Starting phenix.real_space_refine
on Fri Aug 22 13:42:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sc3_40336/08_2025/8sc3_40336.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sc3_40336/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sc3_40336/08_2025/8sc3_40336.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sc3_40336/08_2025/8sc3_40336.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sc3_40336/08_2025/8sc3_40336.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sc3_40336/08_2025/8sc3_40336.map"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.00, per 1000 atoms: 0.29
  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: 0.36
  Conformation dependent library (CDL) restraints added in 99.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.11
  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: 0.49

  Time building geometry restraints manager: 0.42 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:             0.940
  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:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.470
  Find NCS groups from input model:        0.010
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.670
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.38), 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
 ARG   0.008   0.001   ARG A 234 
 TYR   0.021   0.002   TYR A  72 
 PHE   0.017   0.002   PHE A 151 
 TRP   0.015   0.002   TRP A 261 
 HIS   0.002   0.001   HIS A 115 

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

*********************** 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  : 0.108 
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: 0.0509
  time to fit residues: 8.5736
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  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   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 156 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.201506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.161493 restraints weight = 4728.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 3.17
r_work: 0.3631 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2693

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= 0.152
  Angle     :  0.613   5.629   4849  Z= 0.319
  Chirality :  0.039   0.132    562
  Planarity :  0.005   0.047    597
  Dihedral  :  7.308  61.843    492
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  :  8.67 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.41), residues: 441
  helix:  1.49 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop :  1.47 (0.67), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 488 
 TYR   0.019   0.002   TYR A 240 
 PHE   0.021   0.002   PHE A 227 
 TRP   0.010   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 3554)
  covalent geometry    : angle       0.60828 ( 4843)
  SS BOND              : bond        0.00354 (    3)
  SS BOND              : angle       2.34107 (    6)
  hydrogen bonds       : bond        0.04528 (  256)
  hydrogen bonds       : angle       5.09675 (  744)

*********************** 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  : 0.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8567 (m-30) cc_final: 0.8246 (m-30)
REVERT: A   77 LEU cc_start: 0.8165 (tp) cc_final: 0.7503 (mp)
REVERT: A  116 LEU cc_start: 0.8565 (mt) cc_final: 0.8212 (mp)
REVERT: A  239 MET cc_start: 0.7249 (tpt) cc_final: 0.6698 (tpt)
REVERT: A  348 PHE cc_start: 0.8130 (m-10) cc_final: 0.7924 (m-10)
REVERT: A  392 ILE cc_start: 0.8687 (mt) cc_final: 0.8435 (mt)
REVERT: A  410 ASN cc_start: 0.8242 (m-40) cc_final: 0.7962 (m110)
REVERT: A  429 TRP cc_start: 0.7253 (p-90) cc_final: 0.7012 (p90)
REVERT: A  457 TYR cc_start: 0.7808 (m-80) cc_final: 0.7073 (m-80)
REVERT: A  460 PHE cc_start: 0.5790 (t80) cc_final: 0.4960 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 126
  average time/residue: 0.0464
  time to fit residues: 7.4612
Evaluate side-chains
  105 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
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  204 LEU
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 40 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 12 optimal weight:    0.3980
   chunk 6 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   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  97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 156 ASN
A 241 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.203100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.163180 restraints weight = 4684.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 3.06
r_work: 0.3648 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3409

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= 0.137
  Angle     :  0.589   5.853   4849  Z= 0.304
  Chirality :  0.040   0.215    562
  Planarity :  0.004   0.050    597
  Dihedral  :  7.840  92.688    492
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 10.84 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.67 (0.42), residues: 441
  helix:  1.88 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop :  1.77 (0.68), residues: 123

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 488 
 TYR   0.018   0.002   TYR A 361 
 PHE   0.009   0.001   PHE A 227 
 TRP   0.007   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3554)
  covalent geometry    : angle       0.58501 ( 4843)
  SS BOND              : bond        0.00303 (    3)
  SS BOND              : angle       2.05518 (    6)
  hydrogen bonds       : bond        0.04187 (  256)
  hydrogen bonds       : angle       4.88256 (  744)

