Starting phenix.real_space_refine
on Tue Feb  3 16:24:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9oqa_70744/02_2026/9oqa_70744.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9oqa_70744/02_2026/9oqa_70744.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9oqa_70744/02_2026/9oqa_70744.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9oqa_70744/02_2026/9oqa_70744.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9oqa_70744/02_2026/9oqa_70744.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9oqa_70744/02_2026/9oqa_70744.map"
  }
  resolution = 3.87
  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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      13      5.16       5
     C    2980      2.51       5
     N     870      2.21       5
     O     950      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4815
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 622, 4801
          Classifications: {'peptide': 622}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 603}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 14
          Unusual residues: {' ZN': 2}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Modifications used: {'COO': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 1.16, per 1000 atoms: 0.24
  Number of scatterers: 4815
  At special positions: 0
  Unit cell: (62.02, 56.704, 119.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      13     16.00
     O     950      8.00
     N     870      7.00
     C    2980      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 292.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" NE2 HIS A 100 "
      pdb="  ZN A 702 "
        pdb="ZN    ZN A 702 " - pdb=" ND1 HIS A 277 "


  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1086

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 4 sheets defined
      27.8% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 40
      removed outlier: 3.523A  pdb=" N   TYR A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 62
      removed outlier: 3.511A  pdb=" N   LEU A  61 " --> pdb=" O   MET A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 130
    Processing helix  chain 'A' and resid 146 through 150
    Processing helix  chain 'A' and resid 151 through 161
    Processing helix  chain 'A' and resid 162 through 168
    Processing helix  chain 'A' and resid 190 through 194
      removed outlier: 4.020A  pdb=" N   VAL A 193 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 212
    Processing helix  chain 'A' and resid 235 through 240
      removed outlier: 4.321A  pdb=" N   PHE A 239 " --> pdb=" O   ASP A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 292
    Processing helix  chain 'A' and resid 292 through 315
    Processing helix  chain 'A' and resid 316 through 356
    Processing helix  chain 'A' and resid 401 through 404
      removed outlier: 3.856A  pdb=" N   GLU A 404 " --> pdb=" O   ARG A 401 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 401 through 404'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 73
      removed outlier: 6.067A  pdb=" N   LEU A  95 " --> pdb=" O   GLU A 140 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   VAL A 142 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   LEU A  97 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   VAL A  96 " --> pdb=" O   ILE A 173 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   LEU A 175 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   GLY A  98 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ALA A 251 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   THR A 252 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   LYS A 183 " --> pdb=" O   THR A 252 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 501
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 499 through 501
    current: chain 'A' and resid 447 through 468
      removed outlier: 3.839A  pdb=" N   TRP A 432 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ASP A 430 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA A 392 " --> pdb=" O   ARG A 416 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   SER A 389 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA A 623 " --> pdb=" O   ALA A 611 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ALA A 611 " --> pdb=" O   ALA A 623 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA A 566 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ALA A 544 " --> pdb=" O   ARG A 572 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY A 511 " --> pdb=" O   SER A 545 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420
    Processing sheet with id=AA4, first strand: chain 'A' and resid 532 through 533

    231 hydrogen bonds defined for protein.
    666 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: 0.71

  Time building geometry restraints manager: 0.51 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1700
        1.34 -     1.46: 1092
        1.46 -     1.58: 2090
        1.58 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 4906
  Sorted by residual:
  bond pdb=" CA  ASN A 116 "
       pdb=" CB  ASN A 116 "
    ideal  model  delta    sigma   weight residual
    1.535  1.517  0.019 2.75e-02 1.32e+03 4.54e-01
  bond pdb=" CG  LEU A 175 "
