Starting phenix.real_space_refine
on Tue Feb 11 09:53:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ehw_28153/02_2025/8ehw_28153.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ehw_28153/02_2025/8ehw_28153.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ehw_28153/02_2025/8ehw_28153.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ehw_28153/02_2025/8ehw_28153.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ehw_28153/02_2025/8ehw_28153.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ehw_28153/02_2025/8ehw_28153.cif"
  }
  resolution = 3.8
  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=   0.036
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    3410      2.51       5
     N     826      2.21       5
     O     882      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5150
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 630, 5150
          Classifications: {'peptide': 630}
          Link IDs: {'PTRANS': 25, 'TRANS': 604}
          Chain breaks: 2
  Time building chain proxies: 3.66, per 1000 atoms: 0.71
  Number of scatterers: 5150
  At special positions: 0
  Unit cell: (97.35, 107.25, 75.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O     882      8.00
     N     826      7.00
     C    3410      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  32 " - pdb=" SG  CYS A 546 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 308 " - pdb=" SG  CYS A 315 " distance=2.80

  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: 1.27
  Conformation dependent library (CDL) restraints added in 664.0 milliseconds
  

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 2 sheets defined
      70.8% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 48
      removed outlier: 3.722A  pdb=" N   GLY A  48 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 45 through 48'
    Processing helix  chain 'A' and resid 49 through 75
      removed outlier: 3.593A  pdb=" N   VAL A  53 " --> pdb=" O   GLY A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 123
      removed outlier: 3.750A  pdb=" N   ILE A 120 " --> pdb=" O   TRP A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 132
    Processing helix  chain 'A' and resid 134 through 167
      removed outlier: 3.966A  pdb=" N   HIS A 138 " --> pdb=" O   GLU A 134 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   CYS A 159 " --> pdb=" O   PHE A 155 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   VAL A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   LEU A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      Proline residue:  A 163  - end of helix
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 191 through 219
      removed outlier: 4.165A  pdb=" N   LEU A 195 " --> pdb=" O   ASP A 191 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   HIS A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   LEU A 204 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE A 205 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A 218 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 252
    Processing helix  chain 'A' and resid 266 through 294
    Processing helix  chain 'A' and resid 304 through 308
    Processing helix  chain 'A' and resid 320 through 342
      removed outlier: 3.546A  pdb=" N   ARG A 340 " --> pdb=" O   THR A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 368
      removed outlier: 3.822A  pdb=" N   ALA A 360 " --> pdb=" O   GLU A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 391
      removed outlier: 3.585A  pdb=" N   LEU A 390 " --> pdb=" O   HIS A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 395
    Processing helix  chain 'A' and resid 407 through 411
    Processing helix  chain 'A' and resid 415 through 445
      removed outlier: 3.522A  pdb=" N   TRP A 419 " --> pdb=" O   GLY A 415 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   PHE A 427 " --> pdb=" O   LEU A 423 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   THR A 428 " --> pdb=" O   GLY A 424 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   PHE A 434 " --> pdb=" O   PHE A 430 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE A 435 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   THR A 438 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      Proline residue:  A 439  - end of helix
    Processing helix  chain 'A' and resid 466 through 491
      Proline residue:  A 480  - end of helix
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 499 through 515
      removed outlier: 3.645A  pdb=" N   PHE A 509 " --> pdb=" O   LYS A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 534
      removed outlier: 3.682A  pdb=" N   SER A 519 " --> pdb=" O   LEU A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 552
    Processing helix  chain 'A' and resid 553 through 565
      removed outlier: 4.298A  pdb=" N   VAL A 557 " --> pdb=" O   GLY A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
    Processing helix  chain 'A' and resid 574 through 587
      removed outlier: 3.526A  pdb=" N   MET A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 601
    Processing helix  chain 'A' and resid 606 through 624
      removed outlier: 3.740A  pdb=" N   TYR A 624 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 650
      removed outlier: 4.038A  pdb=" N   PHE A 634 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 4.045A  pdb=" N   LEU A 672 " --> pdb=" O   VAL A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 690
      removed outlier: 3.743A  pdb=" N   ILE A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 710
      removed outlier: 3.943A  pdb=" N   LEU A 698 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 264
      removed outlier: 5.626A  pdb=" N   VAL A 257 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   THR A 353 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   ASP A 259 " --> pdb=" O   PHE A 351 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   PHE A 351 " --> pdb=" O   ASP A 259 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   GLN A 261 " --> pdb=" O   MET A 349 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   MET A 349 " --> pdb=" O   GLN A 261 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   CYS A 263 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 299

    306 hydrogen bonds defined for protein.