*********************** 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
  117 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8592 (m-30) cc_final: 0.8314 (m-30)
REVERT: A   72 TYR cc_start: 0.8363 (m-80) cc_final: 0.8143 (m-10)
REVERT: A  242 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7302 (ppp)
REVERT: A  348 PHE cc_start: 0.8115 (m-10) cc_final: 0.7801 (m-10)
REVERT: A  351 MET cc_start: 0.7656 (mtt) cc_final: 0.6804 (tmm)
REVERT: A  408 MET cc_start: 0.8507 (mtp) cc_final: 0.8291 (mtt)
REVERT: A  460 PHE cc_start: 0.5786 (t80) cc_final: 0.4886 (t80)
  outliers start: 14
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0449
  time to fit residues: 6.4667
Evaluate side-chains
  99 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
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   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 9 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0570
   chunk 35 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.4372 r_free = 0.4372 target = 0.203480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.163686 restraints weight = 4615.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 3.07
r_work: 0.3657 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3557  Z= 0.128
  Angle     :  0.571   8.522   4849  Z= 0.294
  Chirality :  0.039   0.230    562
  Planarity :  0.004   0.048    597
  Dihedral  :  7.373  80.964    492
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 13.55 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.79 (0.42), residues: 441
  helix:  2.00 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop :  1.71 (0.69), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 488 
 TYR   0.021   0.001   TYR A 361 
 PHE   0.015   0.001   PHE A 391 
 TRP   0.006   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3554)
  covalent geometry    : angle       0.56749 ( 4843)
  SS BOND              : bond        0.00264 (    3)
  SS BOND              : angle       1.88235 (    6)
  hydrogen bonds       : bond        0.03982 (  256)
  hydrogen bonds       : angle       4.79273 (  744)

*********************** 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
  106 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8610 (m-30) cc_final: 0.8364 (m-30)
REVERT: A  242 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7197 (ppp)
REVERT: A  334 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.8044 (m-10)
REVERT: A  348 PHE cc_start: 0.8101 (m-10) cc_final: 0.7744 (m-10)
REVERT: A  351 MET cc_start: 0.7666 (mtt) cc_final: 0.6818 (tmm)
REVERT: A  352 TYR cc_start: 0.8049 (t80) cc_final: 0.7818 (t80)
REVERT: A  408 MET cc_start: 0.8566 (mtp) cc_final: 0.8326 (mtt)
REVERT: A  511 LEU cc_start: 0.8275 (mt) cc_final: 0.8055 (mm)
  outliers start: 11
  outliers final: 4
  residues processed: 100
  average time/residue: 0.0409
  time to fit residues: 5.4567
Evaluate side-chains
  93 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 PHE
Chi-restraints excluded: chain A residue  242 MET
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  472 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 43 optimal weight:    8.9990
   chunk 36 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 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 = 0.4364 r_free = 0.4364 target = 0.202626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.162903 restraints weight = 4660.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 3.14
r_work: 0.3639 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.3999

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= 0.138
  Angle     :  0.567   6.256   4849  Z= 0.297
  Chirality :  0.040   0.216    562
  Planarity :  0.005   0.047    597
  Dihedral  :  7.266  78.706    492
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.18
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.71 (0.42), residues: 441
  helix:  1.89 (0.28), residues: 321
  sheet:  None (None), residues: 0
  loop :  1.84 (0.70), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 488 
 TYR   0.022   0.002   TYR A 361 
 PHE   0.016   0.001   PHE A 460 
 TRP   0.006   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3554)
  covalent geometry    : angle       0.56417 ( 4843)
  SS BOND              : bond        0.00256 (    3)
  SS BOND              : angle       1.80139 (    6)
  hydrogen bonds       : bond        0.04054 (  256)
  hydrogen bonds       : angle       4.76867 (  744)

*********************** 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  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.7137 (tpt) cc_final: 0.6923 (tpt)
REVERT: A  334 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7930 (m-80)
REVERT: A  348 PHE cc_start: 0.8060 (m-10) cc_final: 0.7667 (m-10)
REVERT: A  351 MET cc_start: 0.7708 (mtt) cc_final: 0.6831 (tmm)
REVERT: A  511 LEU cc_start: 0.8273 (mt) cc_final: 0.8067 (mm)
  outliers start: 16
  outliers final: 10
  residues processed: 96
  average time/residue: 0.0425
  time to fit residues: 5.3773
Evaluate side-chains
  95 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
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  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 18 optimal weight:    0.8980
   chunk 2 optimal weight:    0.1980
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0470
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0470
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 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 = 0.4391 r_free = 0.4391 target = 0.205332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.165698 restraints weight = 4614.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 3.14
r_work: 0.3677 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4317

