Starting phenix.real_space_refine
on Fri Aug 22 15:40:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ehw_28153/08_2025/8ehw_28153.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ehw_28153/08_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_28153/08_2025/8ehw_28153.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ehw_28153/08_2025/8ehw_28153.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ehw_28153/08_2025/8ehw_28153.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ehw_28153/08_2025/8ehw_28153.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.036
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.29, per 1000 atoms: 0.25
  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: 0.47
  Conformation dependent library (CDL) restraints added in 235.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.13
  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: 0.78

  Time building geometry restraints manager: 0.64 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:             1.210
  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:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.650
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.110
-------------------------------------------------------------------------------
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      :  0.012   0.773   5294  Z= 0.620
  Angle     :  1.008  16.655   7195  Z= 0.578
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.001   ARG A 334 
 TYR   0.037   0.003   TYR A 323 
 PHE   0.035   0.002   PHE A 307 
 TRP   0.037   0.003   TRP A 422 
 HIS   0.010   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00558 ( 5292)
  covalent geometry    : angle       0.97031 ( 7191)
  SS BOND              : bond        0.54633 (    2)
  SS BOND              : angle      11.56551 (    4)
  hydrogen bonds       : bond        0.17173 (  306)
  hydrogen bonds       : angle       7.29156 (  873)

*********************** 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  : 0.182 
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: 0.0682
  time to fit residues: 10.1613
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  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.3980
   chunk 24 optimal weight:   30.0000
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   chunk 61 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.4323 r_free = 0.4323 target = 0.172653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.119901 restraints weight = 8685.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.123886 restraints weight = 4778.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.126404 restraints weight = 3489.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.127544 restraints weight = 2960.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.128530 restraints weight = 2725.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.1567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5294  Z= 0.174
  Angle     :  0.696   9.803   7195  Z= 0.348
  Chirality :  0.045   0.239    825
  Planarity :  0.005   0.043    877
  Dihedral  :  4.597  20.433    681
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 27.54 %
    Favored  : 68.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.35), residues: 624
  helix:  0.97 (0.27), residues: 391
  sheet:  0.35 (1.11), residues: 22
  loop : -0.96 (0.47), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 689 
 TYR   0.022   0.002   TYR A 323 
 PHE   0.016   0.001   PHE A 199 
 TRP   0.023   0.002   TRP A 681 
 HIS   0.004   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 5292)
  covalent geometry    : angle       0.69641 ( 7191)
  SS BOND              : bond        0.00028 (    2)
  SS BOND              : angle       0.74426 (    4)
  hydrogen bonds       : bond        0.04659 (  306)
  hydrogen bonds       : angle       4.82349 (  873)

*********************** 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
  124 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 TYR cc_start: 0.8835 (t80) cc_final: 0.8597 (t80)
REVERT: A  324 TYR cc_start: 0.8917 (m-80) cc_final: 0.8530 (m-10)
REVERT: A  327 MET cc_start: 0.9172 (mtp) cc_final: 0.8933 (mtp)
REVERT: A  333 GLU cc_start: 0.8773 (tt0) cc_final: 0.8095 (tp30)
  outliers start: 22
  outliers final: 10
  residues processed: 119
  average time/residue: 0.0542
  time to fit residues: 8.8831
Evaluate side-chains
  100 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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 18 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    3.1588

-------------------------------------------------------------------------------
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 = 0.4242 r_free = 0.4242 target = 0.165947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.125366 restraints weight = 8726.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.125955 restraints weight = 7751.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.126709 restraints weight = 6772.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.127094 restraints weight = 4248.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.127917 restraints weight = 3860.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.074   5294  Z= 0.305
  Angle     :  0.808  12.168   7195  Z= 0.399
  Chirality :  0.047   0.159    825
  Planarity :  0.004   0.034    877
  Dihedral  :  4.740  21.035    681
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 17.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  7.37 %
    Allowed  : 25.26 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.34), residues: 624
  helix:  0.68 (0.26), residues: 392
  sheet:  0.42 (1.10), residues: 22
  loop : -1.02 (0.48), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 330 
 TYR   0.019   0.002   TYR A 286 
 PHE   0.022   0.002   PHE A 430 
 TRP   0.028   0.002   TRP A 681 
 HIS   0.005   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00721 ( 5292)
  covalent geometry    : angle       0.80838 ( 7191)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       0.74803 (    4)
  hydrogen bonds       : bond        0.04633 (  306)
  hydrogen bonds       : angle       4.86034 (  873)

