_final: 0.8120 (mmt)
REVERT: A  394 ASP cc_start: 0.8221 (m-30) cc_final: 0.7687 (m-30)
REVERT: A  486 GLU cc_start: 0.7985 (tt0) cc_final: 0.7747 (tt0)
REVERT: A  571 GLN cc_start: 0.8594 (tt0) cc_final: 0.8191 (tp40)
REVERT: A  576 ASP cc_start: 0.8497 (t0) cc_final: 0.8112 (t0)
  outliers start: 18
  outliers final: 17
  residues processed: 118
  average time/residue: 0.0460
  time to fit residues: 7.4141
Evaluate side-chains
  122 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  374 MET
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 31 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.123334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.098860 restraints weight = 6137.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 2.29
r_work: 0.3101 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4435  Z= 0.158
  Angle     :  0.534   7.379   6041  Z= 0.269
  Chirality :  0.039   0.127    671
  Planarity :  0.003   0.030    735
  Dihedral  :  3.702  15.561    578
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 16.03 %
    Favored  : 79.91 %
  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:  1.55 (0.36), residues: 530
  helix:  1.55 (0.25), residues: 393
  sheet:  None (None), residues: 0
  loop : -0.40 (0.55), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 194 
 TYR   0.017   0.001   TYR A  64 
 PHE   0.014   0.001   PHE A  74 
 TRP   0.008   0.001   TRP A 380 
 HIS   0.002   0.000   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.16 ( 4434)
  covalent geometry    : angle       0.53320 /  0.27 ( 6039)
  SS BOND              : bond        0.00047 /  0.02 (    1)
  SS BOND              : angle       1.34999 /  0.73 (    2)
  hydrogen bonds       : bond        0.03822 /  2.58 (  287)
  hydrogen bonds       : angle       4.43389 /  3.17 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
REVERT: A  158 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7688 (p0)
REVERT: A  189 MET cc_start: 0.8780 (ttm) cc_final: 0.8537 (mtp)
REVERT: A  208 SER cc_start: 0.8603 (m) cc_final: 0.8282 (t)
REVERT: A  264 TYR cc_start: 0.8248 (t80) cc_final: 0.7975 (t80)
REVERT: A  274 ASP cc_start: 0.8194 (t0) cc_final: 0.7892 (t0)
REVERT: A  279 LYS cc_start: 0.7495 (tttp) cc_final: 0.6901 (mmtt)
REVERT: A  280 ASP cc_start: 0.8594 (m-30) cc_final: 0.8101 (p0)
REVERT: A  373 MET cc_start: 0.8629 (mmm) cc_final: 0.8297 (mmt)
REVERT: A  394 ASP cc_start: 0.8383 (m-30) cc_final: 0.7877 (m-30)
REVERT: A  486 GLU cc_start: 0.8203 (tt0) cc_final: 0.7927 (tt0)
REVERT: A  571 GLN cc_start: 0.8776 (tt0) cc_final: 0.8388 (tp40)
REVERT: A  576 ASP cc_start: 0.8632 (t0) cc_final: 0.8244 (t0)
  outliers start: 19
  outliers final: 16
  residues processed: 118
  average time/residue: 0.0495
  time to fit residues: 7.9033
Evaluate side-chains
  123 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 4 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN
A 159 ASN
A 162 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.123504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.099126 restraints weight = 6199.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.29
r_work: 0.3102 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4435  Z= 0.144
  Angle     :  0.537   7.467   6041  Z= 0.273
  Chirality :  0.039   0.138    671
  Planarity :  0.003   0.030    735
  Dihedral  :  3.686  15.698    578
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 16.45 %
    Favored  : 79.70 %
  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:  1.60 (0.36), residues: 530
  helix:  1.57 (0.25), residues: 392
  sheet:  None (None), residues: 0
  loop : -0.31 (0.56), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 416 
 TYR   0.016   0.001   TYR A  64 
 PHE   0.012   0.001   PHE A  74 
 TRP   0.008   0.001   TRP A 108 
 HIS   0.001   0.000   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.14 ( 4434)
  covalent geometry    : angle       0.53610 /  0.27 ( 6039)
  SS BOND              : bond        0.00187 /  0.10 (    1)
  SS BOND              : angle       1.48192 /  0.79 (    2)
  hydrogen bonds       : bond        0.03825 /  2.58 (  287)
  hydrogen bonds       : angle       4.46840 /  3.18 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 MET cc_start: 0.8767 (ttm) cc_final: 0.8516 (mtp)
REVERT: A  205 ASP cc_start: 0.8261 (t70) cc_final: 0.7935 (p0)
REVERT: A  208 SER cc_start: 0.8619 (m) cc_final: 0.8301 (t)
REVERT: A  264 TYR cc_start: 0.8247 (t80) cc_final: 0.7973 (t80)
REVERT: A  274 ASP cc_start: 0.8181 (t0) cc_final: 0.7876 (t0)
REVERT: A  279 LYS cc_start: 0.7492 (tttp) cc_final: 0.6897 (mmtt)
REVERT: A  280 ASP cc_start: 0.8597 (m-30) cc_final: 0.8105 (p0)
REVERT: A  373 MET cc_start: 0.8631 (mmm) cc_final: 0.8306 (mmt)
