Starting phenix.real_space_refine
on Tue Feb 11 02:56:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ouc_20202/02_2025/6ouc_20202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ouc_20202/02_2025/6ouc_20202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ouc_20202/02_2025/6ouc_20202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ouc_20202/02_2025/6ouc_20202.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ouc_20202/02_2025/6ouc_20202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ouc_20202/02_2025/6ouc_20202.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.041
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      1      6.06       5
     S      15      5.16       5
     C    2421      2.51       5
     N     642      2.21       5
     O     820      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3899
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 483, 3774
          Classifications: {'peptide': 483}
          Link IDs: {'PTRANS': 46, 'TRANS': 436}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 125
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1, 'water': 124}
          Link IDs: {None: 124}
  Time building chain proxies: 2.91, per 1000 atoms: 0.75
  Number of scatterers: 3899
  At special positions: 0
  Unit cell: (95.23, 95.23, 78.11, 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      1     29.99
     S      15     16.00
     O     820      8.00
     N     642      7.00
     C    2421      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: 0.92
  Conformation dependent library (CDL) restraints added in 428.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A 299 "
        pdb="ZN    ZN A 601 " - pdb=" NE2 HIS A 293 "


  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  900

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 9 sheets defined
      6.2% alpha, 28.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 85
      removed outlier: 3.522A  pdb=" N   LEU A  85 " --> pdb=" O   GLY A  82 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 82 through 85'
    Processing helix  chain 'A' and resid 86 through 93
    Processing helix  chain 'A' and resid 136 through 141
      removed outlier: 3.628A  pdb=" N   THR A 139 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE A 141 " --> pdb=" O   ILE A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 467
    Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58
    Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 58
      removed outlier: 4.053A  pdb=" N   SER A 199 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 80
      removed outlier: 6.342A  pdb=" N   ALA A 180 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ASN A  78 " --> pdb=" O   ILE A 178 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE A 178 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 168
    Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 116
    Processing sheet with id=AA6, first strand: chain 'A' and resid 450 through 453
      removed outlier: 4.853A  pdb=" N   MET A 249 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 450 through 453
      removed outlier: 4.743A  pdb=" N   MET A 499 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   PHE A 489 " --> pdb=" O   TYR A 479 " (cutoff:3.500A)
      removed outlier: 7.196A  pdb=" N   VAL A 474 " --> pdb=" O   TRP A 522 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   TRP A 522 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LEU A 476 " --> pdb=" O   ASP A 520 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 265 through 266
      removed outlier: 4.565A  pdb=" N   ARG A 265 " --> pdb=" O   GLN A 273 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 360
      removed outlier: 7.700A  pdb=" N   ARG A 331 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   LEU A 396 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   PHE A 333 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ARG A 339 " --> pdb=" O   PRO A 388 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   PHE A 286 " --> pdb=" O   PHE A 391 " (cutoff:3.500A)

    100 hydrogen bonds defined for protein.
    258 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.06