    873 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: 1.44

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1339
        1.34 -     1.46: 1155
        1.46 -     1.58: 2751
        1.58 -     1.70: 0
        1.70 -     1.82: 47
  Bond restraints: 5292
  Sorted by residual:
  bond pdb=" N   VAL A 451 "
       pdb=" CA  VAL A 451 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.02e+01
  bond pdb=" N   VAL A 342 "
       pdb=" CA  VAL A 342 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.38e+00
  bond pdb=" N   LYS A 453 "
       pdb=" CA  LYS A 453 "
    ideal  model  delta    sigma   weight residual
    1.460  1.481 -0.021 7.10e-03 1.98e+04 8.35e+00
  bond pdb=" N   CYS A  32 "
       pdb=" CA  CYS A  32 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.035 1.25e-02 6.40e+03 7.64e+00
  bond pdb=" N   VAL A 266 "
       pdb=" CA  VAL A 266 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 7.08e+00
  ... (remaining 5287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 7001
        2.72 -     5.44: 165
        5.44 -     8.16: 18
        8.16 -    10.88: 3
       10.88 -    13.60: 4
  Bond angle restraints: 7191
  Sorted by residual:
  angle pdb=" C   VAL A 342 "
        pdb=" CA  VAL A 342 "
        pdb=" CB  VAL A 342 "
      ideal   model   delta    sigma   weight residual
     111.29  100.02   11.27 1.64e+00 3.72e-01 4.73e+01
  angle pdb=" C   LEU A 641 "
        pdb=" CA  LEU A 641 "
        pdb=" CB  LEU A 641 "
      ideal   model   delta    sigma   weight residual
     110.81  121.73  -10.92 1.60e+00 3.91e-01 4.66e+01
  angle pdb=" N   VAL A 342 "
        pdb=" CA  VAL A 342 "
        pdb=" C   VAL A 342 "
      ideal   model   delta    sigma   weight residual
     109.34  122.94  -13.60 2.08e+00 2.31e-01 4.28e+01
  angle pdb=" N   LEU A 641 "
        pdb=" CA  LEU A 641 "
        pdb=" C   LEU A 641 "
      ideal   model   delta    sigma   weight residual
     111.11  105.62    5.49 1.20e+00 6.94e-01 2.09e+01
  angle pdb=" N   GLU A 338 "
        pdb=" CA  GLU A 338 "
        pdb=" C   GLU A 338 "
      ideal   model   delta    sigma   weight residual
     111.33  116.13   -4.80 1.21e+00 6.83e-01 1.57e+01
  ... (remaining 7186 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 2651
       17.84 -    35.67: 343
       35.67 -    53.51: 95
       53.51 -    71.34: 9
       71.34 -    89.18: 2
  Dihedral angle restraints: 3100
    sinusoidal: 1236
      harmonic: 1864
  Sorted by residual:
  dihedral pdb=" CB  CYS A 308 "
           pdb=" SG  CYS A 308 "
           pdb=" SG  CYS A 315 "
           pdb=" CB  CYS A 315 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -18.06  -67.94     1      1.00e+01 1.00e-02 5.99e+01
  dihedral pdb=" C   LEU A 641 "
           pdb=" N   LEU A 641 "
           pdb=" CA  LEU A 641 "
           pdb=" CB  LEU A 641 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.39   10.79     0      2.50e+00 1.60e-01 1.86e+01
  dihedral pdb=" CA  PRO A 550 "
           pdb=" C   PRO A 550 "
           pdb=" N   ASP A 551 "
           pdb=" CA  ASP A 551 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.67  -18.33     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 3097 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 660
       0.060 -    0.120: 137
       0.120 -    0.180: 21
       0.180 -    0.240: 5
       0.240 -    0.300: 2
  Chirality restraints: 825
  Sorted by residual:
  chirality pdb=" CA  LEU A 641 "
            pdb=" N   LEU A 641 "
            pdb=" C   LEU A 641 "
            pdb=" CB  LEU A 641 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.25e+00
  chirality pdb=" CA  TYR A 624 "
            pdb=" N   TYR A 624 "
            pdb=" C   TYR A 624 "
            pdb=" CB  TYR A 624 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  ILE A 270 "
            pdb=" N   ILE A 270 "
            pdb=" C   ILE A 270 "
            pdb=" CB  ILE A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 822 not shown)

  Planarity restraints: 877
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 338 "   -0.020 2.00e-02 2.50e+03   4.08e-02 1.66e+01
        pdb=" CD  GLU A 338 "    0.070 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 338 "   -0.025 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 338 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 341 "   -0.034 2.00e-02 2.50e+03   2.57e-02 9.89e+00
