Starting phenix.real_space_refine
on Fri May  9 18:57:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sc3_40336/05_2025/8sc3_40336.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sc3_40336/05_2025/8sc3_40336.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sc3_40336/05_2025/8sc3_40336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sc3_40336/05_2025/8sc3_40336.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sc3_40336/05_2025/8sc3_40336.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sc3_40336/05_2025/8sc3_40336.cif"
  }
  resolution = 3.24
  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=   0.000 sd=   0.016
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      30      5.16       5
     C    2284      2.51       5
     N     559      2.21       5
     O     590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3463
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3441
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 22, 'TRANS': 422}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'ZVJ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.88, per 1000 atoms: 0.83
  Number of scatterers: 3463
  At special positions: 0
  Unit cell: (89.64, 83, 63.91, 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      30     16.00
     O     590      8.00
     N     559      7.00
     C    2284      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A 102 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  88 " - pdb=" SG  CYS A 142 " 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 440.4 milliseconds
  

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  814

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 2 sheets defined
      82.5% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 38
      Proline residue:  A  34  - end of helix
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 54 through 63
    Processing helix  chain 'A' and resid 65 through 74
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 141 through 144
    Processing helix  chain 'A' and resid 145 through 173
      removed outlier: 4.053A  pdb=" N   ASP A 149 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE A 151 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLN A 152 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU A 164 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   GLY A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   TYR A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 195
      removed outlier: 3.600A  pdb=" N   ALA A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE A 195 " --> pdb=" O   VAL A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 228
      removed outlier: 4.241A  pdb=" N   LYS A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   GLY A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 258
    Processing helix  chain 'A' and resid 260 through 278
      Proline residue:  A 271  - end of helix
      removed outlier: 3.560A  pdb=" N   LEU A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   PHE A 275 " --> pdb=" O   PRO A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 338
    Processing helix  chain 'A' and resid 340 through 372
    Processing helix  chain 'A' and resid 374 through 400
      removed outlier: 3.579A  pdb=" N   GLU A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ILE A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      Proline residue:  A 388  - end of helix
      removed outlier: 4.101A  pdb=" N   ASP A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 423
      removed outlier: 3.862A  pdb=" N   PHE A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 456
      removed outlier: 4.116A  pdb=" N   ILE A 433 " --> pdb=" O   TRP A 429 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   CYS A 450 " --> pdb=" O   ILE A 446 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LEU A 451 " --> pdb=" O   GLN A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 487
      removed outlier: 4.432A  pdb=" N   ASN A 463 " --> pdb=" O   THR A 459 " (cutoff:3.500A)
      removed outlier: 5.261A  pdb=" N   LEU A 464 " --> pdb=" O   PHE A 460 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      Proline residue:  A 481  - end of helix
    Processing helix  chain 'A' and resid 488 through 490
      No H-bonds generated for 'chain 'A' and resid 488 through 490'
    Processing helix  chain 'A' and resid 493 through 511
      removed outlier: 3.652A  pdb=" N   LEU A 511 " --> pdb=" O   ALA A 507 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50
    Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91

    256 hydrogen bonds defined for protein.