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 969
        1.33 -     1.45: 735
        1.45 -     1.56: 2154
        1.56 -     1.68: 0
        1.68 -     1.80: 25
  Bond restraints: 3883
  Sorted by residual:
  bond pdb=" CA  TYR A 214 "
       pdb=" C   TYR A 214 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.032 1.22e-02 6.72e+03 6.77e+00
  bond pdb=" CA  GLN A 170 "
       pdb=" C   GLN A 170 "
    ideal  model  delta    sigma   weight residual
    1.528  1.561 -0.033 1.33e-02 5.65e+03 6.30e+00
  bond pdb=" N   TRP A 378 "
       pdb=" CA  TRP A 378 "
    ideal  model  delta    sigma   weight residual
    1.459  1.430  0.029 1.24e-02 6.50e+03 5.52e+00
  bond pdb=" CG  LEU A 455 "
       pdb=" CD1 LEU A 455 "
    ideal  model  delta    sigma   weight residual
    1.521  1.447  0.074 3.30e-02 9.18e+02 5.06e+00
  bond pdb=" CA  GLN A 170 "
       pdb=" CB  GLN A 170 "
    ideal  model  delta    sigma   weight residual
    1.527  1.498  0.029 1.44e-02 4.82e+03 3.96e+00
  ... (remaining 3878 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.39: 5207
        3.39 -     6.79: 93
        6.79 -    10.18: 8
       10.18 -    13.57: 6
       13.57 -    16.97: 1
  Bond angle restraints: 5315
  Sorted by residual:
  angle pdb=" N   GLY A  62 "
        pdb=" CA  GLY A  62 "
        pdb=" C   GLY A  62 "
      ideal   model   delta    sigma   weight residual
     112.73  129.70  -16.97 1.20e+00 6.94e-01 2.00e+02
  angle pdb=" N   THR A 213 "
        pdb=" CA  THR A 213 "
        pdb=" C   THR A 213 "
      ideal   model   delta    sigma   weight residual
     112.68  125.51  -12.83 1.33e+00 5.65e-01 9.31e+01
  angle pdb=" N   ASN A 297 "
        pdb=" CA  ASN A 297 "
        pdb=" C   ASN A 297 "
      ideal   model   delta    sigma   weight residual
     111.28  101.34    9.94 1.09e+00 8.42e-01 8.32e+01
  angle pdb=" N   TYR A 301 "
        pdb=" CA  TYR A 301 "
        pdb=" C   TYR A 301 "
      ideal   model   delta    sigma   weight residual
     111.02  121.74  -10.72 1.25e+00 6.40e-01 7.36e+01
  angle pdb=" N   LEU A 300 "
        pdb=" CA  LEU A 300 "
        pdb=" C   LEU A 300 "
      ideal   model   delta    sigma   weight residual
     114.04  123.08   -9.04 1.24e+00 6.50e-01 5.31e+01
  ... (remaining 5310 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.63: 2184
       13.63 -    27.25: 101
       27.25 -    40.87: 25
       40.87 -    54.49: 3
       54.49 -    68.11: 2
  Dihedral angle restraints: 2315
    sinusoidal: 917
      harmonic: 1398
  Sorted by residual:
  dihedral pdb=" C   LEU A 300 "
           pdb=" N   LEU A 300 "
           pdb=" CA  LEU A 300 "
           pdb=" CB  LEU A 300 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -138.63   16.03     0      2.50e+00 1.60e-01 4.11e+01
  dihedral pdb=" CA  ALA A 344 "
           pdb=" C   ALA A 344 "
           pdb=" N   ALA A 345 "
           pdb=" CA  ALA A 345 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.63  -29.37     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" N   LEU A 300 "
           pdb=" C   LEU A 300 "
           pdb=" CA  LEU A 300 "
           pdb=" CB  LEU A 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  137.25  -14.45     0      2.50e+00 1.60e-01 3.34e+01
  ... (remaining 2312 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.161: 574
       0.161 -    0.321: 11
       0.321 -    0.482: 1
       0.482 -    0.642: 1
       0.642 -    0.802: 1
  Chirality restraints: 588
  Sorted by residual:
  chirality pdb=" CA  LEU A 300 "
            pdb=" N   LEU A 300 "
            pdb=" C   LEU A 300 "
            pdb=" CB  LEU A 300 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.71    0.80 2.00e-01 2.50e+01 1.61e+01
  chirality pdb=" CA  TYR A 301 "
            pdb=" N   TYR A 301 "
            pdb=" C   TYR A 301 "
            pdb=" CB  TYR A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.45e+00
  chirality pdb=" CA  THR A 213 "
            pdb=" N   THR A 213 "
            pdb=" C   THR A 213 "
            pdb=" CB  THR A 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.09    0.43 2.00e-01 2.50e+01 4.66e+00
  ... (remaining 585 not shown)