REVERT: A  389 ILE cc_start: 0.9270 (mp) cc_final: 0.9005 (mp)
REVERT: A  394 ASP cc_start: 0.8376 (m-30) cc_final: 0.7870 (m-30)
REVERT: A  486 GLU cc_start: 0.8170 (tt0) cc_final: 0.7905 (tt0)
REVERT: A  571 GLN cc_start: 0.8743 (tt0) cc_final: 0.8252 (tp40)
REVERT: A  576 ASP cc_start: 0.8630 (t0) cc_final: 0.8242 (t0)
  outliers start: 18
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0567
  time to fit residues: 8.7174
Evaluate side-chains
  118 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 18 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.123395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.098868 restraints weight = 6081.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.28
r_work: 0.3095 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4435  Z= 0.160
  Angle     :  0.554   7.786   6041  Z= 0.279
  Chirality :  0.039   0.141    671
  Planarity :  0.003   0.030    735
  Dihedral  :  3.755  15.970    578
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 17.31 %
    Favored  : 79.06 %
  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:  1.52 (0.36), residues: 530
  helix:  1.54 (0.25), residues: 392
  sheet:  None (None), residues: 0
  loop : -0.42 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 416 
 TYR   0.018   0.001   TYR A  64 
 PHE   0.014   0.001   PHE A  74 
 TRP   0.009   0.001   TRP A 380 
 HIS   0.002   0.001   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.16 ( 4434)
  covalent geometry    : angle       0.54840 /  0.28 ( 6039)
  SS BOND              : bond        0.00147 /  0.08 (    1)
  SS BOND              : angle       4.23287 /  2.37 (    2)
  hydrogen bonds       : bond        0.03863 /  2.61 (  287)
  hydrogen bonds       : angle       4.50112 /  3.21 (  846)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 MET cc_start: 0.8746 (ttm) cc_final: 0.8496 (mtp)
REVERT: A  208 SER cc_start: 0.8572 (m) cc_final: 0.8240 (t)
REVERT: A  264 TYR cc_start: 0.8252 (t80) cc_final: 0.7970 (t80)
REVERT: A  274 ASP cc_start: 0.8199 (t0) cc_final: 0.7870 (t0)
REVERT: A  279 LYS cc_start: 0.7500 (tttp) cc_final: 0.6904 (mmtt)
REVERT: A  280 ASP cc_start: 0.8601 (m-30) cc_final: 0.8098 (p0)
REVERT: A  373 MET cc_start: 0.8629 (mmm) cc_final: 0.8298 (mmt)
REVERT: A  394 ASP cc_start: 0.8309 (m-30) cc_final: 0.7805 (m-30)
REVERT: A  486 GLU cc_start: 0.8175 (tt0) cc_final: 0.7903 (tt0)
REVERT: A  571 GLN cc_start: 0.8769 (tt0) cc_final: 0.8378 (tp40)
REVERT: A  576 ASP cc_start: 0.8636 (t0) cc_final: 0.8247 (t0)
  outliers start: 17
  outliers final: 17
  residues processed: 115
  average time/residue: 0.0554
  time to fit residues: 8.6313
Evaluate side-chains
  118 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue   64 TYR
Chi-restraints excluded: chain A residue  101 SER
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  158 ASN
Chi-restraints excluded: chain A residue  212 GLU
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  464 LEU
Chi-restraints excluded: chain A residue  479 ASP
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  521 THR
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  548 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 18 optimal weight:    5.9990
   chunk 46 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0470
   chunk 17 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.123825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.099418 restraints weight = 6171.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.28
r_work: 0.3108 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4435  Z= 0.138
  Angle     :  0.555   7.712   6041  Z= 0.284
  Chirality :  0.039   0.155    671
  Planarity :  0.003   0.030    735
  Dihedral  :  3.710  15.859    578
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 17.31 %
    Favored  : 79.06 %
  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:  1.50 (0.36), residues: 530
  helix:  1.57 (0.25), residues: 392
  sheet:  None (None), residues: 0
  loop : -0.58 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 416 
 TYR   0.016   0.001   TYR A 132 
 PHE   0.011   0.001   PHE A  74 
 TRP   0.008   0.001   TRP A 380 
 HIS   0.001   0.000   HIS A 312 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 4434)
  covalent geometry    : angle       0.55165 /  0.28 ( 6039)
  SS BOND              : bond        0.00180 /  0.09 (    1)
  SS BOND              : angle       3.25362 /  1.81 (    2)
  hydrogen bonds       : bond        0.03830 /  2.59 (  287)
  hydrogen bonds       : angle       4.52733 /  3.21 (  846)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1207.71 seconds
wall clock time: 21 minutes 25.27 seconds (1285.27 seconds total)