       pdb=" CD2 LEU A 175 "
    ideal  model  delta    sigma   weight residual
    1.521  1.499  0.022 3.30e-02 9.18e+02 4.41e-01
  bond pdb=" C   GLY A 472 "
       pdb=" N   PRO A 473 "
    ideal  model  delta    sigma   weight residual
    1.334  1.318  0.016 2.34e-02 1.83e+03 4.41e-01
  bond pdb=" CG  LEU A  97 "
       pdb=" CD1 LEU A  97 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 3.98e-01
  bond pdb=" CB  ASP A 603 "
       pdb=" CG  ASP A 603 "
    ideal  model  delta    sigma   weight residual
    1.516  1.531 -0.015 2.50e-02 1.60e+03 3.65e-01
  ... (remaining 4901 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 6464
        1.29 -     2.59: 127
        2.59 -     3.88: 33
        3.88 -     5.17: 6
        5.17 -     6.46: 1
  Bond angle restraints: 6631
  Sorted by residual:
  angle pdb=" C   TYR A 402 "
        pdb=" N   SER A 403 "
        pdb=" CA  SER A 403 "
      ideal   model   delta    sigma   weight residual
     121.54  126.24   -4.70 1.91e+00 2.74e-01 6.06e+00
  angle pdb=" N   ALA A 575 "
        pdb=" CA  ALA A 575 "
        pdb=" C   ALA A 575 "
      ideal   model   delta    sigma   weight residual
     108.07  110.89   -2.82 1.38e+00 5.25e-01 4.19e+00
  angle pdb=" N   ASP A 399 "
        pdb=" CA  ASP A 399 "
        pdb=" C   ASP A 399 "
      ideal   model   delta    sigma   weight residual
     108.32  111.64   -3.32 1.64e+00 3.72e-01 4.10e+00
  angle pdb=" CA  LEU A  61 "
        pdb=" CB  LEU A  61 "
        pdb=" CG  LEU A  61 "
      ideal   model   delta    sigma   weight residual
     116.30  122.76   -6.46 3.50e+00 8.16e-02 3.41e+00
  angle pdb=" C   PHE A 381 "
        pdb=" N   ASP A 382 "
        pdb=" CA  ASP A 382 "
      ideal   model   delta    sigma   weight residual
     121.54  125.00   -3.46 1.91e+00 2.74e-01 3.29e+00
  ... (remaining 6626 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 2668
       17.40 -    34.79: 160
       34.79 -    52.19: 37
       52.19 -    69.58: 10
       69.58 -    86.98: 2
  Dihedral angle restraints: 2877
    sinusoidal: 1145
      harmonic: 1732
  Sorted by residual:
  dihedral pdb=" CB  GLU A 451 "
           pdb=" CG  GLU A 451 "
           pdb=" CD  GLU A 451 "
           pdb=" OE1 GLU A 451 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.98  -86.98     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" N   GLN A 264 "
           pdb=" CA  GLN A 264 "
           pdb=" CB  GLN A 264 "
           pdb=" CG  GLN A 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.25  -59.75     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   ASP A 278 "
           pdb=" CA  ASP A 278 "
           pdb=" CB  ASP A 278 "
           pdb=" CG  ASP A 278 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.54  -56.46     3      1.50e+01 4.44e-03 9.40e+00
  ... (remaining 2874 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 397
       0.026 -    0.052: 199
       0.052 -    0.078: 52
       0.078 -    0.104: 23
       0.104 -    0.130: 14
  Chirality restraints: 685
  Sorted by residual:
  chirality pdb=" CA  ILE A 427 "
            pdb=" N   ILE A 427 "
            pdb=" C   ILE A 427 "
            pdb=" CB  ILE A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ASN A 116 "
            pdb=" N   ASN A 116 "
            pdb=" C   ASN A 116 "
            pdb=" CB  ASN A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.17e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.13e-01
  ... (remaining 682 not shown)

  Planarity restraints: 899
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 360 "    0.015 5.00e-02 4.00e+02   2.29e-02 8.41e-01
        pdb=" N   PRO A 361 "   -0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 361 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 361 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 278 "    0.013 5.00e-02 4.00e+02   2.01e-02 6.47e-01
        pdb=" N   PRO A 279 "   -0.035 5.00e-02 4.00e+02
        pdb=" CA  PRO A 279 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO A 279 "    0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  40 "   -0.013 5.00e-02 4.00e+02   1.97e-02 6.18e-01
        pdb=" N   PRO A  41 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO A  41 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO A  41 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 896 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 8
        2.55 -     3.14: 3845
        3.14 -     3.72: 7736
        3.72 -     4.31: 10362
        4.31 -     4.90: 17397
  Nonbonded interactions: 39348
  Sorted by model distance:
  nonbonded pdb="ZN    ZN A 701 "
            pdb=" O   ARG A 703 "
     model   vdw
     1.959 2.230
  nonbonded pdb="ZN    ZN A 702 "
            pdb=" OXT ARG A 703 "
     model   vdw
     2.019 2.230
  nonbonded pdb=" OD1 ASP A 176 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.033 2.230
  nonbonded pdb=" OE1 GLU A 148 "
            pdb="ZN    ZN A 702 "
     model   vdw
     2.053 2.230
  nonbonded pdb=" OE2 GLU A 148 "
            pdb="ZN    ZN A 702 "
     model   vdw
     2.193 2.230
  ... (remaining 39343 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:             1.540
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.980
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