    744 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: 1.02

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1063
        1.35 -     1.47: 914
        1.47 -     1.59: 1531
        1.59 -     1.71: 1
        1.71 -     1.83: 45
  Bond restraints: 3554
  Sorted by residual:
  bond pdb=" C08 ZVJ A 601 "
       pdb=" O09 ZVJ A 601 "
    ideal  model  delta    sigma   weight residual
    1.348  1.451 -0.103 2.00e-02 2.50e+03 2.63e+01
  bond pdb=" C15 ZVJ A 601 "
       pdb=" C16 ZVJ A 601 "
    ideal  model  delta    sigma   weight residual
    1.502  1.601 -0.099 2.00e-02 2.50e+03 2.46e+01
  bond pdb=" C11 ZVJ A 601 "
       pdb=" O12 ZVJ A 601 "
    ideal  model  delta    sigma   weight residual
    1.349  1.438 -0.089 2.00e-02 2.50e+03 1.99e+01
  bond pdb=" C19 ZVJ A 601 "
       pdb=" O22 ZVJ A 601 "
    ideal  model  delta    sigma   weight residual
    1.350  1.428 -0.078 2.00e-02 2.50e+03 1.50e+01
  bond pdb=" C04 ZVJ A 601 "
       pdb=" C05 ZVJ A 601 "
    ideal  model  delta    sigma   weight residual
    1.540  1.482  0.058 2.00e-02 2.50e+03 8.45e+00
  ... (remaining 3549 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 4718
        1.69 -     3.37: 109
        3.37 -     5.06: 11
        5.06 -     6.75: 4
        6.75 -     8.43: 1
  Bond angle restraints: 4843
  Sorted by residual:
  angle pdb=" C05 ZVJ A 601 "
        pdb=" C04 ZVJ A 601 "
        pdb=" N03 ZVJ A 601 "
      ideal   model   delta    sigma   weight residual
     109.71  118.14   -8.43 3.00e+00 1.11e-01 7.90e+00
  angle pdb=" CA  VAL A  37 "
        pdb=" CB  VAL A  37 "
        pdb=" CG1 VAL A  37 "
      ideal   model   delta    sigma   weight residual
     110.40  115.00   -4.60 1.70e+00 3.46e-01 7.34e+00
  angle pdb=" N   VAL A  37 "
        pdb=" CA  VAL A  37 "
        pdb=" CB  VAL A  37 "
      ideal   model   delta    sigma   weight residual
     112.26  109.10    3.16 1.29e+00 6.01e-01 6.00e+00
  angle pdb=" CA  CYS A 102 "
        pdb=" CB  CYS A 102 "
        pdb=" SG  CYS A 102 "
      ideal   model   delta    sigma   weight residual
     114.40  119.97   -5.57 2.30e+00 1.89e-01 5.87e+00
  angle pdb=" N   ARG A 462 "
        pdb=" CA  ARG A 462 "
        pdb=" C   ARG A 462 "
      ideal   model   delta    sigma   weight residual
     111.37  115.02   -3.65 1.65e+00 3.67e-01 4.90e+00
  ... (remaining 4838 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 1942
       16.82 -    33.63: 90
       33.63 -    50.44: 29
       50.44 -    67.26: 4
       67.26 -    84.07: 2
  Dihedral angle restraints: 2067
    sinusoidal: 794
      harmonic: 1273
  Sorted by residual:
  dihedral pdb=" CA  ASN A 374 "
           pdb=" C   ASN A 374 "
           pdb=" N   LEU A 375 "
           pdb=" CA  LEU A 375 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.49  -22.51     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CB  GLU A 515 "
           pdb=" CG  GLU A 515 "
           pdb=" CD  GLU A 515 "
           pdb=" OE1 GLU A 515 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.07   84.07     1      3.00e+01 1.11e-03 9.57e+00
  dihedral pdb=" CB  GLU A 489 "
           pdb=" CG  GLU A 489 "
           pdb=" CD  GLU A 489 "
           pdb=" OE1 GLU A 489 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.08  -81.08     1      3.00e+01 1.11e-03 9.01e+00
  ... (remaining 2064 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 474
       0.052 -    0.104: 76
       0.104 -    0.156: 11
       0.156 -    0.207: 0
       0.207 -    0.259: 1
  Chirality restraints: 562
  Sorted by residual:
  chirality pdb=" C02 ZVJ A 601 "
            pdb=" C01 ZVJ A 601 "
            pdb=" C15 ZVJ A 601 "
            pdb=" N03 ZVJ A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.71    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  VAL A  74 "
            pdb=" N   VAL A  74 "
            pdb=" C   VAL A  74 "
            pdb=" CB  VAL A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  VAL A 126 "
            pdb=" N   VAL A 126 "
            pdb=" C   VAL A 126 "
            pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.47e-01
  ... (remaining 559 not shown)

  Planarity restraints: 597
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 406 "   -0.012 2.00e-02 2.50e+03   2.50e-02 6.27e+00
        pdb=" C   MET A 406 "    0.043 2.00e-02 2.50e+03
