Starting phenix.real_space_refine
on Wed Jul 23 22:38:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yim_33861/07_2025/7yim_33861.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yim_33861/07_2025/7yim_33861.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yim_33861/07_2025/7yim_33861.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yim_33861/07_2025/7yim_33861.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yim_33861/07_2025/7yim_33861.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yim_33861/07_2025/7yim_33861.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.006 sd=   0.095
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      40      5.16       5
     C    2925      2.51       5
     N     791      2.21       5
     O     901      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4657
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4657
          Classifications: {'peptide': 592}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 570}
  Time building chain proxies: 3.36, per 1000 atoms: 0.72
  Number of scatterers: 4657
  At special positions: 0
  Unit cell: (69.5594, 91.3616, 103.82, 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      40     16.00
     O     901      8.00
     N     791      7.00
     C    2925      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  37 " - pdb=" SG  CYS A  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 114 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 113 " - pdb=" SG  CYS A 124 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 148 " - pdb=" SG  CYS A 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 192 " - pdb=" SG  CYS A 201 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 270 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 269 " - pdb=" SG  CYS A 277 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 289 " - pdb=" SG  CYS A 303 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 302 " - pdb=" SG  CYS A 313 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 384 " - pdb=" SG  CYS A 393 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 416 " - pdb=" SG  CYS A 462 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 461 " - pdb=" SG  CYS A 472 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 485 " - pdb=" SG  CYS A 501 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 500 " - pdb=" SG  CYS A 511 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 583 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 582 " - pdb=" SG  CYS A 591 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 646.3 milliseconds
  

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1132

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      75.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 34
      removed outlier: 4.209A  pdb=" N   ASP A  33 " --> pdb=" O   SER A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 55
      removed outlier: 3.750A  pdb=" N   LEU A  46 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 75
      removed outlier: 3.573A  pdb=" N   GLU A  75 " --> pdb=" O   LEU A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 101
    Processing helix  chain 'A' and resid 101 through 108
      removed outlier: 3.546A  pdb=" N   LEU A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
      removed outlier: 3.613A  pdb=" N   SER A 115 " --> pdb=" O   ASP A 112 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLN A 116 " --> pdb=" O   CYS A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 128
    Processing helix  chain 'A' and resid 143 through 154
      removed outlier: 3.629A  pdb=" N   ASP A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 168
    Processing helix  chain 'A' and resid 174 through 193
      Proline residue:  A 190  - end of helix
    Processing helix  chain 'A' and resid 197 through 231
      removed outlier: 3.915A  pdb=" N   THR A 208 " --> pdb=" O   THR A 204 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   VAL A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 247
    Processing helix  chain 'A' and resid 251 through 271
    Processing helix  chain 'A' and resid 273 through 290
    Processing helix  chain 'A' and resid 301 through 305
      removed outlier: 4.018A  pdb=" N   LEU A 305 " --> pdb=" O   CYS A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 317
    Processing helix  chain 'A' and resid 343 through 361
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 3.746A  pdb=" N   PHE A 385 " --> pdb=" O   LEU A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 399
      removed outlier: 4.181A  pdb=" N   CYS A 393 " --> pdb=" O   ASN A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 439