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   0.022   4908  Z= 0.139
  Angle     :  0.500   6.464   6631  Z= 0.259
  Chirality :  0.037   0.130    685
  Planarity :  0.003   0.023    899
  Dihedral  : 12.202  86.977   1791
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 11.78 %
    Favored  : 83.68 %
  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: -0.98 (0.35), residues: 618
  helix:  1.66 (0.39), residues: 164
  sheet: -1.30 (0.32), residues: 262
  loop : -1.52 (0.46), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 391 
 TYR   0.009   0.001   TYR A 565 
 PHE   0.013   0.001   PHE A  94 
 TRP   0.007   0.001   TRP A 548 
 HIS   0.002   0.001   HIS A 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4906)
  covalent geometry    : angle       0.49964 ( 6631)
  hydrogen bonds       : bond        0.16028 (  231)
  hydrogen bonds       : angle       9.35692 (  666)
  metal coordination   : bond        0.00145 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.8044 (pt0) cc_final: 0.7797 (pp30)
REVERT: A  102 ASP cc_start: 0.7868 (t70) cc_final: 0.7412 (t70)
REVERT: A  114 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.5883 (t70)
REVERT: A  140 GLU cc_start: 0.7850 (tt0) cc_final: 0.7622 (tt0)
REVERT: A  155 ARG cc_start: 0.7421 (ttp-110) cc_final: 0.7185 (mtm180)
REVERT: A  170 LEU cc_start: 0.8773 (tp) cc_final: 0.8257 (tt)
REVERT: A  172 MET cc_start: 0.8471 (tmt) cc_final: 0.7426 (tmt)
REVERT: A  187 HIS cc_start: 0.9047 (OUTLIER) cc_final: 0.8754 (p-80)
REVERT: A  198 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8020 (tm)
REVERT: A  256 LEU cc_start: 0.7239 (tp) cc_final: 0.6830 (tp)
REVERT: A  278 ASP cc_start: 0.4517 (OUTLIER) cc_final: 0.4308 (t0)
REVERT: A  291 LEU cc_start: 0.8228 (mp) cc_final: 0.7713 (tt)
REVERT: A  314 GLN cc_start: 0.7902 (tp40) cc_final: 0.7636 (tp-100)
REVERT: A  422 ASP cc_start: 0.7458 (t0) cc_final: 0.7219 (t0)
REVERT: A  423 HIS cc_start: 0.7420 (m90) cc_final: 0.6846 (m90)
REVERT: A  434 LEU cc_start: 0.8949 (tp) cc_final: 0.8703 (mt)
REVERT: A  460 ASP cc_start: 0.8071 (t0) cc_final: 0.7685 (m-30)
REVERT: A  624 GLU cc_start: 0.8065 (tt0) cc_final: 0.7303 (tt0)
REVERT: A  627 SER cc_start: 0.8167 (m) cc_final: 0.7740 (t)
  outliers start: 22
  outliers final: 6
  residues processed: 182
  average time/residue: 0.0992
  time to fit residues: 21.6853
Evaluate side-chains
  133 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  114 ASP
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  643 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
A  82 ASN
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 165 GLN
A 168 ASN
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 187 HIS
A 195 ASN
A 204 GLN
A 298 GLN
A 314 GLN
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 348 HIS
A 516 HIS
A 563 GLN
A 612 GLN
A 618 GLN
** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.167014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.144374 restraints weight = 7306.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.147995 restraints weight = 4876.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150700 restraints weight = 3582.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.152568 restraints weight = 2814.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.153951 restraints weight = 2343.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   4908  Z= 0.209
  Angle     :  0.672   9.797   6631  Z= 0.338
  Chirality :  0.042   0.164    685
  Planarity :  0.004   0.026    899
  Dihedral  :  6.610  56.685    719
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 17.15 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.18 (0.34), residues: 618
  helix:  1.17 (0.38), residues: 168
  sheet: -1.28 (0.32), residues: 251
  loop : -1.59 (0.44), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  78 
 TYR   0.017   0.002   TYR A 185 
 PHE   0.025   0.002   PHE A 414 
 TRP   0.009   0.002   TRP A 447 
 HIS   0.003   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 4906)
  covalent geometry    : angle       0.67237 ( 6631)
  hydrogen bonds       : bond        0.04346 (  231)
  hydrogen bonds       : angle       6.89489 (  666)
  metal coordination   : bond        0.00214 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.7865 (t70) cc_final: 0.7485 (t70)
REVERT: A  125 GLU cc_start: 0.7953 (tp30) cc_final: 0.7714 (tt0)
REVERT: A  147 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6022 (tm-30)
REVERT: A  170 LEU cc_start: 0.8966 (tp) cc_final: 0.8596 (tt)
REVERT: A  172 MET cc_start: 0.8644 (tmt) cc_final: 0.7874 (tmt)
REVERT: A  182 ASP cc_start: 0.7736 (m-30) cc_final: 0.7431 (p0)
REVERT: A  187 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.8554 (p90)
REVERT: A  198 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8353 (tm)
REVERT: A  256 LEU cc_start: 0.7313 (tp) cc_final: 0.7072 (tp)
REVERT: A  264 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6862 (mp10)
REVERT: A  314 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7676 (tp-100)
REVERT: A  423 HIS cc_start: 0.7386 (m90) cc_final: 0.6769 (m90)
REVERT: A  430 ASP cc_start: 0.6342 (OUTLIER) cc_final: 0.5818 (p0)
REVERT: A  587 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.7270 (ttt-90)