        pdb=" O   MET A 406 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ALA A 407 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  28 "   -0.011 2.00e-02 2.50e+03   2.23e-02 4.98e+00
        pdb=" C   LEU A  28 "    0.039 2.00e-02 2.50e+03
        pdb=" O   LEU A  28 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   SER A  29 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 239 "    0.011 2.00e-02 2.50e+03   2.18e-02 4.76e+00
        pdb=" C   MET A 239 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   MET A 239 "    0.014 2.00e-02 2.50e+03
        pdb=" N   TYR A 240 "    0.013 2.00e-02 2.50e+03
  ... (remaining 594 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 294
        2.74 -     3.28: 3746
        3.28 -     3.82: 5805
        3.82 -     4.36: 6758
        4.36 -     4.90: 11725
  Nonbonded interactions: 28328
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 147 "
            pdb=" OH  TYR A 199 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NH1 ARG A  90 "
            pdb=" OD2 ASP A 123 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" O   ALA A 194 "
            pdb=" NH1 ARG A 262 "
     model   vdw
     2.409 3.120
  nonbonded pdb=" O   GLN A 209 "
            pdb=" OG  SER A 213 "
     model   vdw
     2.469 3.040
  nonbonded pdb=" OG1 THR A 182 "
            pdb=" OD1 ASN A 216 "
     model   vdw
     2.488 3.040
  ... (remaining 28323 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:             0.830
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     13.510
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
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      :  0.005   0.103   3557  Z= 0.246
  Angle     :  0.647   8.433   4849  Z= 0.373
  Chirality :  0.039   0.259    562
  Planarity :  0.006   0.037    597
  Dihedral  : 11.841  84.073   1244
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 2.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  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: -0.54 (0.38), residues: 441
  helix: -0.50 (0.26), residues: 317
  sheet:  None (None), residues: 0
  loop :  0.60 (0.61), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 261 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.017   0.002   PHE A 151 
 TYR   0.021   0.002   TYR A  72 
 ARG   0.008   0.001   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12266 (  256)
  hydrogen bonds       : angle       6.58755 (  744)
  SS BOND              : bond        0.00340 (    3)
  SS BOND              : angle       1.94725 (    6)
  covalent geometry    : bond        0.00489 ( 3554)
  covalent geometry    : angle       0.64369 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8137 (m-30) cc_final: 0.7845 (m-30)
REVERT: A  116 LEU cc_start: 0.8525 (mt) cc_final: 0.8271 (mp)
REVERT: A  150 LEU cc_start: 0.8883 (tp) cc_final: 0.8647 (tt)
REVERT: A  154 CYS cc_start: 0.8293 (m) cc_final: 0.8035 (m)
REVERT: A  392 ILE cc_start: 0.8580 (mt) cc_final: 0.8255 (mt)
REVERT: A  460 PHE cc_start: 0.4975 (t80) cc_final: 0.4646 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1374
  time to fit residues: 22.7888
Evaluate side-chains
  106 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   chunk 17 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.202209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.162660 restraints weight = 4619.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 3.18
r_work: 0.3646 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3557  Z= 0.145
  Angle     :  0.603   5.493   4849  Z= 0.315
  Chirality :  0.039   0.138    562
  Planarity :  0.004   0.047    597
  Dihedral  :  7.258  61.432    492
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  :  8.13 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.41), residues: 441
  helix:  1.58 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop :  1.48 (0.67), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.019   0.002   PHE A 227 
 TYR   0.019   0.002   TYR A 240 
 ARG   0.005   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04352 (  256)
  hydrogen bonds       : angle       5.00397 (  744)
  SS BOND              : bond        0.00365 (    3)
  SS BOND              : angle       2.29155 (    6)
  covalent geometry    : bond        0.00315 ( 3554)
  covalent geometry    : angle       0.59841 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8562 (m-30) cc_final: 0.8228 (m-30)