        pdb=" CG  HIS A 341 "    0.028 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 341 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 341 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 341 "   -0.020 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 341 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 549 "    0.050 5.00e-02 4.00e+02   7.56e-02 9.16e+00
        pdb=" N   PRO A 550 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 550 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 550 "    0.042 5.00e-02 4.00e+02
  ... (remaining 874 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1295
        2.79 -     3.32: 5400
        3.32 -     3.84: 8746
        3.84 -     4.37: 9798
        4.37 -     4.90: 16052
  Nonbonded interactions: 41291
  Sorted by model distance:
  nonbonded pdb=" N   PHE A  47 "
            pdb=" O   TYR A 176 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" NZ  LYS A 448 "
            pdb=" OD1 ASP A 551 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" O   ARG A 595 "
            pdb=" NE2 GLN A 599 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" NH1 ARG A 530 "
            pdb=" OD2 ASP A 534 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" O   TRP A 194 "
            pdb=" OG1 THR A 197 "
     model   vdw
     2.412 3.040
  ... (remaining 41286 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.790
  Set stop_for_unknowns flag:              0.010
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.350
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
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      :  0.006   0.043   5292  Z= 0.358
  Angle     :  0.970  13.601   7191  Z= 0.564
  Chirality :  0.053   0.300    825
  Planarity :  0.007   0.076    877
  Dihedral  : 16.572  89.180   1884
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  : 31.23 %
    Favored  : 68.60 %
  Cbeta Deviations :  0.17 %
  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: -0.97 (0.34), residues: 624
  helix: -0.27 (0.26), residues: 386
  sheet:  1.22 (1.35), residues: 16
  loop : -1.29 (0.46), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A 422 
 HIS   0.010   0.001   HIS A 341 
 PHE   0.035   0.002   PHE A 307 
 TYR   0.037   0.003   TYR A 323 
 ARG   0.006   0.001   ARG A 334 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TYR cc_start: 0.8775 (m-80) cc_final: 0.7875 (m-80)
REVERT: A  323 TYR cc_start: 0.8960 (t80) cc_final: 0.8142 (t80)
REVERT: A  332 LEU cc_start: 0.9428 (tp) cc_final: 0.9214 (mt)
REVERT: A  365 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8732 (mmtt)
REVERT: A  502 MET cc_start: 0.7755 (tpt) cc_final: 0.7178 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1972
  time to fit residues: 29.0585
Evaluate side-chains
  96 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0770
   overall best weight:    1.4146

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

Flipped N/Q/H residues before XYZ refinement:
A 216 GLN
A 450 ASN
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.172180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.119396 restraints weight = 8668.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.123381 restraints weight = 4840.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.125760 restraints weight = 3551.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5292  Z= 0.264
  Angle     :  0.697  10.059   7191  Z= 0.350
  Chirality :  0.045   0.225    825
  Planarity :  0.005   0.050    877
  Dihedral  :  4.592  20.216    681
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 27.89 %
    Favored  : 68.42 %
  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 (0.35), residues: 624
  helix:  0.95 (0.27), residues: 391
  sheet:  0.34 (1.11), residues: 22
  loop : -0.95 (0.47), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 681 
 HIS   0.005   0.001   HIS A 341 
 PHE   0.016   0.001   PHE A 199 
 TYR   0.023   0.002   TYR A 286 
 ARG   0.004   0.001   ARG A 330 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  324 TYR cc_start: 0.8970 (m-80) cc_final: 0.8601 (m-80)
REVERT: A  327 MET cc_start: 0.9183 (mtp) cc_final: 0.8858 (mtp)
REVERT: A  333 GLU cc_start: 0.8779 (tt0) cc_final: 0.8103 (tp30)
  outliers start: 21
  outliers final: 10
  residues processed: 118
  average time/residue: 0.1554
  time to fit residues: 25.1014
Evaluate side-chains
  101 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  131 TRP