  Planarity restraints: 708
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  51 "    0.020 2.00e-02 2.50e+03   1.84e-02 8.44e+00
        pdb=" CG  TRP A  51 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  51 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  51 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  51 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  51 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  51 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  51 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  51 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  51 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 405 "   -0.010 2.00e-02 2.50e+03   1.45e-02 5.23e+00
        pdb=" CG  TRP A 405 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 405 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 405 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 405 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 405 "    0.007 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 405 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 405 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 405 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 405 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  49 "    0.038 5.00e-02 4.00e+02   5.68e-02 5.17e+00
        pdb=" N   PRO A  50 "   -0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A  50 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  50 "    0.031 5.00e-02 4.00e+02
  ... (remaining 705 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 158
        2.68 -     3.24: 3304
        3.24 -     3.79: 5839
        3.79 -     4.35: 8181
        4.35 -     4.90: 13624
  Nonbonded interactions: 31106
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 243 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OE1 GLU A  84 "
            pdb=" O   HOH A 702 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" O   ALA A 496 "
            pdb=" O   HOH A 703 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   MET A 532 "
            pdb=" O   HOH A 704 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OD1 ASP A 211 "
            pdb=" N   PHE A 212 "
     model   vdw
     2.197 3.120
  ... (remaining 31101 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.110
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.410
  Find NCS groups from input model:        0.040
  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:11.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
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      :  0.008   0.074   3883  Z= 0.532
  Angle     :  1.153  16.966   5315  Z= 0.699
  Chirality :  0.081   0.802    588
  Planarity :  0.010   0.057    708
  Dihedral  :  9.030  68.110   1415
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.32 (0.31), residues: 479
  helix: -3.43 (0.57), residues: 27
  sheet: -0.80 (0.41), residues: 130
  loop : -1.78 (0.27), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.006   TRP A  51 
 HIS   0.013   0.002   HIS A 494 
 PHE   0.035   0.004   PHE A 498 
 TYR   0.025   0.004   TYR A 410 
 ARG   0.015   0.002   ARG A 495 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.455 
Fit side-chains
REVERT: A   84 GLU cc_start: 0.7264 (mp0) cc_final: 0.7053 (mp0)
REVERT: A  155 LEU cc_start: 0.8987 (mt) cc_final: 0.8739 (mt)
REVERT: A  356 ASP cc_start: 0.8347 (m-30) cc_final: 0.8122 (m-30)
REVERT: A  379 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7605 (mm110)
REVERT: A  443 LYS cc_start: 0.9112 (tttm) cc_final: 0.8850 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 1.1097
  time to fit residues: 128.5353
Evaluate side-chains
  100 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0670
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0010
   overall best weight:    0.5324

