Starting phenix.real_space_refine
on Sat May 10 01:23:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yim_33861/05_2025/7yim_33861.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yim_33861/05_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_33861/05_2025/7yim_33861.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yim_33861/05_2025/7yim_33861.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yim_33861/05_2025/7yim_33861.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yim_33861/05_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-5687/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: 2.92, per 1000 atoms: 0.63
  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: 0.97
  Conformation dependent library (CDL) restraints added in 509.8 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: 0.39
  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: 1.14

  Time building geometry restraints manager: 1.17 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:                  0.010
  Normalize map: mean=0, sd=1:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.570
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.350
-------------------------------------------------------------------------------
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  : 0.562 
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: 1.5090
  time to fit residues: 106.0786
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  : 0.477 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4791 r_free = 0.4791 target = 0.205496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.161462 restraints weight = 5301.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.4378 rms_B_bonded: 2.40
r_work: 0.4249 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work: 0.4114 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6484
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4757  Z= 0.142
  Angle     :  0.587   7.347   6432  Z= 0.317
  Chirality :  0.040   0.154    719
  Planarity :  0.005   0.051    837
  Dihedral  :  5.332  30.320    631
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 13.37 %
    Favored  : 85.47 %
  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: -1.61 (0.31), residues: 590
  helix: -0.47 (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   0.019   0.001   TYR A 185 
 ARG   0.005   0.000   ARG A 168 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04521 (  312)
  hydrogen bonds       : angle       4.70047 (  924)
  SS BOND              : bond        0.00343 (   16)
  SS BOND              : angle       1.68394 (   32)
  covalent geometry    : bond        0.00324 ( 4741)
  covalent geometry    : angle       0.57666 ( 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
  66 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7037 (tp) cc_final: 0.6827 (tp)
REVERT: A   96 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6850 (tm-30)
REVERT: A  228 LYS cc_start: 0.7752 (tttt) cc_final: 0.7109 (mppt)
REVERT: A  548 MET cc_start: 0.6299 (mtp) cc_final: 0.6011 (tpt)
  outliers start: 6
  outliers final: 1
  residues processed: 63
  average time/residue: 1.2551
  time to fit residues: 82.2391
Evaluate side-chains
  48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   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:    1.3786

-------------------------------------------------------------------------------
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 = 0.4784 r_free = 0.4784 target = 0.204507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.158571 restraints weight = 5392.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.4337 rms_B_bonded: 2.45
r_work: 0.4204 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6398
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   4757  Z= 0.151
  Angle     :  0.587   8.447   6432  Z= 0.308
  Chirality :  0.041   0.148    719
  Planarity :  0.004   0.042    837
  Dihedral  :  4.883  27.109    631
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 14.34 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.32), residues: 590
  helix:  0.25 (0.23), residues: 430
  sheet:  None (None), residues: 0
  loop : -2.14 (0.45), residues: 160

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   0.027   0.002   PHE A  50 
 TYR   0.021   0.002   TYR A 164 
 ARG   0.008   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04664 (  312)
  hydrogen bonds       : angle       4.53753 (  924)
  SS BOND              : bond        0.00392 (   16)
  SS BOND              : angle       1.19834 (   32)
  covalent geometry    : bond        0.00352 ( 4741)
  covalent geometry    : angle       0.58246 ( 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
  62 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.488 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7108 (tp) cc_final: 0.6869 (tp)
REVERT: A  228 LYS cc_start: 0.7842 (tttt) cc_final: 0.7138 (mppt)
REVERT: A  534 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6911 (p-80)
  outliers start: 14
  outliers final: 3
  residues processed: 57
  average time/residue: 1.0864
  time to fit residues: 64.8762
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  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  393 CYS
Chi-restraints excluded: chain A residue  534 HIS
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:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0980
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4801 r_free = 0.4801 target = 0.205751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.160165 restraints weight = 5354.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.4365 rms_B_bonded: 2.42
r_work: 0.4232 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.4232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6362
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4757  Z= 0.136
  Angle     :  0.561   7.580   6432  Z= 0.298
  Chirality :  0.040   0.135    719
  Planarity :  0.004   0.037    837
  Dihedral  :  4.642  23.941    631
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.28 %
    Favored  : 80.62 %
  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: -0.06 (0.33), residues: 590
  helix:  0.72 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -2.08 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 181 
 HIS   0.006   0.001   HIS A 483 
 PHE   0.032   0.002   PHE A  50 
 TYR   0.016   0.001   TYR A 164 
 ARG   0.004   0.000   ARG A 332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04326 (  312)
  hydrogen bonds       : angle       4.38576 (  924)
  SS BOND              : bond        0.00393 (   16)
  SS BOND              : angle       1.43538 (   32)
  covalent geometry    : bond        0.00315 ( 4741)
  covalent geometry    : angle       0.55362 ( 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
  63 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7112 (tp) cc_final: 0.6877 (tp)
REVERT: A  228 LYS cc_start: 0.7790 (tttt) cc_final: 0.7089 (mppt)
REVERT: A  291 GLN cc_start: 0.5705 (OUTLIER) cc_final: 0.5394 (mt0)
REVERT: A  448 MET cc_start: 0.6758 (mtp) cc_final: 0.6313 (mtt)
REVERT: A  499 GLN cc_start: 0.7232 (tt0) cc_final: 0.7028 (mt0)
REVERT: A  536 ASP cc_start: 0.6187 (p0) cc_final: 0.5892 (p0)
  outliers start: 16
  outliers final: 5
  residues processed: 56
  average time/residue: 0.9096
  time to fit residues: 53.7780
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  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  291 GLN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0980
   chunk 58 optimal weight:   10.0000
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.4817 r_free = 0.4817 target = 0.207700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.162532 restraints weight = 5381.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.4391 rms_B_bonded: 2.45
r_work: 0.4262 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6331
moved from start:          0.3155