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  603 PHE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  653 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 6 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.171835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.118578 restraints weight = 8767.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.122596 restraints weight = 4853.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.124960 restraints weight = 3562.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5292  Z= 0.232
  Angle     :  0.689  10.916   7191  Z= 0.335
  Chirality :  0.043   0.155    825
  Planarity :  0.004   0.036    877
  Dihedral  :  4.487  19.184    681
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 26.84 %
    Favored  : 67.37 %
  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:  0.60 (0.35), residues: 624
  helix:  1.11 (0.27), residues: 390
  sheet:  0.44 (1.11), residues: 22
  loop : -0.87 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 681 
 HIS   0.004   0.001   HIS A 341 
 PHE   0.010   0.001   PHE A 583 
 TYR   0.018   0.002   TYR A 286 
 ARG   0.004   0.000   ARG A 689 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 99
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7356 (t0) cc_final: 0.6610 (t0)
REVERT: A  324 TYR cc_start: 0.8919 (m-80) cc_final: 0.8659 (m-80)
REVERT: A  333 GLU cc_start: 0.8919 (tt0) cc_final: 0.8142 (tp30)
REVERT: A  502 MET cc_start: 0.7767 (tpt) cc_final: 0.7541 (tpt)
REVERT: A  570 MET cc_start: 0.8773 (tpt) cc_final: 0.8305 (tpt)
REVERT: A  606 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7651 (pm20)
  outliers start: 33
  outliers final: 15
  residues processed: 124
  average time/residue: 0.1462
  time to fit residues: 24.7879
Evaluate side-chains
  113 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  131 TRP
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  603 PHE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  653 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0070
   chunk 19 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   chunk 25 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7000

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.174267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.121024 restraints weight = 8773.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.125151 restraints weight = 4765.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.127073 restraints weight = 3487.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5292  Z= 0.187
  Angle     :  0.683  11.724   7191  Z= 0.325
  Chirality :  0.042   0.126    825
  Planarity :  0.004   0.037    877
  Dihedral  :  4.396  18.680    681
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 25.79 %
    Favored  : 68.77 %
  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:  0.69 (0.35), residues: 624
  helix:  1.10 (0.27), residues: 390
  sheet:  0.46 (1.04), residues: 22
  loop : -0.65 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.013   0.001   PHE A 583 
 TYR   0.019   0.001   TYR A 286 
 ARG   0.004   0.000   ARG A 227 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 103
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7381 (t0) cc_final: 0.6641 (t0)
REVERT: A  286 TYR cc_start: 0.8978 (m-80) cc_final: 0.8749 (m-10)
REVERT: A  327 MET cc_start: 0.9230 (mtm) cc_final: 0.8827 (mtm)
REVERT: A  333 GLU cc_start: 0.8940 (tt0) cc_final: 0.8090 (tp30)
REVERT: A  443 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7417 (mp)
REVERT: A  502 MET cc_start: 0.7875 (tpt) cc_final: 0.7525 (tpt)
REVERT: A  570 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8279 (tpt)
REVERT: A  606 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7556 (pm20)
  outliers start: 31
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1443
  time to fit residues: 24.3663
Evaluate side-chains
  120 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  116 TRP
Chi-restraints excluded: chain A residue  131 TRP
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  653 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 23 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 GLN
** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 648 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.174166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.121158 restraints weight = 8712.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.125194 restraints weight = 4754.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.127733 restraints weight = 3478.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5292  Z= 0.205
  Angle     :  0.685  12.704   7191  Z= 0.325
  Chirality :  0.042   0.153    825
  Planarity :  0.004   0.036    877
  Dihedral  :  4.361  18.383    681
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 26.67 %
    Favored  : 67.37 %
  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:  0.67 (0.35), residues: 624
  helix:  1.07 (0.27), residues: 391
  sheet:  0.29 (0.99), residues: 22
  loop : -0.61 (0.48), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 681 
 HIS   0.008   0.001   HIS A 648 
 PHE   0.012   0.001   PHE A 583 
 TYR   0.029   0.002   TYR A 286 
 ARG   0.003   0.000   ARG A 689 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7320 (t0) cc_final: 0.6588 (t0)
REVERT: A  327 MET cc_start: 0.9155 (mtm) cc_final: 0.8887 (mtp)
REVERT: A  333 GLU cc_start: 0.8968 (tt0) cc_final: 0.8118 (tp30)
REVERT: A  443 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7393 (mp)
REVERT: A  502 MET cc_start: 0.7853 (tpt) cc_final: 0.7425 (tpt)
REVERT: A  606 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7745 (pm20)
  outliers start: 34
  outliers final: 21
  residues processed: 125
  average time/residue: 0.1454
  time to fit residues: 25.1924
Evaluate side-chains
  121 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  116 TRP
Chi-restraints excluded: chain A residue  131 TRP
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  653 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 22 optimal weight:    0.0060
   chunk 51 optimal weight:   20.0000
   chunk 15 optimal weight:    5.9990
   chunk 48 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 16 optimal weight:    9.9990
   chunk 5 optimal weight:    0.2980
   overall best weight:    1.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
A 290 GLN
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.171100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.118123 restraints weight = 8495.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.122002 restraints weight = 4670.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.124318 restraints weight = 3437.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5292  Z= 0.275
  Angle     :  0.718  12.127   7191  Z= 0.344
  Chirality :  0.043   0.135    825
  Planarity :  0.004   0.035    877
  Dihedral  :  4.383  19.015    681
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 28.60 %
    Favored  : 66.32 %
  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:  0.42 (0.35), residues: 624
  helix:  0.82 (0.26), residues: 398
  sheet:  0.26 (0.97), residues: 22
  loop : -0.65 (0.48), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.012   0.001   PHE A 583 
 TYR   0.022   0.002   TYR A 324 
 ARG   0.003   0.000   ARG A 689 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7575 (t0) cc_final: 0.6760 (t0)
REVERT: A  327 MET cc_start: 0.9135 (mtm) cc_final: 0.8636 (ptm)
REVERT: A  333 GLU cc_start: 0.8954 (tt0) cc_final: 0.8177 (tp30)
REVERT: A  422 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.7388 (t60)
REVERT: A  443 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7440 (mp)
REVERT: A  502 MET cc_start: 0.7983 (tpt) cc_final: 0.7487 (tpt)
REVERT: A  606 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7793 (pm20)
  outliers start: 29
  outliers final: 20
  residues processed: 124
  average time/residue: 0.1592
  time to fit residues: 26.2509
Evaluate side-chains
  122 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  116 TRP
Chi-restraints excluded: chain A residue  131 TRP
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  422 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  653 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 41 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 47 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.173963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.122832 restraints weight = 8386.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.126655 restraints weight = 4744.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.129018 restraints weight = 3512.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5292  Z= 0.181
  Angle     :  0.692  14.190   7191  Z= 0.326
  Chirality :  0.042   0.139    825