REVERT: A  627 SER cc_start: 0.7855 (m) cc_final: 0.7398 (t)
  outliers start: 26
  outliers final: 13
  residues processed: 144
  average time/residue: 0.0905
  time to fit residues: 16.1140
Evaluate side-chains
  127 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  647 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS
A 537 GLN
A 626 ASN
A 646 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.162643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.139936 restraints weight = 7345.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143346 restraints weight = 4948.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.145868 restraints weight = 3675.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.147665 restraints weight = 2919.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.148688 restraints weight = 2452.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   4908  Z= 0.299
  Angle     :  0.758  10.040   6631  Z= 0.384
  Chirality :  0.045   0.184    685
  Planarity :  0.005   0.043    899
  Dihedral  :  6.633  56.104    715
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  7.02 %
    Allowed  : 18.60 %
    Favored  : 74.38 %
  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: -1.70 (0.33), residues: 618
  helix:  0.58 (0.38), residues: 168
  sheet: -1.52 (0.32), residues: 249
  loop : -1.82 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 518 
 TYR   0.016   0.002   TYR A  44 
 PHE   0.027   0.003   PHE A 414 
 TRP   0.011   0.002   TRP A 548 
 HIS   0.004   0.001   HIS A 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00656 ( 4906)
  covalent geometry    : angle       0.75780 ( 6631)
  hydrogen bonds       : bond        0.04658 (  231)
  hydrogen bonds       : angle       6.75289 (  666)
  metal coordination   : bond        0.00313 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.7956 (t70) cc_final: 0.7606 (t70)
REVERT: A  125 GLU cc_start: 0.8200 (tp30) cc_final: 0.7832 (tt0)
REVERT: A  147 GLU cc_start: 0.7305 (tm-30) cc_final: 0.5930 (tm-30)
REVERT: A  170 LEU cc_start: 0.8994 (tp) cc_final: 0.8651 (tt)
REVERT: A  172 MET cc_start: 0.8734 (tmt) cc_final: 0.7984 (tmt)
REVERT: A  187 HIS cc_start: 0.9166 (OUTLIER) cc_final: 0.8779 (p90)
REVERT: A  198 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8326 (tm)
REVERT: A  202 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7739 (ttt180)
REVERT: A  256 LEU cc_start: 0.7391 (tp) cc_final: 0.7148 (tp)
REVERT: A  264 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6760 (mp10)
REVERT: A  518 ARG cc_start: 0.6769 (mmm-85) cc_final: 0.6120 (ttt180)
REVERT: A  587 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7172 (ttp80)
REVERT: A  627 SER cc_start: 0.7975 (m) cc_final: 0.7449 (t)
  outliers start: 34
  outliers final: 20
  residues processed: 128
  average time/residue: 0.0916
  time to fit residues: 14.4299
Evaluate side-chains
  125 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  202 ARG
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  264 GLN
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  374 GLU
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  512 LEU
Chi-restraints excluded: chain A residue  516 HIS
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  647 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.168089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.145967 restraints weight = 7269.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.149668 restraints weight = 4781.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.152279 restraints weight = 3474.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.154089 restraints weight = 2727.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.155509 restraints weight = 2266.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4908  Z= 0.150
  Angle     :  0.660  10.611   6631  Z= 0.322
  Chirality :  0.042   0.238    685
  Planarity :  0.004   0.038    899
  Dihedral  :  6.257  53.121    715
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 21.07 %
    Favored  : 72.52 %
  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 (0.33), residues: 618
  helix:  0.88 (0.38), residues: 168
  sheet: -1.55 (0.31), residues: 262
  loop : -1.64 (0.45), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 351 
 TYR   0.018   0.001   TYR A  44 
 PHE   0.023   0.002   PHE A 414 
 TRP   0.011   0.001   TRP A 645 
 HIS   0.005   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4906)
  covalent geometry    : angle       0.66023 ( 6631)
  hydrogen bonds       : bond        0.03697 (  231)
  hydrogen bonds       : angle       6.02245 (  666)
  metal coordination   : bond        0.00149 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.8055 (tp30) cc_final: 0.7761 (tt0)
REVERT: A  147 GLU cc_start: 0.7198 (tm-30) cc_final: 0.5766 (tm-30)
REVERT: A  170 LEU cc_start: 0.8938 (tp) cc_final: 0.8720 (tp)
REVERT: A  172 MET cc_start: 0.8721 (tmt) cc_final: 0.7809 (tmt)
REVERT: A  187 HIS cc_start: 0.9126 (OUTLIER) cc_final: 0.8607 (p90)
REVERT: A  198 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8390 (tm)
REVERT: A  202 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7636 (ttt180)
REVERT: A  256 LEU cc_start: 0.7163 (tp) cc_final: 0.6920 (tp)