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= 0.127
  Angle     :  0.550   7.788   6432  Z= 0.292
  Chirality :  0.040   0.136    719
  Planarity :  0.004   0.034    837
  Dihedral  :  4.436  21.935    631
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.44 %
    Favored  : 80.23 %
  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:  0.34 (0.34), residues: 590
  helix:  0.99 (0.25), residues: 432
  sheet:  None (None), residues: 0
  loop : -1.86 (0.46), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 181 
 HIS   0.006   0.001   HIS A 483 
 PHE   0.031   0.002   PHE A  54 
 TYR   0.009   0.001   TYR A 185 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04117 (  312)
  hydrogen bonds       : angle       4.30233 (  924)
  SS BOND              : bond        0.00340 (   16)
  SS BOND              : angle       1.28848 (   32)
  covalent geometry    : bond        0.00291 ( 4741)
  covalent geometry    : angle       0.54393 ( 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
  53 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7103 (tp) cc_final: 0.6865 (tp)
REVERT: A  228 LYS cc_start: 0.7756 (tttt) cc_final: 0.7084 (mppt)
REVERT: A  403 LYS cc_start: 0.6450 (pttt) cc_final: 0.5805 (tptp)
REVERT: A  448 MET cc_start: 0.6805 (mtp) cc_final: 0.6269 (mtt)
  outliers start: 12
  outliers final: 4
  residues processed: 51
  average time/residue: 1.0530
  time to fit residues: 56.3430
Evaluate side-chains
  43 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 39
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A  24 ASN
A 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4796 r_free = 0.4796 target = 0.205387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.160349 restraints weight = 5337.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.4363 rms_B_bonded: 2.40
r_work: 0.4231 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4757  Z= 0.139
  Angle     :  0.559   8.638   6432  Z= 0.297
  Chirality :  0.040   0.131    719
  Planarity :  0.004   0.036    837
  Dihedral  :  4.443  22.288    631
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 19.38 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.36 (0.34), residues: 590
  helix:  0.99 (0.24), residues: 430
  sheet:  None (None), residues: 0
  loop : -1.80 (0.46), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 181 
 HIS   0.009   0.001   HIS A 534 
 PHE   0.025   0.002   PHE A  50 
 TYR   0.015   0.002   TYR A 151 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04273 (  312)
  hydrogen bonds       : angle       4.32296 (  924)
  SS BOND              : bond        0.00323 (   16)
  SS BOND              : angle       1.17382 (   32)
  covalent geometry    : bond        0.00323 ( 4741)
  covalent geometry    : angle       0.55433 ( 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
  48 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7114 (tp) cc_final: 0.6857 (tp)
REVERT: A  228 LYS cc_start: 0.7763 (tttt) cc_final: 0.7142 (mppt)
REVERT: A  403 LYS cc_start: 0.6574 (pttt) cc_final: 0.5990 (tptp)
REVERT: A  448 MET cc_start: 0.6922 (mtp) cc_final: 0.6550 (mtt)
  outliers start: 7
  outliers final: 4
  residues processed: 46
  average time/residue: 1.0845
  time to fit residues: 52.4446
Evaluate side-chains
  37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   chunk 7 optimal weight:    3.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
A 122 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.202057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.156678 restraints weight = 5338.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.4321 rms_B_bonded: 2.38
r_work: 0.4186 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6437
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   4757  Z= 0.195
  Angle     :  0.620   9.184   6432  Z= 0.330
  Chirality :  0.043   0.136    719
  Planarity :  0.004   0.041    837
  Dihedral  :  4.641  20.646    631
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.35 %
    Favored  : 77.91 %
  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: -0.03 (0.33), residues: 590
  helix:  0.66 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -1.81 (0.47), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 181 
 HIS   0.008   0.002   HIS A 534 
 PHE   0.026   0.002   PHE A  54 
 TYR   0.015   0.002   TYR A 185 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04939 (  312)
  hydrogen bonds       : angle       4.56353 (  924)
  SS BOND              : bond        0.00470 (   16)
  SS BOND              : angle       1.34316 (   32)
  covalent geometry    : bond        0.00463 ( 4741)
  covalent geometry    : angle       0.61454 ( 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
  46 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7121 (tp) cc_final: 0.6866 (tp)
REVERT: A  228 LYS cc_start: 0.7795 (tttt) cc_final: 0.7131 (mppt)
REVERT: A  403 LYS cc_start: 0.6612 (pttt) cc_final: 0.6099 (tptp)
REVERT: A  448 MET cc_start: 0.7013 (mtp) cc_final: 0.6792 (mtm)
  outliers start: 9
  outliers final: 4
  residues processed: 45
  average time/residue: 0.9158
  time to fit residues: 43.6146
Evaluate side-chains
  38 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 SER
Chi-restraints excluded: chain A residue   99 CYS
Chi-restraints excluded: chain A residue  384 CYS
Chi-restraints excluded: chain A residue  393 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:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0270
   chunk 19 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7438