REVERT: A  116 LEU cc_start: 0.8549 (mt) cc_final: 0.8200 (mp)
REVERT: A  200 MET cc_start: 0.7633 (mmt) cc_final: 0.7427 (mmt)
REVERT: A  239 MET cc_start: 0.7230 (tpt) cc_final: 0.6625 (tpt)
REVERT: A  348 PHE cc_start: 0.8067 (m-10) cc_final: 0.7814 (m-10)
REVERT: A  392 ILE cc_start: 0.8670 (mt) cc_final: 0.8443 (mt)
REVERT: A  410 ASN cc_start: 0.8226 (m-40) cc_final: 0.7933 (m110)
REVERT: A  429 TRP cc_start: 0.7222 (p-90) cc_final: 0.6996 (p90)
REVERT: A  460 PHE cc_start: 0.5759 (t80) cc_final: 0.4941 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 126
  average time/residue: 0.1260
  time to fit residues: 19.9175
Evaluate side-chains
  103 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  112 ASN
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.3980
   chunk 40 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 156 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.202088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.161505 restraints weight = 4636.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 3.02
r_work: 0.3636 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3557  Z= 0.145
  Angle     :  0.605  10.264   4849  Z= 0.309
  Chirality :  0.040   0.222    562
  Planarity :  0.004   0.049    597
  Dihedral  :  7.763  91.264    492
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 10.30 %
    Favored  : 85.91 %
  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:  2.61 (0.42), residues: 441
  helix:  1.83 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop :  1.77 (0.68), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.010   0.001   PHE A 151 
 TYR   0.018   0.002   TYR A 361 
 ARG   0.006   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04279 (  256)
  hydrogen bonds       : angle       4.90060 (  744)
  SS BOND              : bond        0.00334 (    3)
  SS BOND              : angle       2.01756 (    6)
  covalent geometry    : bond        0.00323 ( 3554)
  covalent geometry    : angle       0.60157 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 TYR cc_start: 0.8360 (m-80) cc_final: 0.8138 (m-10)
REVERT: A  200 MET cc_start: 0.7584 (mmt) cc_final: 0.7381 (mmt)
REVERT: A  242 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7248 (ppp)
REVERT: A  348 PHE cc_start: 0.8087 (m-10) cc_final: 0.7750 (m-10)
REVERT: A  351 MET cc_start: 0.7724 (mtt) cc_final: 0.6859 (tmm)
REVERT: A  408 MET cc_start: 0.8535 (mtp) cc_final: 0.8317 (mtt)
  outliers start: 14
  outliers final: 9
  residues processed: 109
  average time/residue: 0.1114
  time to fit residues: 15.7787
Evaluate side-chains
  107 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  112 ASN
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 23 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0020
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.203246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.163176 restraints weight = 4652.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 3.16
r_work: 0.3647 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3557  Z= 0.135
  Angle     :  0.570   5.696   4849  Z= 0.299
  Chirality :  0.040   0.221    562
  Planarity :  0.004   0.048    597
  Dihedral  :  7.407  83.874    492
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 13.01 %
    Favored  : 83.20 %
  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:  2.74 (0.42), residues: 441
  helix:  1.94 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop :  1.76 (0.70), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.015   0.001   PHE A 391 
 TYR   0.017   0.002   TYR A 361 
 ARG   0.008   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04093 (  256)
  hydrogen bonds       : angle       4.78838 (  744)
  SS BOND              : bond        0.00270 (    3)
  SS BOND              : angle       1.86735 (    6)
  covalent geometry    : bond        0.00299 ( 3554)
  covalent geometry    : angle       0.56668 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.7168 (tpt) cc_final: 0.6967 (tpt)
REVERT: A  334 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.8117 (m-10)
REVERT: A  348 PHE cc_start: 0.8085 (m-10) cc_final: 0.7711 (m-10)
REVERT: A  351 MET cc_start: 0.7670 (mtt) cc_final: 0.6817 (tmm)
REVERT: A  352 TYR cc_start: 0.8095 (t80) cc_final: 0.7861 (t80)
REVERT: A  408 MET cc_start: 0.8497 (mtp) cc_final: 0.8279 (mtt)
REVERT: A  498 LEU cc_start: 0.8250 (mm) cc_final: 0.7930 (mm)