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
A 167 HIS
A 189 ASN
A 347 GLN
A 386 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.112020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.096778 restraints weight = 4609.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.58
r_work: 0.2870 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3883  Z= 0.136
  Angle     :  0.539   6.936   5315  Z= 0.283
  Chirality :  0.045   0.129    588
  Planarity :  0.006   0.037    708
  Dihedral  :  5.077  20.881    519
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  7.21 %
    Favored  : 91.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.34), residues: 479
  helix: -1.60 (0.85), residues: 27
  sheet: -0.35 (0.40), residues: 155
  loop : -1.01 (0.31), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A  51 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.014   0.001   PHE A  64 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.003   0.001   ARG A 495 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A  187 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7459 (ttp80)
REVERT: A  225 LYS cc_start: 0.9001 (ttmm) cc_final: 0.8796 (ttmm)
REVERT: A  238 SER cc_start: 0.9166 (m) cc_final: 0.8831 (p)
REVERT: A  398 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8384 (p0)
REVERT: A  443 LYS cc_start: 0.9239 (tttm) cc_final: 0.8923 (tttm)
  outliers start: 6
  outliers final: 0
  residues processed: 101
  average time/residue: 1.0986
  time to fit residues: 114.8925
Evaluate side-chains
  96 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 26 optimal weight:    0.3980
   chunk 19 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 338 GLN
A 386 ASN
A 461 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.109283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.093742 restraints weight = 4921.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 1.59
r_work: 0.2842 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3883  Z= 0.192
  Angle     :  0.549   6.718   5315  Z= 0.280
  Chirality :  0.045   0.124    588
  Planarity :  0.006   0.035    708
  Dihedral  :  4.816  21.235    519
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  :  9.62 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.34), residues: 479
  helix: -1.45 (0.83), residues: 33
  sheet:  0.01 (0.42), residues: 140
  loop : -0.85 (0.31), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.014   0.001   PHE A  64 
 TYR   0.011   0.001   TYR A 168 
 ARG   0.003   0.001   ARG A 437 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 THR cc_start: 0.9321 (p) cc_final: 0.9083 (m)
REVERT: A  443 LYS cc_start: 0.9172 (tttm) cc_final: 0.8906 (tttm)
REVERT: A  525 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7747 (pm20)
  outliers start: 12
  outliers final: 7
  residues processed: 101
  average time/residue: 1.1153
  time to fit residues: 116.5746
Evaluate side-chains
  98 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0970
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
A 386 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.106851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.091267 restraints weight = 4882.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.2898 rms_B_bonded: 1.57
r_work: 0.2823 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3883  Z= 0.205
  Angle     :  0.541   6.477   5315  Z= 0.275
  Chirality :  0.045   0.126    588
  Planarity :  0.006   0.036    708
  Dihedral  :  4.654  21.324    519
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 12.26 %
    Favored  : 85.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.35), residues: 479
  helix: -1.23 (0.85), residues: 33
  sheet: -0.16 (0.41), residues: 154
  loop : -0.59 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 299 
 PHE   0.012   0.001   PHE A  64 
 TYR   0.011   0.001   TYR A 214 
 ARG   0.003   0.001   ARG A 437 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  187 ARG cc_start: 0.8087 (mtm180) cc_final: 0.7608 (mtp85)
REVERT: A  204 THR cc_start: 0.9300 (p) cc_final: 0.9078 (m)
REVERT: A  238 SER cc_start: 0.9197 (m) cc_final: 0.8883 (p)
REVERT: A  398 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8571 (p0)
REVERT: A  443 LYS cc_start: 0.9163 (tttm) cc_final: 0.8919 (tttm)
REVERT: A  525 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7832 (pm20)
  outliers start: 11
  outliers final: 5
  residues processed: 102
  average time/residue: 1.1468
  time to fit residues: 121.0056
Evaluate side-chains
  104 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 37 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 293 HIS
A 372 GLN
A 374 GLN
A 386 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.120178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.104818 restraints weight = 4740.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.2807 rms_B_bonded: 1.65
r_work: 0.2723 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2619 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8807
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3883  Z= 0.389
  Angle     :  0.632   6.648   5315  Z= 0.322
  Chirality :  0.049   0.150    588
  Planarity :  0.006   0.040    708
  Dihedral  :  5.073  21.376    519
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 12.26 %
    Favored  : 83.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.35), residues: 479
  helix: -1.53 (0.80), residues: 33
  sheet: -0.12 (0.41), residues: 154
  loop : -0.64 (0.32), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  51 
 HIS   0.006   0.002   HIS A 299 
 PHE   0.013   0.002   PHE A  64 
 TYR   0.018   0.002   TYR A 214 
 ARG   0.005   0.001   ARG A 201 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A  171 LYS cc_start: 0.8320 (tppt) cc_final: 0.7807 (mmmt)
REVERT: A  204 THR cc_start: 0.9331 (p) cc_final: 0.9109 (m)
REVERT: A  398 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8561 (p0)
REVERT: A  443 LYS cc_start: 0.9305 (tttm) cc_final: 0.9103 (tttm)
REVERT: A  525 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7963 (pm20)
  outliers start: 16
  outliers final: 8
  residues processed: 105
  average time/residue: 1.1053
  time to fit residues: 120.1348
Evaluate side-chains
  102 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  398 ASP
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  525 GLN
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0670
   chunk 46 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 29 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7520