      removed outlier: 7.982A  pdb=" N   GLU A 424 " --> pdb=" O   GLN A 420 " (cutoff:3.500A)
      removed outlier: 9.376A  pdb=" N   TYR A 425 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   TYR A 426 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 462
    Processing helix  chain 'A' and resid 467 through 491
      removed outlier: 4.204A  pdb=" N   ALA A 471 " --> pdb=" O   ASP A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 503
      removed outlier: 3.527A  pdb=" N   GLY A 498 " --> pdb=" O   ASN A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 514
    Processing helix  chain 'A' and resid 527 through 531
      removed outlier: 3.999A  pdb=" N   LYS A 530 " --> pdb=" O   SER A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 560
    Processing helix  chain 'A' and resid 565 through 582
    Processing helix  chain 'A' and resid 587 through 608
      removed outlier: 3.913A  pdb=" N   CYS A 591 " --> pdb=" O   GLU A 587 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   GLN A 597 " --> pdb=" O   ALA A 593 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   LYS A 598 " --> pdb=" O   GLU A 594 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    924 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1072
        1.33 -     1.46: 1193
        1.46 -     1.58: 2428
        1.58 -     1.71: 0
        1.71 -     1.84: 48
  Bond restraints: 4741
  Sorted by residual:
  bond pdb=" CB  VAL A 355 "
       pdb=" CG2 VAL A 355 "
    ideal  model  delta    sigma   weight residual
    1.521  1.408  0.113 3.30e-02 9.18e+02 1.17e+01
  bond pdb=" C   TYR A 174 "
       pdb=" N   ALA A 175 "
    ideal  model  delta    sigma   weight residual
    1.332  1.297  0.035 1.09e-02 8.42e+03 1.04e+01
  bond pdb=" CG  GLN A 245 "
       pdb=" CD  GLN A 245 "
    ideal  model  delta    sigma   weight residual
    1.516  1.439  0.077 2.50e-02 1.60e+03 9.56e+00
  bond pdb=" CB  GLN A 245 "
       pdb=" CG  GLN A 245 "
    ideal  model  delta    sigma   weight residual
    1.520  1.427  0.093 3.00e-02 1.11e+03 9.55e+00
  bond pdb=" CG1 ILE A 314 "
       pdb=" CD1 ILE A 314 "
    ideal  model  delta    sigma   weight residual
    1.513  1.400  0.113 3.90e-02 6.57e+02 8.40e+00
  ... (remaining 4736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 6228
        2.87 -     5.74: 147
        5.74 -     8.61: 23
        8.61 -    11.48: 1
       11.48 -    14.36: 1
  Bond angle restraints: 6400
  Sorted by residual:
  angle pdb=" CA  CYS A 591 "
        pdb=" CB  CYS A 591 "
        pdb=" SG  CYS A 591 "
      ideal   model   delta    sigma   weight residual
     114.40  128.76  -14.36 2.30e+00 1.89e-01 3.90e+01
  angle pdb=" C   CYS A 591 "
        pdb=" CA  CYS A 591 "
        pdb=" CB  CYS A 591 "
      ideal   model   delta    sigma   weight residual
     110.88  103.82    7.06 1.57e+00 4.06e-01 2.02e+01
  angle pdb=" CA  GLU A  81 "
        pdb=" CB  GLU A  81 "
        pdb=" CG  GLU A  81 "
      ideal   model   delta    sigma   weight residual
     114.10  122.78   -8.68 2.00e+00 2.50e-01 1.88e+01
  angle pdb=" C   GLU A 398 "
        pdb=" N   GLU A 399 "
        pdb=" CA  GLU A 399 "
      ideal   model   delta    sigma   weight residual
     122.60  116.29    6.31 1.56e+00 4.11e-01 1.64e+01
  angle pdb=" C   LYS A 581 "
        pdb=" N   CYS A 582 "
        pdb=" CA  CYS A 582 "
      ideal   model   delta    sigma   weight residual
     122.54  115.64    6.90 1.82e+00 3.02e-01 1.44e+01
  ... (remaining 6395 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 2536
       17.11 -    34.21: 342
       34.21 -    51.31: 60
       51.31 -    68.42: 19
       68.42 -    85.52: 5
  Dihedral angle restraints: 2962
    sinusoidal: 1222
      harmonic: 1740
  Sorted by residual:
  dihedral pdb=" CB  CYS A 582 "
           pdb=" SG  CYS A 582 "
           pdb=" SG  CYS A 591 "
           pdb=" CB  CYS A 591 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.66  -80.66     1      1.00e+01 1.00e-02 8.04e+01
  dihedral pdb=" CA  LYS A  76 "
           pdb=" C   LYS A  76 "
           pdb=" N   PRO A  77 "
           pdb=" CA  PRO A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.61  -35.39     0      5.00e+00 4.00e-02 5.01e+01
  dihedral pdb=" CA  SER A 117 "
           pdb=" C   SER A 117 "
           pdb=" N   GLU A 118 "
           pdb=" CA  GLU A 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.39  -33.61     0      5.00e+00 4.00e-02 4.52e+01
  ... (remaining 2959 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 519
       0.070 -    0.139: 176
       0.139 -    0.209: 19
       0.209 -    0.278: 4
       0.278 -    0.348: 1