REVERT: A  511 LEU cc_start: 0.8234 (mt) cc_final: 0.8034 (mm)
  outliers start: 14
  outliers final: 9
  residues processed: 106
  average time/residue: 0.1177
  time to fit residues: 16.0721
Evaluate side-chains
  102 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  112 ASN
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 26 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4367 r_free = 0.4367 target = 0.203263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.162955 restraints weight = 4713.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 3.15
r_work: 0.3644 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3557  Z= 0.136
  Angle     :  0.552   5.563   4849  Z= 0.292
  Chirality :  0.040   0.215    562
  Planarity :  0.004   0.047    597
  Dihedral  :  7.225  72.899    492
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 14.63 %
    Favored  : 81.03 %
  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:  2.73 (0.42), residues: 441
  helix:  1.96 (0.29), residues: 320
  sheet:  None (None), residues: 0
  loop :  1.69 (0.70), residues: 121

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.010   0.001   PHE A  22 
 TYR   0.018   0.001   TYR A 361 
 ARG   0.009   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  256)
  hydrogen bonds       : angle       4.73868 (  744)
  SS BOND              : bond        0.00266 (    3)
  SS BOND              : angle       1.82457 (    6)
  covalent geometry    : bond        0.00303 ( 3554)
  covalent geometry    : angle       0.54904 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 MET cc_start: 0.7595 (mmt) cc_final: 0.7383 (mmt)
REVERT: A  239 MET cc_start: 0.7141 (tpt) cc_final: 0.6821 (tpt)
REVERT: A  334 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7960 (m-80)
REVERT: A  348 PHE cc_start: 0.8080 (m-10) cc_final: 0.7692 (m-10)
REVERT: A  351 MET cc_start: 0.7693 (mtt) cc_final: 0.6821 (tmm)
REVERT: A  352 TYR cc_start: 0.8110 (t80) cc_final: 0.7876 (t80)
  outliers start: 16
  outliers final: 11
  residues processed: 97
  average time/residue: 0.1083
  time to fit residues: 13.7984
Evaluate side-chains
  103 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  459 THR
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0870
   chunk 10 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.4366 r_free = 0.4366 target = 0.203021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.163498 restraints weight = 4814.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 3.08
r_work: 0.3653 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.4247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3557  Z= 0.136
  Angle     :  0.565   6.139   4849  Z= 0.296
  Chirality :  0.040   0.210    562
  Planarity :  0.005   0.046    597
  Dihedral  :  7.078  73.946    492
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.45 %
    Favored  : 80.22 %
  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:  2.73 (0.42), residues: 441
  helix:  1.91 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop :  1.84 (0.71), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.019   0.001   PHE A 391 
 TYR   0.018   0.002   TYR A 361 
 ARG   0.010   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04096 (  256)
  hydrogen bonds       : angle       4.75736 (  744)
  SS BOND              : bond        0.00236 (    3)
  SS BOND              : angle       1.77877 (    6)
  covalent geometry    : bond        0.00305 ( 3554)
  covalent geometry    : angle       0.56233 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.7161 (tpt) cc_final: 0.6954 (tpt)
REVERT: A  334 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7767 (m-80)
REVERT: A  348 PHE cc_start: 0.8039 (m-10) cc_final: 0.7686 (m-10)
REVERT: A  351 MET cc_start: 0.7666 (mtt) cc_final: 0.7233 (ttt)
  outliers start: 16
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1197
  time to fit residues: 16.2278
Evaluate side-chains
  96 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0000
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 447 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.204247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.164575 restraints weight = 4728.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 3.16
r_work: 0.3668 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.4544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3557  Z= 0.127