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.108281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.092669 restraints weight = 4946.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 1.60
r_work: 0.2821 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.2726 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8743
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3883  Z= 0.140
  Angle     :  0.498   6.612   5315  Z= 0.253
  Chirality :  0.044   0.132    588
  Planarity :  0.006   0.041    708
  Dihedral  :  4.478  21.337    519
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.42 %
    Favored  : 83.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.35), residues: 479
  helix: -0.93 (0.89), residues: 33
  sheet: -0.04 (0.41), residues: 153
  loop : -0.46 (0.33), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 522 
 HIS   0.004   0.001   HIS A 299 
 PHE   0.011   0.001   PHE A  64 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.002   0.000   ARG A 187 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.454 
Fit side-chains
REVERT: A  187 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7603 (ttp80)
REVERT: A  238 SER cc_start: 0.9175 (m) cc_final: 0.8892 (p)
REVERT: A  443 LYS cc_start: 0.9120 (tttm) cc_final: 0.8897 (tttm)
  outliers start: 9
  outliers final: 4
  residues processed: 100
  average time/residue: 1.1499
  time to fit residues: 118.8896
Evaluate side-chains
  98 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.107535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.091902 restraints weight = 4835.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 1.58
r_work: 0.2812 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3883  Z= 0.189
  Angle     :  0.521   6.394   5315  Z= 0.264
  Chirality :  0.045   0.134    588
  Planarity :  0.006   0.040    708
  Dihedral  :  4.496  19.597    519
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 14.90 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.36), residues: 479
  helix: -0.94 (0.89), residues: 33
  sheet:  0.06 (0.41), residues: 154
  loop : -0.38 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 522 
 HIS   0.004   0.001   HIS A 299 
 PHE   0.012   0.001   PHE A  64 
 TYR   0.011   0.001   TYR A 214 
 ARG   0.005   0.001   ARG A 409 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  114 PHE cc_start: 0.8227 (m-80) cc_final: 0.7940 (m-80)
REVERT: A  187 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7574 (ttp80)
REVERT: A  238 SER cc_start: 0.9179 (m) cc_final: 0.8890 (p)
REVERT: A  398 ASP cc_start: 0.8459 (p0) cc_final: 0.7925 (p0)
REVERT: A  443 LYS cc_start: 0.9214 (tttm) cc_final: 0.9010 (tttm)
  outliers start: 8
  outliers final: 6
  residues processed: 101
  average time/residue: 1.1068
  time to fit residues: 115.7431
Evaluate side-chains
  100 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 23 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0020
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   overall best weight:    1.0792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.106847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.091333 restraints weight = 4815.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.2905 rms_B_bonded: 1.56
r_work: 0.2833 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8794
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3883  Z= 0.170
  Angle     :  0.516   6.342   5315  Z= 0.260
  Chirality :  0.045   0.132    588
  Planarity :  0.005   0.040    708
  Dihedral  :  4.420  19.971    519
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 2.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.62 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.36), residues: 479
  helix: -0.85 (0.90), residues: 33
  sheet:  0.09 (0.41), residues: 154
  loop : -0.32 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 522 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.011   0.001   PHE A  64 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.005   0.001   ARG A 409 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A  114 PHE cc_start: 0.8208 (m-80) cc_final: 0.7965 (m-80)
REVERT: A  187 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7663 (ttp80)
REVERT: A  238 SER cc_start: 0.9161 (m) cc_final: 0.8960 (p)
REVERT: A  302 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.7928 (m-40)
REVERT: A  379 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7704 (mm-40)
REVERT: A  384 LYS cc_start: 0.8408 (mttt) cc_final: 0.8139 (mttt)
REVERT: A  398 ASP cc_start: 0.8491 (p0) cc_final: 0.8003 (p0)
REVERT: A  443 LYS cc_start: 0.9224 (tttm) cc_final: 0.9018 (tttm)
REVERT: A  452 ASP cc_start: 0.8819 (m-30) cc_final: 0.8427 (m-30)
  outliers start: 7
  outliers final: 5
  residues processed: 101
  average time/residue: 1.1367
  time to fit residues: 118.6700
Evaluate side-chains
  99 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  302 ASN
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.122334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.107085 restraints weight = 4441.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.61
r_work: 0.2761 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2657 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3883  Z= 0.270
  Angle     :  0.567   6.300   5315  Z= 0.286
  Chirality :  0.046   0.137    588
  Planarity :  0.006   0.039    708
  Dihedral  :  4.675  19.317    519
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.35 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.35), residues: 479
  helix: -1.07 (0.87), residues: 33
  sheet:  0.08 (0.41), residues: 154
  loop : -0.38 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 378 
 HIS   0.004   0.001   HIS A 299 
 PHE   0.013   0.002   PHE A  64 
 TYR   0.013   0.001   TYR A 214 
 ARG   0.003   0.001   ARG A 201 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  114 PHE cc_start: 0.8270 (m-80) cc_final: 0.8001 (m-80)
REVERT: A  187 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7684 (ttp80)
REVERT: A  302 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8208 (m110)
REVERT: A  379 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7729 (mm-40)
REVERT: A  398 ASP cc_start: 0.8601 (p0) cc_final: 0.8261 (p0)
REVERT: A  415 ASN cc_start: 0.8336 (m-40) cc_final: 0.7766 (m-40)
  outliers start: 8
  outliers final: 7
  residues processed: 101
  average time/residue: 1.1396
  time to fit residues: 119.2233
Evaluate side-chains
  102 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  302 ASN
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 24 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0370
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.2662