  Chirality restraints: 719
  Sorted by residual:
  chirality pdb=" CB  ILE A 481 "
            pdb=" CA  ILE A 481 "
            pdb=" CG1 ILE A 481 "
            pdb=" CG2 ILE A 481 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" CB  VAL A 355 "
            pdb=" CA  VAL A 355 "
            pdb=" CG1 VAL A 355 "
            pdb=" CG2 VAL A 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CA  PRO A 510 "
            pdb=" N   PRO A 510 "
            pdb=" C   PRO A 510 "
            pdb=" CB  PRO A 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.46    0.25 2.00e-01 2.50e+01 1.61e+00
  ... (remaining 716 not shown)

  Planarity restraints: 837
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 509 "    0.059 5.00e-02 4.00e+02   8.92e-02 1.27e+01
        pdb=" N   PRO A 510 "   -0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO A 510 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 510 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 592 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.25e+00
        pdb=" C   PHE A 592 "    0.047 2.00e-02 2.50e+03
        pdb=" O   PHE A 592 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A 593 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 175 "    0.045 5.00e-02 4.00e+02   6.65e-02 7.07e+00
        pdb=" N   PRO A 176 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 176 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 176 "    0.038 5.00e-02 4.00e+02
  ... (remaining 834 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1194
        2.80 -     3.32: 4406
        3.32 -     3.85: 7985
        3.85 -     4.37: 9276
        4.37 -     4.90: 15248
  Nonbonded interactions: 38109
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 165 "
            pdb=" NH1 ARG A 169 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" O   ARG A 509 "
            pdb=" OG  SER A 513 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OE1 GLU A  62 "
            pdb=" OH  TYR A 108 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG  SER A  42 "
            pdb=" OD2 ASP A  45 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   ALA A  44 "
            pdb=" OG1 THR A  48 "
     model   vdw
     2.311 3.040
  ... (remaining 38104 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.250
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.470
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6532
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      :  0.013   0.113   4757  Z= 0.530
  Angle     :  1.155  14.355   6432  Z= 0.642
  Chirality :  0.068   0.348    719
  Planarity :  0.009   0.089    837
  Dihedral  : 15.893  85.522   1782
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  6.59 %
    Favored  : 92.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.17 (0.25), residues: 590
  helix: -2.57 (0.18), residues: 420
  sheet:  None (None), residues: 0
  loop : -2.74 (0.38), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.007   TRP A 181 
 HIS   0.012   0.003   HIS A 483 
 PHE   0.031   0.005   PHE A 235 
 TYR   0.043   0.005   TYR A 185 
 ARG   0.008   0.001   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13229 (  312)
  hydrogen bonds       : angle       6.74957 (  924)
  SS BOND              : bond        0.01411 (   16)
  SS BOND              : angle       3.19771 (   32)
  covalent geometry    : bond        0.01290 ( 4741)
  covalent geometry    : angle       1.13553 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
REVERT: A  519 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6959 (tm-30)
  outliers start: 4
  outliers final: 0
  residues processed: 68
  average time/residue: 1.6014
  time to fit residues: 112.4698
Evaluate side-chains
  37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 116 GLN
A 220 ASN
A 389 ASN
A 420 GLN
A 534 HIS
A 555 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.205396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.161412 restraints weight = 5299.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.4379 rms_B_bonded: 2.39
r_work: 0.4249 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.4114 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6485
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4757  Z= 0.142
  Angle     :  0.587   7.137   6432  Z= 0.317
  Chirality :  0.040   0.158    719
  Planarity :  0.005   0.051    837
  Dihedral  :  5.350  30.476    631
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 13.37 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.76 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.31), residues: 590
  helix: -0.48 (0.23), residues: 429