-------------------------------------------------------------------------------
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 = 0.4806 r_free = 0.4806 target = 0.206337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.161510 restraints weight = 5352.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.4384 rms_B_bonded: 2.44
r_work: 0.4249 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6352
moved from start:          0.3440

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= 0.128
  Angle     :  0.567   9.786   6432  Z= 0.300
  Chirality :  0.040   0.158    719
  Planarity :  0.004   0.034    837
  Dihedral  :  4.301  22.092    631
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 20.16 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.34), residues: 590
  helix:  1.22 (0.25), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.51 (0.48), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 181 
 HIS   0.006   0.001   HIS A 483 
 PHE   0.027   0.002   PHE A  54 
 TYR   0.017   0.002   TYR A 164 
 ARG   0.003   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04035 (  312)
  hydrogen bonds       : angle       4.26658 (  924)
  SS BOND              : bond        0.00263 (   16)
  SS BOND              : angle       1.66403 (   32)
  covalent geometry    : bond        0.00295 ( 4741)
  covalent geometry    : angle       0.55571 ( 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
  52 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7099 (tp) cc_final: 0.6853 (tp)
REVERT: A  124 CYS cc_start: 0.6452 (t) cc_final: 0.6031 (t)
REVERT: A  228 LYS cc_start: 0.7725 (tttt) cc_final: 0.7060 (mppt)
REVERT: A  291 GLN cc_start: 0.5692 (OUTLIER) cc_final: 0.5375 (mt0)
REVERT: A  403 LYS cc_start: 0.6480 (pttt) cc_final: 0.6044 (tptp)
REVERT: A  448 MET cc_start: 0.6993 (mtp) cc_final: 0.6716 (mtp)
  outliers start: 8
  outliers final: 5
  residues processed: 51
  average time/residue: 1.0570
  time to fit residues: 56.6307
Evaluate side-chains
  40 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 CYS
Chi-restraints excluded: chain A residue  291 GLN
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=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:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 2 optimal weight:    8.9990
   chunk 52 optimal weight:    0.2980
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0870
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
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 = 0.4821 r_free = 0.4821 target = 0.207636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.163558 restraints weight = 5384.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.4395 rms_B_bonded: 2.40
r_work: 0.4264 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.4264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6343
moved from start:          0.3596