  Angle     :  0.572   7.492   4849  Z= 0.294
  Chirality :  0.040   0.203    562
  Planarity :  0.005   0.048    597
  Dihedral  :  7.037  73.355    492
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 17.89 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.42), residues: 441
  helix:  1.96 (0.28), residues: 321
  sheet:  None (None), residues: 0
  loop :  1.69 (0.70), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.018   0.001   PHE A 460 
 TYR   0.017   0.001   TYR A 361 
 ARG   0.011   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  256)
  hydrogen bonds       : angle       4.73668 (  744)
  SS BOND              : bond        0.00176 (    3)
  SS BOND              : angle       1.74514 (    6)
  covalent geometry    : bond        0.00279 ( 3554)
  covalent geometry    : angle       0.56872 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.6577 (m100) cc_final: 0.6242 (m100)
REVERT: A  334 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7780 (m-80)
REVERT: A  348 PHE cc_start: 0.8051 (m-10) cc_final: 0.7666 (m-10)
REVERT: A  351 MET cc_start: 0.7685 (mtt) cc_final: 0.7212 (ttt)
  outliers start: 14
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1169
  time to fit residues: 14.5702
Evaluate side-chains
  94 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 24 optimal weight:    0.3980
   chunk 15 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4369 r_free = 0.4369 target = 0.203031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.163592 restraints weight = 4748.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3956 rms_B_bonded: 3.13
r_work: 0.3663 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3557  Z= 0.140
  Angle     :  0.604   6.298   4849  Z= 0.308
  Chirality :  0.041   0.200    562
  Planarity :  0.005   0.047    597
  Dihedral  :  7.016  72.948    492
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 18.97 %
    Favored  : 77.78 %
  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:  2.70 (0.42), residues: 441
  helix:  1.92 (0.28), residues: 322
  sheet:  None (None), residues: 0
  loop :  1.72 (0.70), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.022   0.001   PHE A 391 
 TYR   0.020   0.002   TYR A 361 
 ARG   0.012   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04112 (  256)
  hydrogen bonds       : angle       4.81662 (  744)
  SS BOND              : bond        0.00281 (    3)
  SS BOND              : angle       2.72861 (    6)
  covalent geometry    : bond        0.00319 ( 3554)
  covalent geometry    : angle       0.59649 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7670 (m-80)
REVERT: A  348 PHE cc_start: 0.8050 (m-10) cc_final: 0.7670 (m-10)
REVERT: A  351 MET cc_start: 0.7712 (mtt) cc_final: 0.7245 (ttt)
  outliers start: 12
  outliers final: 9
  residues processed: 92
  average time/residue: 0.1090
  time to fit residues: 13.1138
Evaluate side-chains
  94 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 9 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0770
   chunk 37 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 = 0.4380 r_free = 0.4380 target = 0.204288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.164966 restraints weight = 4632.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3971 rms_B_bonded: 3.13
r_work: 0.3673 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.4671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3557  Z= 0.135
  Angle     :  0.590   6.072   4849  Z= 0.303
  Chirality :  0.041   0.199    562
  Planarity :  0.005   0.047    597
  Dihedral  :  6.946  71.210    492
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 19.78 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.42), residues: 441
  helix:  1.76 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop :  1.84 (0.72), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.016   0.001   PHE A 460 
 TYR   0.019   0.001   TYR A 361 
 ARG   0.010   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04070 (  256)
  hydrogen bonds       : angle       4.83595 (  744)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       2.67689 (    6)
  covalent geometry    : bond        0.00301 ( 3554)
  covalent geometry    : angle       0.58320 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A  242 MET cc_start: 0.7510 (ptt) cc_final: 0.7184 (ppp)
REVERT: A  334 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7648 (m-80)