REVERT: A  266 ASP cc_start: 0.8350 (m-30) cc_final: 0.8095 (m-30)
REVERT: A  518 ARG cc_start: 0.6594 (mmm-85) cc_final: 0.6123 (ttt180)
REVERT: A  580 ASP cc_start: 0.7954 (m-30) cc_final: 0.7603 (t0)
REVERT: A  627 SER cc_start: 0.8042 (m) cc_final: 0.7567 (t)
  outliers start: 31
  outliers final: 16
  residues processed: 131
  average time/residue: 0.0859
  time to fit residues: 13.9146
Evaluate side-chains
  121 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  202 ARG
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  516 HIS
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  647 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.165479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.142887 restraints weight = 7446.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.146447 restraints weight = 4959.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.149006 restraints weight = 3658.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.150721 restraints weight = 2891.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.152123 restraints weight = 2429.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4908  Z= 0.205
  Angle     :  0.683   9.366   6631  Z= 0.340
  Chirality :  0.042   0.151    685
  Planarity :  0.004   0.034    899
  Dihedral  :  6.439  54.295    715
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  6.82 %
    Allowed  : 20.66 %
    Favored  : 72.52 %
  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: -1.66 (0.33), residues: 618
  helix:  0.78 (0.38), residues: 168
  sheet: -1.54 (0.32), residues: 249
  loop : -1.90 (0.42), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 351 
 TYR   0.017   0.002   TYR A  44 
 PHE   0.026   0.002   PHE A 414 
 TRP   0.016   0.002   TRP A 645 
 HIS   0.008   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 4906)
  covalent geometry    : angle       0.68335 ( 6631)
  hydrogen bonds       : bond        0.03936 (  231)
  hydrogen bonds       : angle       6.03014 (  666)
  metal coordination   : bond        0.00160 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 110
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 ARG cc_start: 0.7972 (mpp80) cc_final: 0.7717 (mpp80)
REVERT: A  102 ASP cc_start: 0.7973 (t70) cc_final: 0.7622 (t70)
REVERT: A  125 GLU cc_start: 0.8176 (tp30) cc_final: 0.7971 (tp30)
REVERT: A  147 GLU cc_start: 0.7263 (tm-30) cc_final: 0.5706 (tm-30)
REVERT: A  170 LEU cc_start: 0.8996 (tp) cc_final: 0.8715 (tp)
REVERT: A  172 MET cc_start: 0.8774 (tmt) cc_final: 0.7881 (tmt)
REVERT: A  187 HIS cc_start: 0.9104 (OUTLIER) cc_final: 0.8623 (p90)
REVERT: A  198 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8329 (tm)
REVERT: A  202 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7679 (ttt180)
REVERT: A  256 LEU cc_start: 0.7311 (tp) cc_final: 0.7041 (tp)
REVERT: A  266 ASP cc_start: 0.8440 (m-30) cc_final: 0.8182 (m-30)
REVERT: A  282 ASP cc_start: 0.8006 (t0) cc_final: 0.7692 (t70)
REVERT: A  518 ARG cc_start: 0.6510 (mmm-85) cc_final: 0.6081 (ttt180)
REVERT: A  580 ASP cc_start: 0.7961 (m-30) cc_final: 0.7716 (t0)
REVERT: A  587 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7085 (ttp80)
REVERT: A  627 SER cc_start: 0.8111 (m) cc_final: 0.7589 (t)
  outliers start: 33
  outliers final: 25
  residues processed: 130
  average time/residue: 0.0813
  time to fit residues: 13.1553
Evaluate side-chains
  128 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  202 ARG
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  516 HIS
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  647 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0470
   chunk 27 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 342 GLN
A 433 GLN
A 516 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.169552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.147417 restraints weight = 7383.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.151023 restraints weight = 4818.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.153657 restraints weight = 3508.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.155554 restraints weight = 2742.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.156754 restraints weight = 2273.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.3741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4908  Z= 0.135
  Angle     :  0.638   8.860   6631  Z= 0.313
  Chirality :  0.041   0.202    685
  Planarity :  0.003   0.035    899
  Dihedral  :  6.180  52.876    715
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.53 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 21.28 %
    Favored  : 72.11 %
  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: -1.47 (0.33), residues: 618
  helix:  0.97 (0.38), residues: 167
  sheet: -1.47 (0.32), residues: 254
  loop : -1.73 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 351 
 TYR   0.017   0.001   TYR A  44 
 PHE   0.024   0.002   PHE A 414 
 TRP   0.015   0.001   TRP A 645 
 HIS   0.005   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4906)
  covalent geometry    : angle       0.63800 ( 6631)
  hydrogen bonds       : bond        0.03527 (  231)
  hydrogen bonds       : angle       5.61406 (  666)
  metal coordination   : bond        0.00089 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.7846 (t70) cc_final: 0.7498 (t70)