  sheet:  None (None), residues: 0
  loop : -2.47 (0.41), residues: 161

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP A 181 
 HIS   0.008   0.001   HIS A 534 
 PHE   0.016   0.002   PHE A 235 
 TYR   0.018   0.001   TYR A 185 
 ARG   0.001   0.000   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04555 (  312)
  hydrogen bonds       : angle       4.71027 (  924)
  SS BOND              : bond        0.00321 (   16)
  SS BOND              : angle       1.67092 (   32)
  covalent geometry    : bond        0.00325 ( 4741)
  covalent geometry    : angle       0.57669 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7034 (tp) cc_final: 0.6821 (tp)
REVERT: A  228 LYS cc_start: 0.7759 (tttt) cc_final: 0.7112 (mppt)
REVERT: A  548 MET cc_start: 0.6323 (mtp) cc_final: 0.6022 (tpt)
  outliers start: 5
  outliers final: 1
  residues processed: 62
  average time/residue: 1.2470
  time to fit residues: 80.4149
Evaluate side-chains
  46 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4762 r_free = 0.4762 target = 0.202495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.156459 restraints weight = 5401.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.4317 rms_B_bonded: 2.42
r_work: 0.4184 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6438
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4757  Z= 0.176
  Angle     :  0.614   8.262   6432  Z= 0.324
  Chirality :  0.043   0.150    719
  Planarity :  0.005   0.045    837
  Dihedral  :  5.020  27.460    631
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.12 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.32), residues: 590
  helix:  0.17 (0.23), residues: 422
  sheet:  None (None), residues: 0
  loop : -2.06 (0.45), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 181 
 HIS   0.007   0.001   HIS A 483 
 PHE   0.025   0.002   PHE A  50 
 TYR   0.018   0.002   TYR A 164 
 ARG   0.008   0.001   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05016 (  312)
  hydrogen bonds       : angle       4.65768 (  924)
  SS BOND              : bond        0.00460 (   16)
  SS BOND              : angle       1.25171 (   32)
  covalent geometry    : bond        0.00416 ( 4741)
  covalent geometry    : angle       0.60872 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7130 (tp) cc_final: 0.6868 (tp)
REVERT: A  228 LYS cc_start: 0.7891 (tttt) cc_final: 0.7205 (mppt)
  outliers start: 12
  outliers final: 4
  residues processed: 53
  average time/residue: 1.0656
  time to fit residues: 59.3771
Evaluate side-chains
  42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  393 CYS
Chi-restraints excluded: chain A residue  583 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0570
   chunk 53 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0030
   chunk 5 optimal weight:    0.0980
   overall best weight:    0.3708

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4830 r_free = 0.4830 target = 0.208885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.164791 restraints weight = 5389.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.4412 rms_B_bonded: 2.45
r_work: 0.4283 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6284
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4757  Z= 0.121
  Angle     :  0.542   7.773   6432  Z= 0.288
  Chirality :  0.039   0.130    719
  Planarity :  0.004   0.033    837
  Dihedral  :  4.522  23.416    631
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 16.67 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.34), residues: 590
  helix:  0.84 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop : -2.01 (0.44), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 181 
 HIS   0.006   0.001   HIS A 534 
 PHE   0.031   0.002   PHE A  50 
 TYR   0.009   0.001   TYR A 185 
 ARG   0.004   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04026 (  312)
  hydrogen bonds       : angle       4.28041 (  924)
  SS BOND              : bond        0.00439 (   16)
  SS BOND              : angle       1.38127 (   32)
  covalent geometry    : bond        0.00269 ( 4741)
  covalent geometry    : angle       0.53470 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 48
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.6138 (tp30) cc_final: 0.5677 (tp30)
REVERT: A  228 LYS cc_start: 0.7669 (tttt) cc_final: 0.7038 (mppt)
REVERT: A  448 MET cc_start: 0.6648 (mtp) cc_final: 0.6208 (mtt)
  outliers start: 12
  outliers final: 5
  residues processed: 56
  average time/residue: 1.0865
  time to fit residues: 63.7503
Evaluate side-chains
  41 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  384 CYS
Chi-restraints excluded: chain A residue  393 CYS