  Planarity :  0.004   0.037    877
  Dihedral  :  4.355  18.449    681
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 28.42 %
    Favored  : 66.84 %
  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: 624
  helix:  0.93 (0.26), residues: 397
  sheet:  0.30 (1.00), residues: 22
  loop : -0.54 (0.49), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 681 
 HIS   0.003   0.000   HIS A 341 
 PHE   0.011   0.001   PHE A 583 
 TYR   0.025   0.002   TYR A 324 
 ARG   0.003   0.000   ARG A 689 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7504 (t0) cc_final: 0.6667 (t0)
REVERT: A  327 MET cc_start: 0.9153 (mtm) cc_final: 0.8844 (ptm)
REVERT: A  333 GLU cc_start: 0.8947 (tt0) cc_final: 0.8158 (tp30)
REVERT: A  443 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7510 (mp)
REVERT: A  502 MET cc_start: 0.7927 (tpt) cc_final: 0.7687 (tpt)
REVERT: A  571 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: A  606 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7659 (pm20)
  outliers start: 27
  outliers final: 17
  residues processed: 122
  average time/residue: 0.1496
  time to fit residues: 24.7275
Evaluate side-chains
  116 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  116 TRP
Chi-restraints excluded: chain A residue  131 TRP
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  653 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 21 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 4 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 48 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.173182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.125020 restraints weight = 8559.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.125829 restraints weight = 5008.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.126648 restraints weight = 3888.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5292  Z= 0.205
  Angle     :  0.729  15.660   7191  Z= 0.339
  Chirality :  0.042   0.142    825
  Planarity :  0.004   0.036    877
  Dihedral  :  4.399  18.482    681
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 30.18 %
    Favored  : 65.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: 624
  helix:  0.81 (0.26), residues: 397
  sheet:  0.18 (1.01), residues: 22
  loop : -0.50 (0.50), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 681 
 HIS   0.002   0.000   HIS A 341 
 PHE   0.011   0.001   PHE A 583 
 TYR   0.026   0.002   TYR A 323 
 ARG   0.003   0.000   ARG A 689 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7504 (t0) cc_final: 0.6668 (t0)
REVERT: A  327 MET cc_start: 0.9122 (mtm) cc_final: 0.8718 (ptm)
REVERT: A  328 LYS cc_start: 0.9482 (OUTLIER) cc_final: 0.9127 (pptt)
REVERT: A  333 GLU cc_start: 0.8972 (tt0) cc_final: 0.8168 (tp30)
REVERT: A  502 MET cc_start: 0.7971 (tpt) cc_final: 0.7588 (tpt)
REVERT: A  570 MET cc_start: 0.8607 (tpt) cc_final: 0.8318 (tpt)
REVERT: A  571 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8179 (tm-30)
REVERT: A  606 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7671 (pm20)
  outliers start: 23
  outliers final: 15
  residues processed: 117
  average time/residue: 0.1434
  time to fit residues: 22.6650
Evaluate side-chains
  110 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  116 TRP
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  690 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 58 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 54 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.173528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.130616 restraints weight = 8508.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.132960 restraints weight = 6975.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.133365 restraints weight = 6471.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.3001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5292  Z= 0.196
  Angle     :  0.736  16.148   7191  Z= 0.340
  Chirality :  0.043   0.145    825
  Planarity :  0.004   0.036    877
  Dihedral  :  4.381  18.309    681
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 29.82 %
    Favored  : 66.32 %
  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:  0.56 (0.35), residues: 624
  helix:  0.84 (0.26), residues: 397
  sheet:  0.70 (1.19), residues: 17
  loop : -0.38 (0.50), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP A 681 
 HIS   0.002   0.000   HIS A 341 
 PHE   0.016   0.001   PHE A 556 