REVERT: A  125 GLU cc_start: 0.7933 (tp30) cc_final: 0.7683 (tt0)
REVERT: A  147 GLU cc_start: 0.7090 (tm-30) cc_final: 0.5578 (tm-30)
REVERT: A  172 MET cc_start: 0.8751 (tmt) cc_final: 0.7783 (tmt)
REVERT: A  182 ASP cc_start: 0.7535 (m-30) cc_final: 0.7301 (p0)
REVERT: A  187 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.8629 (p90)
REVERT: A  198 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8420 (tm)
REVERT: A  202 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7705 (ttt180)
REVERT: A  256 LEU cc_start: 0.7261 (tp) cc_final: 0.7007 (tp)
REVERT: A  266 ASP cc_start: 0.8332 (m-30) cc_final: 0.8082 (m-30)
REVERT: A  322 SER cc_start: 0.8708 (p) cc_final: 0.8403 (p)
REVERT: A  399 ASP cc_start: 0.7647 (t0) cc_final: 0.7271 (t0)
REVERT: A  518 ARG cc_start: 0.6345 (mmm-85) cc_final: 0.6025 (ttt180)
REVERT: A  587 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7165 (ttt-90)
REVERT: A  627 SER cc_start: 0.7984 (m) cc_final: 0.7509 (t)
  outliers start: 32
  outliers final: 21
  residues processed: 134
  average time/residue: 0.0881
  time to fit residues: 14.4790
Evaluate side-chains
  129 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  202 ARG
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  516 HIS
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  647 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0170
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.7822

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.169009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.146982 restraints weight = 7322.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.150562 restraints weight = 4793.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.152963 restraints weight = 3498.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.154987 restraints weight = 2770.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.156093 restraints weight = 2282.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4908  Z= 0.151
  Angle     :  0.644   8.967   6631  Z= 0.319
  Chirality :  0.042   0.147    685
  Planarity :  0.003   0.032    899
  Dihedral  :  6.055  52.644    713
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.50 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 22.73 %
    Favored  : 70.87 %
  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: -1.50 (0.33), residues: 618
  helix:  0.90 (0.38), residues: 167
  sheet: -1.42 (0.32), residues: 254
  loop : -1.83 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 351 
 TYR   0.012   0.001   TYR A 459 
 PHE   0.025   0.002   PHE A 414 
 TRP   0.013   0.001   TRP A 645 
 HIS   0.006   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4906)
  covalent geometry    : angle       0.64431 ( 6631)
  hydrogen bonds       : bond        0.03604 (  231)
  hydrogen bonds       : angle       5.58751 (  666)
  metal coordination   : bond        0.00081 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ARG cc_start: 0.8711 (mmp80) cc_final: 0.8349 (mmp80)
REVERT: A  147 GLU cc_start: 0.7070 (tm-30) cc_final: 0.5624 (tm-30)
REVERT: A  172 MET cc_start: 0.8740 (tmt) cc_final: 0.7848 (tmt)
REVERT: A  187 HIS cc_start: 0.9086 (OUTLIER) cc_final: 0.8618 (p90)
REVERT: A  198 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8382 (tm)
REVERT: A  202 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7639 (ttt180)
REVERT: A  256 LEU cc_start: 0.7275 (tp) cc_final: 0.7009 (tp)
REVERT: A  266 ASP cc_start: 0.8342 (m-30) cc_final: 0.8078 (m-30)
REVERT: A  518 ARG cc_start: 0.6321 (mmm-85) cc_final: 0.6009 (ttt180)
REVERT: A  587 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7160 (ttt-90)
REVERT: A  627 SER cc_start: 0.8076 (m) cc_final: 0.7632 (t)
  outliers start: 31
  outliers final: 24
  residues processed: 126
  average time/residue: 0.0918
  time to fit residues: 14.2903
Evaluate side-chains
  127 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  202 ARG
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  516 HIS
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  647 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 56 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.166882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.144440 restraints weight = 7346.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.148106 restraints weight = 4769.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.150764 restraints weight = 3458.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.152621 restraints weight = 2696.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.153864 restraints weight = 2236.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4908  Z= 0.179
  Angle     :  0.682   8.994   6631  Z= 0.337
  Chirality :  0.044   0.255    685
  Planarity :  0.004   0.033    899
  Dihedral  :  6.093  53.143    713
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.99 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  6.40 %
    Allowed  : 22.93 %
    Favored  : 70.66 %
  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: -1.57 (0.33), residues: 618
  helix:  0.81 (0.37), residues: 167
  sheet: -1.47 (0.31), residues: 254
  loop : -1.82 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 351 