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  583 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0870
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:    8.9990
   chunk 48 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 58 optimal weight:   10.0000
   overall best weight:    1.3362

-------------------------------------------------------------------------------
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 = 0.4787 r_free = 0.4787 target = 0.204786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.159079 restraints weight = 5393.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.4337 rms_B_bonded: 2.45
r_work: 0.4202 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6369
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4757  Z= 0.150
  Angle     :  0.568   7.950   6432  Z= 0.302
  Chirality :  0.041   0.135    719
  Planarity :  0.004   0.038    837
  Dihedral  :  4.509  22.243    631
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.44 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.34), residues: 590
  helix:  0.94 (0.24), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.79 (0.46), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 181 
 HIS   0.007   0.001   HIS A 483 
 PHE   0.043   0.002   PHE A  50 
 TYR   0.014   0.001   TYR A 164 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04486 (  312)
  hydrogen bonds       : angle       4.37477 (  924)
  SS BOND              : bond        0.00329 (   16)
  SS BOND              : angle       1.33061 (   32)
  covalent geometry    : bond        0.00355 ( 4741)
  covalent geometry    : angle       0.56142 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A  228 LYS cc_start: 0.7781 (tttt) cc_final: 0.7099 (mppt)
REVERT: A  403 LYS cc_start: 0.6603 (pttt) cc_final: 0.5954 (tptp)
REVERT: A  448 MET cc_start: 0.6852 (mtp) cc_final: 0.6312 (mtt)
  outliers start: 13
  outliers final: 5
  residues processed: 55
  average time/residue: 1.1746
  time to fit residues: 67.6070
Evaluate side-chains
  40 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  384 CYS
Chi-restraints excluded: chain A residue  393 CYS
Chi-restraints excluded: chain A residue  583 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 53 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4782 r_free = 0.4782 target = 0.204073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.159024 restraints weight = 5374.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.4345 rms_B_bonded: 2.42
r_work: 0.4210 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.3087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4757  Z= 0.146
  Angle     :  0.576   8.510   6432  Z= 0.306
  Chirality :  0.041   0.130    719
  Planarity :  0.004   0.038    837
  Dihedral  :  4.471  21.632    631
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 19.38 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.34), residues: 590
  helix:  0.92 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -1.87 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 181 
 HIS   0.009   0.001   HIS A 534 
 PHE   0.037   0.002   PHE A  50 
 TYR   0.011   0.001   TYR A 185 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  312)
  hydrogen bonds       : angle       4.41295 (  924)
  SS BOND              : bond        0.00346 (   16)
  SS BOND              : angle       1.44724 (   32)
  covalent geometry    : bond        0.00342 ( 4741)
  covalent geometry    : angle       0.56838 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 CYS cc_start: 0.6394 (t) cc_final: 0.5925 (t)
REVERT: A  228 LYS cc_start: 0.7802 (tttt) cc_final: 0.7151 (mppt)
REVERT: A  314 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.6978 (mp)
REVERT: A  403 LYS cc_start: 0.6566 (pttt) cc_final: 0.5972 (tptp)
REVERT: A  448 MET cc_start: 0.6959 (mtp) cc_final: 0.6569 (mtt)
  outliers start: 10
  outliers final: 5
  residues processed: 50
  average time/residue: 0.9297
  time to fit residues: 49.2234
Evaluate side-chains
  43 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  365 LEU
Chi-restraints excluded: chain A residue  384 CYS
Chi-restraints excluded: chain A residue  393 CYS
Chi-restraints excluded: chain A residue  462 CYS
Chi-restraints excluded: chain A residue  583 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0670
   chunk 58 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 54 optimal weight:    0.4980
   chunk 37 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
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 = 0.4815 r_free = 0.4815 target = 0.207317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.162940 restraints weight = 5348.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.4391 rms_B_bonded: 2.42