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= 0.125
  Angle     :  0.572  10.568   6432  Z= 0.304
  Chirality :  0.039   0.133    719
  Planarity :  0.004   0.032    837
  Dihedral  :  4.186  21.262    631
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 20.74 %
    Favored  : 77.91 %
  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:  1.00 (0.35), residues: 590
  helix:  1.43 (0.25), residues: 426
  sheet:  None (None), residues: 0
  loop : -1.37 (0.49), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 181 
 HIS   0.005   0.001   HIS A 483 
 PHE   0.030   0.002   PHE A  54 
 TYR   0.008   0.001   TYR A 505 
 ARG   0.002   0.000   ARG A 169 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03900 (  312)
  hydrogen bonds       : angle       4.21947 (  924)
  SS BOND              : bond        0.00273 (   16)
  SS BOND              : angle       1.52749 (   32)
  covalent geometry    : bond        0.00286 ( 4741)
  covalent geometry    : angle       0.56349 ( 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
  47 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7107 (tp) cc_final: 0.6858 (tp)
REVERT: A  228 LYS cc_start: 0.7740 (tttt) cc_final: 0.7092 (mppt)
REVERT: A  403 LYS cc_start: 0.6305 (pttt) cc_final: 0.6020 (tptp)
REVERT: A  448 MET cc_start: 0.7036 (mtp) cc_final: 0.6780 (mtp)
REVERT: A  490 MET cc_start: 0.6477 (mpt) cc_final: 0.5624 (mpt)
  outliers start: 7
  outliers final: 4
  residues processed: 46
  average time/residue: 1.1080
  time to fit residues: 53.7440
Evaluate side-chains
  37 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
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  583 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 54 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 5 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 45 optimal weight:    0.6980
   chunk 23 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.4800 r_free = 0.4800 target = 0.205732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.160809 restraints weight = 5363.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.4374 rms_B_bonded: 2.40
r_work: 0.4244 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6367
moved from start:          0.3607

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= 0.142
  Angle     :  0.599  10.484   6432  Z= 0.320
  Chirality :  0.041   0.157    719
  Planarity :  0.004   0.035    837
  Dihedral  :  4.221  20.742    631
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 21.51 %
    Favored  : 77.33 %
  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:  0.88 (0.34), residues: 590
  helix:  1.30 (0.24), residues: 426
  sheet:  None (None), residues: 0
  loop : -1.29 (0.49), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 181 
 HIS   0.006   0.001   HIS A 483 
 PHE   0.029   0.002   PHE A  54 
 TYR   0.015   0.002   TYR A 151 
 ARG   0.006   0.000   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04263 (  312)
  hydrogen bonds       : angle       4.31914 (  924)
  SS BOND              : bond        0.00365 (   16)
  SS BOND              : angle       1.63145 (   32)
  covalent geometry    : bond        0.00331 ( 4741)
  covalent geometry    : angle       0.58969 ( 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
  42 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.7122 (tp) cc_final: 0.6861 (tp)
REVERT: A  228 LYS cc_start: 0.7704 (tttt) cc_final: 0.7072 (mppt)
REVERT: A  403 LYS cc_start: 0.6407 (pttt) cc_final: 0.6119 (tptp)
REVERT: A  448 MET cc_start: 0.7071 (mtp) cc_final: 0.6821 (mtp)
REVERT: A  490 MET cc_start: 0.6492 (mpt) cc_final: 0.5547 (mpt)
  outliers start: 6
  outliers final: 4
  residues processed: 41
  average time/residue: 0.9387
  time to fit residues: 40.8399
Evaluate side-chains
  36 residues out of total 516 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
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  583 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:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.4793 r_free = 0.4793 target = 0.205265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.159876 restraints weight = 5384.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.4351 rms_B_bonded: 2.41
r_work: 0.4219 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4757  Z= 0.152
  Angle     :  0.615  10.871   6432  Z= 0.327
  Chirality :  0.042   0.173    719
  Planarity :  0.004   0.036    837
  Dihedral  :  4.279  20.405    631
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 21.90 %
    Favored  : 76.94 %
  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:  0.75 (0.34), residues: 590
  helix:  1.18 (0.24), residues: 427
  sheet:  None (None), residues: 0
  loop : -1.29 (0.50), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A 181 
 HIS   0.006   0.001   HIS A 483 
 PHE   0.037   0.002   PHE A 252 
 TYR   0.015   0.002   TYR A 151 
 ARG   0.007   0.000   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  312)
  hydrogen bonds       : angle       4.37678 (  924)
  SS BOND              : bond        0.00397 (   16)
  SS BOND              : angle       1.65439 (   32)
  covalent geometry    : bond        0.00354 ( 4741)
  covalent geometry    : angle       0.60548 ( 6400)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4173.17 seconds
wall clock time: 72 minutes 22.53 seconds (4342.53 seconds total)