 TYR   0.017   0.001   TYR A  44 
 PHE   0.025   0.002   PHE A 414 
 TRP   0.009   0.001   TRP A 432 
 HIS   0.005   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 4906)
  covalent geometry    : angle       0.68244 ( 6631)
  hydrogen bonds       : bond        0.03757 (  231)
  hydrogen bonds       : angle       5.69464 (  666)
  metal coordination   : bond        0.00120 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.7856 (t70) cc_final: 0.7521 (t70)
REVERT: A  125 GLU cc_start: 0.7995 (tp30) cc_final: 0.7524 (tt0)
REVERT: A  147 GLU cc_start: 0.7122 (tm-30) cc_final: 0.5668 (tm-30)
REVERT: A  172 MET cc_start: 0.8767 (tmt) cc_final: 0.7821 (tmt)
REVERT: A  187 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8575 (p90)
REVERT: A  198 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8342 (tm)
REVERT: A  202 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7731 (ttt180)
REVERT: A  256 LEU cc_start: 0.7326 (tp) cc_final: 0.7036 (tp)
REVERT: A  266 ASP cc_start: 0.8350 (m-30) cc_final: 0.8096 (m-30)
REVERT: A  333 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8225 (ttp)
REVERT: A  518 ARG cc_start: 0.6340 (mmm-85) cc_final: 0.6015 (ttt180)
REVERT: A  582 MET cc_start: 0.6770 (ttt) cc_final: 0.6395 (ttt)
REVERT: A  587 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7183 (tmt170)
REVERT: A  627 SER cc_start: 0.8152 (m) cc_final: 0.7680 (t)
  outliers start: 31
  outliers final: 25
  residues processed: 123
  average time/residue: 0.0932
  time to fit residues: 14.1122
Evaluate side-chains
  129 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  202 ARG
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  516 HIS
Chi-restraints excluded: chain A residue  530 THR
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  647 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.170010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.147769 restraints weight = 7276.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.151448 restraints weight = 4698.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.154115 restraints weight = 3391.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.155957 restraints weight = 2644.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.157010 restraints weight = 2189.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.4022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4908  Z= 0.143
  Angle     :  0.678   9.967   6631  Z= 0.331
  Chirality :  0.042   0.201    685
  Planarity :  0.003   0.033    899
  Dihedral  :  6.023  52.269    713
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.85 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 23.35 %
    Favored  : 69.01 %
  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: -1.47 (0.33), residues: 618
  helix:  0.92 (0.37), residues: 167
  sheet: -1.42 (0.32), residues: 253
  loop : -1.78 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 351 
 TYR   0.019   0.001   TYR A  44 
 PHE   0.024   0.002   PHE A 414 
 TRP   0.011   0.001   TRP A 432 
 HIS   0.006   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4906)
  covalent geometry    : angle       0.67806 ( 6631)
  hydrogen bonds       : bond        0.03482 (  231)
  hydrogen bonds       : angle       5.52316 (  666)
  metal coordination   : bond        0.00085 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 106
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.7819 (t70) cc_final: 0.7465 (t70)
REVERT: A  125 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7520 (tt0)
REVERT: A  147 GLU cc_start: 0.7056 (tm-30) cc_final: 0.5649 (tm-30)
REVERT: A  172 MET cc_start: 0.8754 (tmt) cc_final: 0.7833 (tmt)
REVERT: A  187 HIS cc_start: 0.9100 (OUTLIER) cc_final: 0.8592 (p90)
REVERT: A  198 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8369 (tm)
REVERT: A  202 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7742 (ttt180)
REVERT: A  256 LEU cc_start: 0.7376 (tp) cc_final: 0.7107 (tp)
REVERT: A  266 ASP cc_start: 0.8375 (m-30) cc_final: 0.8131 (m-30)
REVERT: A  333 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8136 (ttp)
REVERT: A  399 ASP cc_start: 0.7641 (t0) cc_final: 0.7266 (t0)
REVERT: A  518 ARG cc_start: 0.6276 (mmm-85) cc_final: 0.5963 (ttt180)
REVERT: A  528 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.5564 (mp)
REVERT: A  582 MET cc_start: 0.6694 (ttt) cc_final: 0.6316 (ttt)
REVERT: A  587 ARG cc_start: 0.7857 (mmm-85) cc_final: 0.7244 (tmt170)
REVERT: A  627 SER cc_start: 0.8100 (m) cc_final: 0.7637 (t)
  outliers start: 37
  outliers final: 27
  residues processed: 128
  average time/residue: 0.0944
  time to fit residues: 15.1303
Evaluate side-chains
  132 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 99
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  202 ARG
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  516 HIS
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  647 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0060
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.170689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.148438 restraints weight = 7336.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.152154 restraints weight = 4732.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.154854 restraints weight = 3410.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.156740 restraints weight = 2653.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.157768 restraints weight = 2193.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4908  Z= 0.146