 TYR   0.017   0.001   TYR A 323 
 ARG   0.003   0.000   ARG A 689 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7541 (t0) cc_final: 0.6713 (t0)
REVERT: A  328 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9099 (pptt)
REVERT: A  333 GLU cc_start: 0.8803 (tt0) cc_final: 0.8043 (tp30)
REVERT: A  349 MET cc_start: 0.6793 (mmp) cc_final: 0.6478 (mmp)
REVERT: A  502 MET cc_start: 0.7878 (tpt) cc_final: 0.7652 (tpt)
REVERT: A  570 MET cc_start: 0.8542 (tpt) cc_final: 0.8283 (tpt)
REVERT: A  571 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: A  606 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7567 (pm20)
  outliers start: 22
  outliers final: 19
  residues processed: 114
  average time/residue: 0.1675
  time to fit residues: 25.3932
Evaluate side-chains
  115 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  116 TRP
Chi-restraints excluded: chain A residue  131 TRP
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  511 ILE
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  690 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0870
   overall best weight:    0.7564

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

Flipped N/Q/H residues before XYZ refinement:
A 185 ASN
A 345 GLN
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 GLN
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.172746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.123282 restraints weight = 8426.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.124147 restraints weight = 5754.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.125665 restraints weight = 4265.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5292  Z= 0.204
  Angle     :  0.755  16.529   7191  Z= 0.346
  Chirality :  0.044   0.227    825
  Planarity :  0.004   0.038    877
  Dihedral  :  4.364  18.249    681
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 30.18 %
    Favored  : 66.32 %
  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: 624
  helix:  0.78 (0.26), residues: 403
  sheet:  0.68 (1.20), residues: 17
  loop : -0.24 (0.51), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 341 
 PHE   0.009   0.001   PHE A 583 
 TYR   0.017   0.001   TYR A 271 
 ARG   0.003   0.000   ARG A 689 

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7426 (t0) cc_final: 0.6721 (t0)
REVERT: A  328 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9136 (pptt)
REVERT: A  333 GLU cc_start: 0.8942 (tt0) cc_final: 0.8200 (tp30)
REVERT: A  349 MET cc_start: 0.7051 (mmp) cc_final: 0.6718 (mmp)
REVERT: A  502 MET cc_start: 0.7927 (tpt) cc_final: 0.7564 (tpt)
REVERT: A  606 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7611 (pm20)
  outliers start: 20
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1499
  time to fit residues: 21.9634
Evaluate side-chains
  109 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  116 TRP
Chi-restraints excluded: chain A residue  131 TRP
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  440 SER
Chi-restraints excluded: chain A residue  516 ILE
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  607 PHE
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  690 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 2 optimal weight:    0.1980
   chunk 57 optimal weight:    0.0870
   chunk 43 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.174691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.122545 restraints weight = 8525.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.126215 restraints weight = 5045.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.128506 restraints weight = 3778.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5292  Z= 0.174
  Angle     :  0.748  16.477   7191  Z= 0.343
  Chirality :  0.043   0.223    825
  Planarity :  0.004   0.038    877
  Dihedral  :  4.356  17.965    681
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 29.82 %
    Favored  : 66.32 %
  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:  0.64 (0.35), residues: 624
  helix:  0.79 (0.26), residues: 403
  sheet:  1.54 (1.46), residues: 12
  loop : -0.18 (0.51), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 681 
 HIS   0.002   0.000   HIS A 341 
 PHE   0.011   0.001   PHE A 583 
 TYR   0.016   0.001   TYR A 286 
 ARG   0.003   0.000   ARG A 689 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1980.96 seconds
wall clock time: 36 minutes 29.63 seconds (2189.63 seconds total)