r_work: 0.4257 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6325
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4757  Z= 0.119
  Angle     :  0.539   9.333   6432  Z= 0.288
  Chirality :  0.039   0.122    719
  Planarity :  0.004   0.033    837
  Dihedral  :  4.256  22.930    631
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 20.35 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.35), residues: 590
  helix:  1.26 (0.25), residues: 431
  sheet:  None (None), residues: 0
  loop : -1.63 (0.48), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 181 
 HIS   0.007   0.001   HIS A 534 
 PHE   0.027   0.002   PHE A  50 
 TYR   0.016   0.001   TYR A 164 
 ARG   0.002   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  312)
  hydrogen bonds       : angle       4.22290 (  924)
  SS BOND              : bond        0.00248 (   16)
  SS BOND              : angle       1.23585 (   32)
  covalent geometry    : bond        0.00271 ( 4741)
  covalent geometry    : angle       0.53283 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.509 
Fit side-chains
REVERT: A  228 LYS cc_start: 0.7744 (tttt) cc_final: 0.7059 (mppt)
REVERT: A  403 LYS cc_start: 0.6377 (pttt) cc_final: 0.5907 (tptp)
  outliers start: 8
  outliers final: 3
  residues processed: 46
  average time/residue: 1.0642
  time to fit residues: 51.5955
Evaluate side-chains
  36 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 33
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 CYS
Chi-restraints excluded: chain A residue  384 CYS
Chi-restraints excluded: chain A residue  583 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.204971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.159776 restraints weight = 5391.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 2.44
r_work: 0.4199 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.4199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6380
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4757  Z= 0.139
  Angle     :  0.574   9.825   6432  Z= 0.305
  Chirality :  0.040   0.129    719
  Planarity :  0.004   0.036    837
  Dihedral  :  4.277  21.622    631
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 20.35 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.34), residues: 590
  helix:  1.20 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop : -1.56 (0.49), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 181 
 HIS   0.006   0.001   HIS A 483 
 PHE   0.027   0.002   PHE A  50 
 TYR   0.010   0.001   TYR A 185 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04205 (  312)
  hydrogen bonds       : angle       4.30518 (  924)
  SS BOND              : bond        0.00362 (   16)
  SS BOND              : angle       1.43437 (   32)
  covalent geometry    : bond        0.00322 ( 4741)
  covalent geometry    : angle       0.56683 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  228 LYS cc_start: 0.7735 (tttt) cc_final: 0.7077 (mppt)
REVERT: A  403 LYS cc_start: 0.6475 (pttt) cc_final: 0.6046 (tptp)
REVERT: A  490 MET cc_start: 0.6471 (mpt) cc_final: 0.5540 (mpt)
  outliers start: 8
  outliers final: 5
  residues processed: 45
  average time/residue: 0.9811
  time to fit residues: 46.6920
Evaluate side-chains
  36 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 CYS
Chi-restraints excluded: chain A residue  384 CYS
Chi-restraints excluded: chain A residue  462 CYS
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  583 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0770
   chunk 2 optimal weight:    0.2980
   chunk 52 optimal weight:    0.0270
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
A 128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.208758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.164752 restraints weight = 5360.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.4413 rms_B_bonded: 2.43
r_work: 0.4284 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6296
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4757  Z= 0.118
  Angle     :  0.552  10.629   6432  Z= 0.293
  Chirality :  0.039   0.127    719
  Planarity :  0.004   0.033    837
  Dihedral  :  4.097  21.000    631
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 19.77 %
    Favored  : 78.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.35), residues: 590
  helix:  1.49 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop : -1.42 (0.49), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 181 
 HIS   0.005   0.001   HIS A 483 
 PHE   0.023   0.002   PHE A  50 
 TYR   0.019   0.001   TYR A 164 