  Angle     :  0.685  10.249   6631  Z= 0.334
  Chirality :  0.043   0.257    685
  Planarity :  0.004   0.071    899
  Dihedral  :  6.009  52.040    713
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.83 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  7.02 %
    Allowed  : 23.97 %
    Favored  : 69.01 %
  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: -1.42 (0.33), residues: 618
  helix:  0.99 (0.37), residues: 167
  sheet: -1.40 (0.32), residues: 253
  loop : -1.77 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 351 
 TYR   0.019   0.001   TYR A  44 
 PHE   0.024   0.002   PHE A 414 
 TRP   0.011   0.001   TRP A 432 
 HIS   0.006   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4906)
  covalent geometry    : angle       0.68501 ( 6631)
  hydrogen bonds       : bond        0.03504 (  231)
  hydrogen bonds       : angle       5.49626 (  666)
  metal coordination   : bond        0.00074 (    2)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 ASP cc_start: 0.7802 (t70) cc_final: 0.7455 (t70)
REVERT: A  125 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7550 (tt0)
REVERT: A  128 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6999 (tpt90)
REVERT: A  147 GLU cc_start: 0.7067 (tm-30) cc_final: 0.5586 (tm-30)
REVERT: A  172 MET cc_start: 0.8721 (tmt) cc_final: 0.7753 (tmt)
REVERT: A  187 HIS cc_start: 0.9079 (OUTLIER) cc_final: 0.8577 (p90)
REVERT: A  198 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8341 (tm)
REVERT: A  202 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8165 (ttt180)
REVERT: A  256 LEU cc_start: 0.7363 (tp) cc_final: 0.7099 (tp)
REVERT: A  266 ASP cc_start: 0.8421 (m-30) cc_final: 0.8185 (m-30)
REVERT: A  399 ASP cc_start: 0.7652 (t0) cc_final: 0.7297 (t0)
REVERT: A  518 ARG cc_start: 0.6250 (mmm-85) cc_final: 0.5939 (ttt180)
REVERT: A  528 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5483 (mp)
REVERT: A  582 MET cc_start: 0.6690 (ttt) cc_final: 0.6310 (ttt)
REVERT: A  587 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7208 (tmt170)
REVERT: A  627 SER cc_start: 0.8080 (m) cc_final: 0.7633 (t)
  outliers start: 34
  outliers final: 26
  residues processed: 126
  average time/residue: 0.0894
  time to fit residues: 13.9660
Evaluate side-chains
  131 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 TYR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   71 ASP
Chi-restraints excluded: chain A residue   93 LYS
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  116 ASN
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  128 ARG
Chi-restraints excluded: chain A residue  187 HIS
Chi-restraints excluded: chain A residue  194 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  202 ARG
Chi-restraints excluded: chain A residue  296 ILE
Chi-restraints excluded: chain A residue  320 LEU
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  430 ASP
Chi-restraints excluded: chain A residue  461 SER
Chi-restraints excluded: chain A residue  516 HIS
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  560 MET
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  621 VAL
Chi-restraints excluded: chain A residue  643 VAL
Chi-restraints excluded: chain A residue  647 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 GLN
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 516 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.170877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.148416 restraints weight = 7401.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.152128 restraints weight = 4790.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.154777 restraints weight = 3468.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.156499 restraints weight = 2718.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.158009 restraints weight = 2274.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.4172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4908  Z= 0.152
  Angle     :  0.690  10.256   6631  Z= 0.337
  Chirality :  0.044   0.239    685
  Planarity :  0.004   0.062    899
  Dihedral  :  6.035  51.880    713
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.50 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  7.02 %
    Allowed  : 23.97 %
    Favored  : 69.01 %
  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: -1.45 (0.33), residues: 618
  helix:  0.95 (0.37), residues: 167
  sheet: -1.40 (0.32), residues: 253
  loop : -1.79 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 351 
 TYR   0.019   0.001   TYR A  44 
 PHE   0.027   0.002   PHE A 414 
 TRP   0.010   0.001   TRP A 432 
 HIS   0.005   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4906)
  covalent geometry    : angle       0.69024 ( 6631)
  hydrogen bonds       : bond        0.03485 (  231)
  hydrogen bonds       : angle       5.44959 (  666)
  metal coordination   : bond        0.00072 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 966.97 seconds
wall clock time: 17 minutes 25.62 seconds (1045.62 seconds total)