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= 0.121
  Angle     :  0.556   7.440   4849  Z= 0.289
  Chirality :  0.040   0.213    562
  Planarity :  0.005   0.047    597
  Dihedral  :  7.123  77.508    492
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 15.45 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.42), residues: 441
  helix:  1.98 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop :  1.71 (0.69), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 488 
 TYR   0.018   0.001   TYR A 361 
 PHE   0.018   0.001   PHE A 391 
 TRP   0.005   0.001   TRP A 261 
 HIS   0.001   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 3554)
  covalent geometry    : angle       0.55350 ( 4843)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       1.69863 (    6)
  hydrogen bonds       : bond        0.03843 (  256)
  hydrogen bonds       : angle       4.65891 (  744)

*********************** 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
  107 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  242 MET cc_start: 0.7745 (ptt) cc_final: 0.7077 (ppp)
REVERT: A  334 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7797 (m-80)
REVERT: A  348 PHE cc_start: 0.8068 (m-10) cc_final: 0.7674 (m-10)
REVERT: A  351 MET cc_start: 0.7648 (mtt) cc_final: 0.6773 (tmm)
REVERT: A  352 TYR cc_start: 0.8003 (t80) cc_final: 0.7794 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0450
  time to fit residues: 5.9241
Evaluate side-chains
  95 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
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  238 ILE
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  459 THR
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 31 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0570
   chunk 35 optimal weight:    0.0070
   chunk 34 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.5716

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 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 = 0.4383 r_free = 0.4383 target = 0.204346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.164544 restraints weight = 4735.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 3.10
r_work: 0.3666 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4406

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= 0.129
  Angle     :  0.571   7.589   4849  Z= 0.296
  Chirality :  0.041   0.203    562
  Planarity :  0.005   0.047    597
  Dihedral  :  7.055  76.242    492
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 15.99 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.42), residues: 441
  helix:  1.88 (0.29), residues: 322
  sheet:  None (None), residues: 0
  loop :  1.71 (0.69), residues: 119

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 488 
 TYR   0.021   0.001   TYR A 361 
 PHE   0.010   0.001   PHE A  22 
 TRP   0.005   0.001   TRP A 261 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3554)
  covalent geometry    : angle       0.56869 ( 4843)
  SS BOND              : bond        0.00208 (    3)
  SS BOND              : angle       1.64609 (    6)
  hydrogen bonds       : bond        0.03995 (  256)
  hydrogen bonds       : angle       4.68262 (  744)

*********************** 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
  102 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TRP cc_start: 0.7681 (m-10) cc_final: 0.7231 (m-10)
REVERT: A  200 MET cc_start: 0.7603 (mmt) cc_final: 0.7397 (mmt)
REVERT: A  239 MET cc_start: 0.7159 (tpt) cc_final: 0.6862 (tpt)
REVERT: A  334 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7784 (m-80)
REVERT: A  348 PHE cc_start: 0.8049 (m-10) cc_final: 0.7672 (m-10)
REVERT: A  351 MET cc_start: 0.7672 (mtt) cc_final: 0.7225 (ttt)
  outliers start: 17
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0371
  time to fit residues: 4.6517
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  : 0.132 
-------------------------------------------------------------------------------
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  238 ILE
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  490 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 23 optimal weight:    0.2980
   chunk 0 optimal weight:    7.9990
   chunk 36 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 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 = 0.4380 r_free = 0.4380 target = 0.204363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.164518 restraints weight = 4725.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3968 rms_B_bonded: 3.13
r_work: 0.3670 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4530

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= 0.132
  Angle     :  0.569   5.678   4849  Z= 0.296
  Chirality :  0.041   0.203    562
  Planarity :  0.005   0.047    597
  Dihedral  :  7.049  73.971    492
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 16.80 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.64 (0.41), residues: 441
  helix:  1.85 (0.28), residues: 323
  sheet:  None (None), residues: 0
  loop :  1.76 (0.69), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 488 
 TYR   0.021   0.002   TYR A 361 
 PHE   0.022   0.001   PHE A 391 
 TRP   0.006   0.001   TRP A 217 
 HIS   0.002   0.001   HIS A 260 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3554)
  covalent geometry    : angle       0.56533 ( 4843)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       1.86515 (    6)
  hydrogen bonds       : bond        0.03965 (  256)
  hydrogen bonds       : angle       4.68359 (  744)