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.123799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.108592 restraints weight = 4473.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 1.62
r_work: 0.2782 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3883  Z= 0.192
  Angle     :  0.530   6.320   5315  Z= 0.267
  Chirality :  0.045   0.131    588
  Planarity :  0.005   0.040    708
  Dihedral  :  4.510  19.726    519
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.59 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.35), residues: 479
  helix: -0.94 (0.89), residues: 33
  sheet:  0.10 (0.41), residues: 154
  loop : -0.29 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 522 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.012   0.001   PHE A  64 
 TYR   0.010   0.001   TYR A 214 
 ARG   0.004   0.000   ARG A 409 

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

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

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

  958 Ramachandran restraints generated.
    479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.424 
Fit side-chains
REVERT: A  114 PHE cc_start: 0.8254 (m-80) cc_final: 0.7980 (m-80)
REVERT: A  187 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7671 (ttp80)
REVERT: A  238 SER cc_start: 0.9192 (m) cc_final: 0.8883 (p)
REVERT: A  302 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8207 (m110)
REVERT: A  379 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7685 (mm-40)
REVERT: A  384 LYS cc_start: 0.8441 (mttt) cc_final: 0.8024 (mttt)
REVERT: A  398 ASP cc_start: 0.8552 (p0) cc_final: 0.8069 (p0)
REVERT: A  415 ASN cc_start: 0.8336 (m-40) cc_final: 0.7787 (m-40)
  outliers start: 8
  outliers final: 7
  residues processed: 101
  average time/residue: 1.1697
  time to fit residues: 122.1723
Evaluate side-chains
  103 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 LYS
Chi-restraints excluded: chain A residue  249 MET
Chi-restraints excluded: chain A residue  272 LEU
Chi-restraints excluded: chain A residue  302 ASN
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain A residue  528 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   chunk 31 optimal weight:    0.0570
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0030
   chunk 3 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.3708

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.112473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.097116 restraints weight = 4742.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.2992 rms_B_bonded: 1.58
r_work: 0.2920 rms_B_bonded: 1.72 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3883  Z= 0.114
  Angle     :  0.478   6.270   5315  Z= 0.239
  Chirality :  0.044   0.126    588
  Planarity :  0.005   0.041    708
  Dihedral  :  4.014  18.982    519
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 17.07 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.36), residues: 479
  helix: -0.64 (0.95), residues: 33
  sheet:  0.21 (0.42), residues: 149
  loop : -0.09 (0.33), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 522 
 HIS   0.002   0.001   HIS A 494 
 PHE   0.010   0.001   PHE A  64 
 TYR   0.009   0.001   TYR A 168 
 ARG   0.003   0.000   ARG A 409 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3547.42 seconds
wall clock time: 63 minutes 22.62 seconds (3802.62 seconds total)