REVERT: A  348 PHE cc_start: 0.8031 (m-10) cc_final: 0.7651 (m-10)
REVERT: A  351 MET cc_start: 0.7708 (mtt) cc_final: 0.7238 (ttt)
REVERT: A  447 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7794 (tp40)
  outliers start: 13
  outliers final: 10
  residues processed: 90
  average time/residue: 0.1149
  time to fit residues: 13.4749
Evaluate side-chains
  92 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  447 GLN
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 12 optimal weight:    0.2980
   chunk 10 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 2 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4392 r_free = 0.4392 target = 0.205074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.165536 restraints weight = 4722.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 3.20
r_work: 0.3679 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.4812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3557  Z= 0.130
  Angle     :  0.589   6.537   4849  Z= 0.302
  Chirality :  0.041   0.194    562
  Planarity :  0.005   0.047    597
  Dihedral  :  6.891  69.293    492
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 21.14 %
    Favored  : 75.88 %
  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:  2.58 (0.42), residues: 441
  helix:  1.76 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop :  1.90 (0.72), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.026   0.001   PHE A 391 
 TYR   0.019   0.001   TYR A 361 
 ARG   0.010   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04008 (  256)
  hydrogen bonds       : angle       4.80911 (  744)
  SS BOND              : bond        0.00204 (    3)
  SS BOND              : angle       2.74078 (    6)
  covalent geometry    : bond        0.00282 ( 3554)
  covalent geometry    : angle       0.58107 ( 4843)

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

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

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  882 Ramachandran restraints generated.
    441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.8219 (t0) cc_final: 0.7945 (t0)
REVERT: A  242 MET cc_start: 0.7449 (ptt) cc_final: 0.7145 (ppp)
REVERT: A  334 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7658 (m-80)
REVERT: A  348 PHE cc_start: 0.8053 (m-10) cc_final: 0.7663 (m-10)
REVERT: A  351 MET cc_start: 0.7686 (mtt) cc_final: 0.7212 (ttt)
  outliers start: 11
  outliers final: 9
  residues processed: 92
  average time/residue: 0.1089
  time to fit residues: 13.1505
Evaluate side-chains
  94 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  102 CYS
Chi-restraints excluded: chain A residue  204 LEU
Chi-restraints excluded: chain A residue  334 PHE
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain A residue  505 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0980
   chunk 41 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0030
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 17 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.3790

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.206200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.166897 restraints weight = 4719.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 3.16
r_work: 0.3697 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3557  Z= 0.123
  Angle     :  0.598   9.656   4849  Z= 0.303
  Chirality :  0.041   0.201    562
  Planarity :  0.005   0.047    597
  Dihedral  :  6.780  70.076    492
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 21.68 %
    Favored  : 75.88 %
  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:  2.62 (0.42), residues: 441
  helix:  1.81 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop :  1.83 (0.71), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  64 
 HIS   0.001   0.000   HIS A  49 
 PHE   0.016   0.001   PHE A 460 
 TYR   0.018   0.001   TYR A 361 
 ARG   0.008   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03846 (  256)
  hydrogen bonds       : angle       4.78049 (  744)
  SS BOND              : bond        0.00151 (    3)
  SS BOND              : angle       2.49635 (    6)
  covalent geometry    : bond        0.00262 ( 3554)
  covalent geometry    : angle       0.59217 ( 4843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2190.02 seconds
wall clock time: 38 minutes 35.60 seconds (2315.60 seconds total)