*********************** 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
  140 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 98
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7341 (t0) cc_final: 0.6599 (t0)
REVERT: A  286 TYR cc_start: 0.8624 (m-80) cc_final: 0.8316 (m-10)
REVERT: A  333 GLU cc_start: 0.8790 (tt0) cc_final: 0.7946 (tp30)
REVERT: A  585 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.5609 (mpp)
  outliers start: 42
  outliers final: 21
  residues processed: 128
  average time/residue: 0.0477
  time to fit residues: 8.5729
Evaluate side-chains
  110 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
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  143 GLN
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  227 ARG
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  429 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  585 MET
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  645 VAL
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 52 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 48 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   chunk 54 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.170113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.117267 restraints weight = 8724.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.121288 restraints weight = 4776.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.123284 restraints weight = 3485.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.124952 restraints weight = 2995.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.125338 restraints weight = 2735.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5294  Z= 0.140
  Angle     :  0.702  13.269   7195  Z= 0.337
  Chirality :  0.043   0.162    825
  Planarity :  0.004   0.037    877
  Dihedral  :  4.615  19.761    681
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 26.84 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.35), residues: 624
  helix:  1.01 (0.27), residues: 390
  sheet:  0.31 (1.07), residues: 22
  loop : -0.76 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 689 
 TYR   0.026   0.002   TYR A 286 
 PHE   0.012   0.001   PHE A 583 
 TRP   0.022   0.001   TRP A 681 
 HIS   0.004   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5292)
  covalent geometry    : angle       0.70239 ( 7191)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.65356 (    4)
  hydrogen bonds       : bond        0.03931 (  306)
  hydrogen bonds       : angle       4.46113 (  873)

*********************** 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
  136 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7498 (t0) cc_final: 0.6603 (t0)
REVERT: A  327 MET cc_start: 0.9198 (mtm) cc_final: 0.8926 (mtm)
REVERT: A  333 GLU cc_start: 0.8933 (tt0) cc_final: 0.8164 (tp30)
REVERT: A  443 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7370 (mp)
REVERT: A  502 MET cc_start: 0.7829 (tpt) cc_final: 0.7364 (tpt)
REVERT: A  570 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8162 (tpt)
REVERT: A  585 MET cc_start: 0.5928 (OUTLIER) cc_final: 0.5718 (mpp)
REVERT: A  606 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7671 (pm20)
  outliers start: 36
  outliers final: 14
  residues processed: 126
  average time/residue: 0.0501
  time to fit residues: 8.7479
Evaluate side-chains
  114 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
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  225 LEU
Chi-restraints excluded: chain A residue  411 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  566 ILE
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  585 MET
Chi-restraints excluded: chain A residue  606 GLU
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 26 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0270
   chunk 23 optimal weight:   30.0000
   chunk 37 optimal weight:    0.4980
   chunk 46 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
A 648 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.173349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.122080 restraints weight = 8572.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.125986 restraints weight = 4805.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.128464 restraints weight = 3518.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.129814 restraints weight = 2974.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.130074 restraints weight = 2731.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5294  Z= 0.127
  Angle     :  0.710  12.901   7195  Z= 0.334
  Chirality :  0.043   0.149    825
  Planarity :  0.004   0.037    877
  Dihedral  :  4.481  18.853    681
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 27.54 %
    Favored  : 67.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.35), residues: 624
  helix:  1.00 (0.26), residues: 391
  sheet:  0.03 (1.01), residues: 22
  loop : -0.68 (0.47), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 689 
 TYR   0.021   0.002   TYR A 286 
 PHE   0.012   0.001   PHE A 583 
 TRP   0.020   0.001   TRP A 681 
 HIS   0.009   0.001   HIS A 648 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5292)
  covalent geometry    : angle       0.70979 ( 7191)
  SS BOND              : bond        0.00307 (    2)
  SS BOND              : angle       1.12994 (    4)
  hydrogen bonds       : bond        0.03652 (  306)
  hydrogen bonds       : angle       4.29273 (  873)