 ARG   0.002   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03744 (  312)
  hydrogen bonds       : angle       4.12521 (  924)
  SS BOND              : bond        0.00297 (   16)
  SS BOND              : angle       1.40603 (   32)
  covalent geometry    : bond        0.00265 ( 4741)
  covalent geometry    : angle       0.54402 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.551 
Fit side-chains
REVERT: A  228 LYS cc_start: 0.7715 (tttt) cc_final: 0.7025 (mppt)
REVERT: A  254 GLU cc_start: 0.6928 (mp0) cc_final: 0.6593 (mp0)
REVERT: A  403 LYS cc_start: 0.6321 (pttt) cc_final: 0.6032 (tptp)
REVERT: A  448 MET cc_start: 0.6759 (mtm) cc_final: 0.6452 (mtp)
REVERT: A  490 MET cc_start: 0.6474 (mpt) cc_final: 0.5571 (mpt)
  outliers start: 8
  outliers final: 5
  residues processed: 50
  average time/residue: 1.1015
  time to fit residues: 57.9811
Evaluate side-chains
  41 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 CYS
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  384 CYS
Chi-restraints excluded: chain A residue  462 CYS
Chi-restraints excluded: chain A residue  583 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.0786

-------------------------------------------------------------------------------
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 = 0.4803 r_free = 0.4803 target = 0.206317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.161322 restraints weight = 5348.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.4373 rms_B_bonded: 2.42
r_work: 0.4242 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6361
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4757  Z= 0.139
  Angle     :  0.592  10.878   6432  Z= 0.314
  Chirality :  0.041   0.176    719
  Planarity :  0.004   0.035    837
  Dihedral  :  4.175  21.336    631
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.16 %
    Favored  : 78.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.35), residues: 590
  helix:  1.34 (0.25), residues: 433
  sheet:  None (None), residues: 0
  loop : -1.44 (0.50), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 181 
 HIS   0.007   0.001   HIS A 534 
 PHE   0.035   0.002   PHE A 252 
 TYR   0.009   0.001   TYR A 185 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04155 (  312)
  hydrogen bonds       : angle       4.24798 (  924)
  SS BOND              : bond        0.00360 (   16)
  SS BOND              : angle       1.39850 (   32)
  covalent geometry    : bond        0.00322 ( 4741)
  covalent geometry    : angle       0.58537 ( 6400)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A  228 LYS cc_start: 0.7715 (tttt) cc_final: 0.7065 (mppt)
REVERT: A  254 GLU cc_start: 0.7049 (mp0) cc_final: 0.6643 (mp0)
REVERT: A  403 LYS cc_start: 0.6332 (pttt) cc_final: 0.6050 (tptp)
REVERT: A  490 MET cc_start: 0.6472 (mpt) cc_final: 0.5542 (mpt)
  outliers start: 9
  outliers final: 4
  residues processed: 47
  average time/residue: 0.9832
  time to fit residues: 49.0250
Evaluate side-chains
  40 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 CYS
Chi-restraints excluded: chain A residue  276 ASP
Chi-restraints excluded: chain A residue  384 CYS
Chi-restraints excluded: chain A residue  462 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 36 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4797 r_free = 0.4797 target = 0.206025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.160778 restraints weight = 5351.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.4355 rms_B_bonded: 2.40
r_work: 0.4219 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6392
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4757  Z= 0.149
  Angle     :  0.615  10.843   6432  Z= 0.323
  Chirality :  0.042   0.165    719
  Planarity :  0.004   0.036    837
  Dihedral  :  4.313  23.694    631
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 21.71 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.35), residues: 590
  helix:  1.16 (0.24), residues: 434
  sheet:  None (None), residues: 0
  loop : -1.39 (0.51), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 181 
 HIS   0.007   0.001   HIS A 534 
 PHE   0.025   0.002   PHE A 252 
 TYR   0.018   0.002   TYR A 164 
 ARG   0.002   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04328 (  312)
  hydrogen bonds       : angle       4.29132 (  924)
  SS BOND              : bond        0.00426 (   16)
  SS BOND              : angle       1.60763 (   32)
  covalent geometry    : bond        0.00344 ( 4741)
  covalent geometry    : angle       0.60559 ( 6400)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4687.84 seconds
wall clock time: 80 minutes 41.65 seconds (4841.65 seconds total)