*********************** 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
  101 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 GLU cc_start: 0.8903 (pt0) cc_final: 0.8542 (pt0)
REVERT: A  334 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7705 (m-80)
REVERT: A  348 PHE cc_start: 0.8058 (m-10) cc_final: 0.7674 (m-10)
REVERT: A  351 MET cc_start: 0.7675 (mtt) cc_final: 0.7222 (ttt)
  outliers start: 15
  outliers final: 9
  residues processed: 92
  average time/residue: 0.0397
  time to fit residues: 4.9044
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  : 0.074 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain A residue  490 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0270
   chunk 30 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.4387 r_free = 0.4387 target = 0.204784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.165398 restraints weight = 4651.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 3.23
r_work: 0.3675 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3557  Z= 0.131
  Angle     :  0.617   7.171   4849  Z= 0.315
  Chirality :  0.043   0.240    562
  Planarity :  0.005   0.047    597
  Dihedral  :  6.997  72.698    492
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 19.24 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.42), residues: 441
  helix:  1.71 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop :  1.89 (0.71), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 488 
 TYR   0.020   0.002   TYR A 361 
 PHE   0.009   0.001   PHE A 244 
 TRP   0.014   0.001   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3554)
  covalent geometry    : angle       0.61031 ( 4843)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       2.67325 (    6)
  hydrogen bonds       : bond        0.03948 (  256)
  hydrogen bonds       : angle       4.74873 (  744)

*********************** 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
  95 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7633 (m-80)
REVERT: A  348 PHE cc_start: 0.8087 (m-10) cc_final: 0.7695 (m-10)
REVERT: A  351 MET cc_start: 0.7685 (mtt) cc_final: 0.7206 (ttt)
REVERT: A  447 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7733 (tp40)
  outliers start: 13
  outliers final: 9
  residues processed: 87
  average time/residue: 0.0364
  time to fit residues: 4.2770
Evaluate side-chains
  92 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0980
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4374 r_free = 0.4374 target = 0.203658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.164150 restraints weight = 4677.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 3.18
r_work: 0.3660 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.4748

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= 0.143
  Angle     :  0.610   6.432   4849  Z= 0.317
  Chirality :  0.043   0.226    562
  Planarity :  0.005   0.046    597
  Dihedral  :  6.986  70.429    492
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.78 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.42), residues: 441
  helix:  1.66 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop :  1.98 (0.72), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 488 
 TYR   0.020   0.002   TYR A 361 
 PHE   0.027   0.001   PHE A 391 
 TRP   0.019   0.002   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3554)
  covalent geometry    : angle       0.60247 ( 4843)
  SS BOND              : bond        0.00208 (    3)
  SS BOND              : angle       2.86752 (    6)
  hydrogen bonds       : bond        0.04108 (  256)
  hydrogen bonds       : angle       4.83794 (  744)

********************** 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
  94 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A  233 ARG cc_start: 0.7665 (ptp-170) cc_final: 0.7232 (ptp-170)
REVERT: A  242 MET cc_start: 0.7588 (ptt) cc_final: 0.7199 (ppp)
REVERT: A  334 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7636 (m-80)
REVERT: A  344 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7487 (ptp-170)
REVERT: A  348 PHE cc_start: 0.8091 (m-10) cc_final: 0.7857 (m-10)
REVERT: A  447 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7741 (tp40)
  outliers start: 11
  outliers final: 9
  residues processed: 87
  average time/residue: 0.0417
  time to fit residues: 4.8715
Evaluate side-chains
  94 residues out of total 369 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
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  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  447 GLN
Chi-restraints excluded: chain A residue  471 SER
Chi-restraints excluded: chain A residue  472 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4365 r_free = 0.4365 target = 0.202702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.163502 restraints weight = 4736.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3958 rms_B_bonded: 3.08
r_work: 0.3664 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3557  Z= 0.151
  Angle     :  0.611   6.309   4849  Z= 0.321
  Chirality :  0.044   0.217    562
  Planarity :  0.005   0.046    597
  Dihedral  :  6.945  67.384    492
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.87 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.45 (0.42), residues: 441
  helix:  1.62 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop :  2.04 (0.74), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 488 
 TYR   0.021   0.002   TYR A 361 
 PHE   0.008   0.001   PHE A 355 
 TRP   0.028   0.002   TRP A  64 
 HIS   0.002   0.001   HIS A  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3554)
  covalent geometry    : angle       0.60596 ( 4843)
  SS BOND              : bond        0.00220 (    3)
  SS BOND              : angle       2.37413 (    6)
  hydrogen bonds       : bond        0.04244 (  256)
  hydrogen bonds       : angle       4.87153 (  744)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 974.51 seconds
wall clock time: 17 minutes 17.50 seconds (1037.50 seconds total)