*********************** 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
  129 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 99
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7532 (t0) cc_final: 0.6697 (t0)
REVERT: A  327 MET cc_start: 0.9029 (mtm) cc_final: 0.8752 (mtm)
REVERT: A  333 GLU cc_start: 0.8897 (tt0) cc_final: 0.8066 (tp30)
REVERT: A  443 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7471 (mp)
REVERT: A  502 MET cc_start: 0.7806 (tpt) cc_final: 0.7516 (tpt)
REVERT: A  606 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7689 (pm20)
  outliers start: 30
  outliers final: 19
  residues processed: 119
  average time/residue: 0.0515
  time to fit residues: 8.3457
Evaluate side-chains
  117 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
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  225 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  411 LEU
Chi-restraints excluded: chain A residue  438 THR
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  566 ILE
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
Chi-restraints excluded: chain A residue  690 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 51 optimal weight:   20.0000
   chunk 46 optimal weight:    0.5980
   chunk 54 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 187 GLN
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 670 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.171707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.119349 restraints weight = 9158.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.123283 restraints weight = 5021.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.125728 restraints weight = 3685.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.126689 restraints weight = 3137.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.127769 restraints weight = 2901.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5294  Z= 0.128
  Angle     :  0.695  13.866   7195  Z= 0.328
  Chirality :  0.042   0.144    825
  Planarity :  0.004   0.038    877
  Dihedral  :  4.423  18.651    681
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 28.77 %
    Favored  : 66.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.35), residues: 624
  helix:  0.88 (0.26), residues: 398
  sheet:  0.58 (1.14), residues: 17
  loop : -0.54 (0.47), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 689 
 TYR   0.019   0.001   TYR A 286 
 PHE   0.013   0.001   PHE A 583 
 TRP   0.018   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 5292)
  covalent geometry    : angle       0.69488 ( 7191)
  SS BOND              : bond        0.00113 (    2)
  SS BOND              : angle       1.16370 (    4)
  hydrogen bonds       : bond        0.03510 (  306)
  hydrogen bonds       : angle       4.22962 (  873)

*********************** 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
  128 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7534 (t0) cc_final: 0.6797 (t0)
REVERT: A  323 TYR cc_start: 0.9097 (t80) cc_final: 0.8838 (t80)
REVERT: A  333 GLU cc_start: 0.8969 (tt0) cc_final: 0.8141 (tp30)
REVERT: A  443 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7403 (mp)
REVERT: A  502 MET cc_start: 0.7858 (tpt) cc_final: 0.7439 (tpt)
REVERT: A  606 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7648 (pm20)
  outliers start: 29
  outliers final: 22
  residues processed: 118
  average time/residue: 0.0528
  time to fit residues: 8.6216
Evaluate side-chains
  118 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
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  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  438 THR
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  615 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  690 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4316 r_free = 0.4316 target = 0.172614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.119956 restraints weight = 8595.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.123748 restraints weight = 5013.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.126129 restraints weight = 3730.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.126985 restraints weight = 3183.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.128042 restraints weight = 2958.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5294  Z= 0.138
  Angle     :  0.726  14.799   7195  Z= 0.338
  Chirality :  0.042   0.142    825
  Planarity :  0.004   0.037    877
  Dihedral  :  4.371  18.537    681
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 27.72 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.35), residues: 624
  helix:  0.93 (0.26), residues: 398
  sheet:  0.73 (1.17), residues: 17
  loop : -0.41 (0.48), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 689 
 TYR   0.016   0.001   TYR A 286 
 PHE   0.012   0.001   PHE A 583 
 TRP   0.021   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 5292)
  covalent geometry    : angle       0.72563 ( 7191)
  SS BOND              : bond        0.00080 (    2)
  SS BOND              : angle       0.74133 (    4)
  hydrogen bonds       : bond        0.03529 (  306)
  hydrogen bonds       : angle       4.19934 (  873)

*********************** 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
  127 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7677 (t0) cc_final: 0.6866 (t0)
REVERT: A  328 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9126 (pptt)
REVERT: A  333 GLU cc_start: 0.8948 (tt0) cc_final: 0.8131 (tp30)
REVERT: A  443 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7486 (mp)
REVERT: A  502 MET cc_start: 0.7949 (tpt) cc_final: 0.7571 (tpt)
REVERT: A  585 MET cc_start: 0.5493 (mpp) cc_final: 0.5250 (mpp)
REVERT: A  606 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7668 (pm20)
  outliers start: 31
  outliers final: 24
  residues processed: 120
  average time/residue: 0.0442
  time to fit residues: 7.4829
Evaluate side-chains
  120 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 93
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   52 THR
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  160 VAL
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  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  438 THR
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  615 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  690 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   chunk 48 optimal weight:    0.7980
   chunk 31 optimal weight:    8.9990
   chunk 54 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 17 optimal weight:    0.0270
   overall best weight:    0.7040

-------------------------------------------------------------------------------
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 = 0.4329 r_free = 0.4329 target = 0.173582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.120720 restraints weight = 8636.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.124696 restraints weight = 4782.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.127185 restraints weight = 3497.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.128587 restraints weight = 2968.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.128922 restraints weight = 2724.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5294  Z= 0.128
  Angle     :  0.719  15.767   7195  Z= 0.335
  Chirality :  0.042   0.145    825
  Planarity :  0.004   0.037    877
  Dihedral  :  4.368  18.279    681
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 29.12 %
    Favored  : 65.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.35), residues: 624
  helix:  0.96 (0.26), residues: 398
  sheet:  0.70 (1.18), residues: 17
  loop : -0.36 (0.49), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 689 
 TYR   0.016   0.002   TYR A 286 
 PHE   0.012   0.001   PHE A 583 
 TRP   0.019   0.001   TRP A 681 
 HIS   0.002   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5292)
  covalent geometry    : angle       0.71930 ( 7191)
  SS BOND              : bond        0.00069 (    2)
  SS BOND              : angle       0.67110 (    4)
  hydrogen bonds       : bond        0.03479 (  306)
  hydrogen bonds       : angle       4.14063 (  873)

*********************** 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
  126 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 ASN cc_start: 0.7659 (t0) cc_final: 0.6875 (t0)
REVERT: A  333 GLU cc_start: 0.8967 (tt0) cc_final: 0.8147 (tp30)
REVERT: A  443 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7326 (mp)
REVERT: A  502 MET cc_start: 0.7911 (tpt) cc_final: 0.7642 (tpt)
REVERT: A  606 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7669 (pm20)
  outliers start: 28
  outliers final: 21
  residues processed: 118
  average time/residue: 0.0451
  time to fit residues: 7.5710
Evaluate side-chains
  115 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   52 THR
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  193 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  438 THR
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  615 LEU
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 47 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 42 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0970
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.4324 r_free = 0.4324 target = 0.173240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.120463 restraints weight = 8511.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.124379 restraints weight = 4774.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.126851 restraints weight = 3527.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.127945 restraints weight = 2986.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.128897 restraints weight = 2754.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5294  Z= 0.124
  Angle     :  0.729  16.340   7195  Z= 0.337
  Chirality :  0.042   0.140    825
  Planarity :  0.004   0.037    877
  Dihedral  :  4.334  18.087    681
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 30.18 %
    Favored  : 65.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.35), residues: 624
  helix:  0.97 (0.26), residues: 399
  sheet:  0.66 (1.19), residues: 17
  loop : -0.36 (0.50), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 689 
 TYR   0.029   0.002   TYR A 324 
 PHE   0.028   0.001   PHE A 680 
 TRP   0.022   0.001   TRP A 681 
 HIS   0.002   0.000   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 5292)
  covalent geometry    : angle       0.72945 ( 7191)
  SS BOND              : bond        0.00065 (    2)
  SS BOND              : angle       0.75687 (    4)
  hydrogen bonds       : bond        0.03455 (  306)
  hydrogen bonds       : angle       4.13737 (  873)

*********************** 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
  122 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ASP cc_start: 0.6987 (m-30) cc_final: 0.6466 (t0)
REVERT: A  185 ASN cc_start: 0.7651 (t0) cc_final: 0.6870 (t0)
REVERT: A  333 GLU cc_start: 0.8986 (tt0) cc_final: 0.8193 (tp30)
REVERT: A  502 MET cc_start: 0.7873 (tpt) cc_final: 0.7599 (tpt)
REVERT: A  606 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7565 (pm20)
  outliers start: 27
  outliers final: 22
  residues processed: 114
  average time/residue: 0.0459
  time to fit residues: 7.4294
Evaluate side-chains
  118 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   52 THR
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  225 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  438 THR
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  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  615 LEU
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 3 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 62 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4303 r_free = 0.4303 target = 0.171414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.118610 restraints weight = 8648.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.122493 restraints weight = 4830.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.124529 restraints weight = 3537.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.126285 restraints weight = 3030.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.126717 restraints weight = 2764.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7511
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5294  Z= 0.143
  Angle     :  0.759  16.616   7195  Z= 0.352
  Chirality :  0.043   0.146    825
  Planarity :  0.004   0.038    877
  Dihedral  :  4.355  17.929    681
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 30.70 %
    Favored  : 65.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.35), residues: 624
  helix:  0.90 (0.26), residues: 399
  sheet:  0.62 (1.20), residues: 17
  loop : -0.34 (0.50), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 689 
 TYR   0.031   0.002   TYR A 324 
 PHE   0.019   0.001   PHE A  63 
 TRP   0.019   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 5292)
  covalent geometry    : angle       0.75853 ( 7191)
  SS BOND              : bond        0.00053 (    2)
  SS BOND              : angle       0.70841 (    4)
  hydrogen bonds       : bond        0.03524 (  306)
  hydrogen bonds       : angle       4.20095 (  873)

********************** 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
  120 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ASP cc_start: 0.6936 (m-30) cc_final: 0.6389 (t0)
REVERT: A  185 ASN cc_start: 0.7710 (t0) cc_final: 0.6905 (t0)
REVERT: A  329 ASP cc_start: 0.9296 (m-30) cc_final: 0.9061 (m-30)
REVERT: A  333 GLU cc_start: 0.8997 (tt0) cc_final: 0.8207 (tp30)
REVERT: A  349 MET cc_start: 0.6974 (mmp) cc_final: 0.6665 (mmp)
REVERT: A  502 MET cc_start: 0.7904 (tpt) cc_final: 0.7447 (tpt)
REVERT: A  571 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8248 (tm-30)
REVERT: A  606 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7592 (pm20)
  outliers start: 23
  outliers final: 22
  residues processed: 114
  average time/residue: 0.0484
  time to fit residues: 7.7687
Evaluate side-chains
  117 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 VAL
Chi-restraints excluded: chain A residue   52 THR
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  225 LEU
Chi-restraints excluded: chain A residue  328 LYS
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  438 THR
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  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  615 LEU
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 14 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0980
   chunk 25 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 1 optimal weight:    0.0670
   chunk 40 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4322 r_free = 0.4322 target = 0.173016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.120796 restraints weight = 8601.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.124792 restraints weight = 4765.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.127271 restraints weight = 3487.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.128185 restraints weight = 2951.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.128744 restraints weight = 2736.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5294  Z= 0.128
  Angle     :  0.761  16.551   7195  Z= 0.353
  Chirality :  0.043   0.142    825
  Planarity :  0.004   0.037    877
  Dihedral  :  4.354  17.789    681
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 30.88 %
    Favored  : 65.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.35), residues: 624
  helix:  0.95 (0.26), residues: 396
  sheet:  0.68 (1.21), residues: 17
  loop : -0.35 (0.50), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 689 
 TYR   0.030   0.002   TYR A 324 
 PHE   0.029   0.001   PHE A 680 
 TRP   0.022   0.001   TRP A 681 
 HIS   0.003   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 5292)
  covalent geometry    : angle       0.76071 ( 7191)
  SS BOND              : bond        0.00033 (    2)
  SS BOND              : angle       0.63266 (    4)
  hydrogen bonds       : bond        0.03426 (  306)
  hydrogen bonds       : angle       4.17788 (  873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 975.08 seconds
wall clock time: 17 minutes 30.12 seconds (1050.12 seconds total)