Starting phenix.real_space_refine
on Fri Aug 22 15:23:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b57_44202/08_2025/9b57_44202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b57_44202/08_2025/9b57_44202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b57_44202/08_2025/9b57_44202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b57_44202/08_2025/9b57_44202.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b57_44202/08_2025/9b57_44202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b57_44202/08_2025/9b57_44202.cif"
  }
  resolution = 3.37
  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=   0.039
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      14      5.16       5
     C    3110      2.51       5
     N     824      2.21       5
     O     923      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: 4871
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1162
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1162
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "B"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 596
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 3107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 377, 3099
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 14, 'TRANS': 362}
      Conformer: "B"
        Number of residues, atoms: 377, 3099
          Classifications: {'peptide': 377}
          Link IDs: {'PTRANS': 14, 'TRANS': 362}
          bond proxies already assigned to first conformer: 3161
    Chain: "B"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.97, per 1000 atoms: 0.40
  Number of scatterers: 4871
  At special positions: 0
  Unit cell: (63.84, 82.992, 103.208, 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      14     16.00
     O     923      8.00
     N     824      7.00
     C    3110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 314.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 6 sheets defined
      48.4% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
    Processing helix  chain 'A' and resid 98 through 110
      removed outlier: 3.827A  pdb=" N   VAL A 102 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 130
    Processing helix  chain 'A' and resid 130 through 146
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 37 through 41
    Processing helix  chain 'B' and resid 56 through 60
    Processing helix  chain 'C' and resid 293 through 306
    Processing helix  chain 'C' and resid 325 through 335
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 357 through 374
    Processing helix  chain 'C' and resid 375 through 379
    Processing helix  chain 'C' and resid 395 through 400
      removed outlier: 3.547A  pdb=" N   SER C 398 " --> pdb=" O   PRO C 395 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 420
      removed outlier: 4.472A  pdb=" N   TYR C 406 " --> pdb=" O   ASP C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 437
      removed outlier: 3.610A  pdb=" N   TYR C 433 " --> pdb=" O   VAL C 429 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 442 through 444
      No H-bonds generated for 'chain 'C' and resid 442 through 444'
    Processing helix  chain 'C' and resid 445 through 450
      removed outlier: 3.816A  pdb=" N   VAL C 449 " --> pdb=" O   ASP C 445 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 450 through 463
    Processing helix  chain 'C' and resid 491 through 495
      removed outlier: 3.937A  pdb=" N   ASN C 494 " --> pdb=" O   ASN C 491 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 501 through 515
    Processing helix  chain 'C' and resid 518 through 533
      removed outlier: 4.315A  pdb=" N   LEU C 532 " --> pdb=" O   GLY C 528 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 534 through 539
      removed outlier: 3.585A  pdb=" N   LEU C 538 " --> pdb=" O   PRO C 534 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 544 through 552
    Processing helix  chain 'C' and resid 558 through 564
    Processing helix  chain 'C' and resid 574 through 586
      removed outlier: 3.893A  pdb=" N   PHE C 580 " --> pdb=" O   ILE C 576 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 588 through 600
    Processing helix  chain 'C' and resid 638 through 640
      No H-bonds generated for 'chain 'C' and resid 638 through 640'
    Processing helix  chain 'C' and resid 650 through 662
      removed outlier: 3.569A  pdb=" N   ILE C 662 " --> pdb=" O   LEU C 658 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25
    Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16
      removed outlier: 3.963A  pdb=" N   SER B  65 " --> pdb=" O   GLN B   2 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ARG B  42 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 313 through 321
      removed outlier: 3.707A  pdb=" N   VAL C 321 " --> pdb=" O   ARG C 349 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 381 through 383
    Processing sheet with id=AA5, first strand: chain 'C' and resid 475 through 479
      removed outlier: 3.675A  pdb=" N   GLU C 482 " --> pdb=" O   ARG C 479 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 565 through 568

    223 hydrogen bonds defined for protein.
    623 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: 0.75

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 820
        1.27 -     1.41: 1241
        1.41 -     1.55: 2898
        1.55 -     1.69: 0
        1.69 -     1.83: 24
  Bond restraints: 4983
  Sorted by residual:
  bond pdb=" C04 A1AIV B 101 "
       pdb=" C05 A1AIV B 101 "
    ideal  model  delta    sigma   weight residual
    1.453  1.526 -0.073 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.93e+00
  bond pdb=" N   MET A   1 "
       pdb=" CA  MET A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.85e+00
  bond pdb=" C05 A1AIV B 101 "
       pdb=" N06 A1AIV B 101 "
    ideal  model  delta    sigma   weight residual
    1.151  1.133  0.018 2.00e-02 2.50e+03 8.36e-01
  bond pdb=" CG  LEU C 595 "
       pdb=" CD2 LEU C 595 "
    ideal  model  delta    sigma   weight residual
    1.521  1.499  0.022 3.30e-02 9.18e+02 4.35e-01
  ... (remaining 4978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 6513
        1.05 -     2.10: 185
        2.10 -     3.15: 24
        3.15 -     4.20: 24
        4.20 -     5.26: 1
  Bond angle restraints: 6747
  Sorted by residual:
  angle pdb=" C03 A1AIV B 101 "
        pdb=" C02 A1AIV B 101 "
        pdb=" N01 A1AIV B 101 "
      ideal   model   delta    sigma   weight residual
     111.06  105.80    5.26 3.00e+00 1.11e-01 3.07e+00
  angle pdb=" N   LEU C 424 "
        pdb=" CA  LEU C 424 "
        pdb=" C   LEU C 424 "
      ideal   model   delta    sigma   weight residual
     110.35  108.12    2.23 1.38e+00 5.25e-01 2.62e+00
  angle pdb=" CA  CYS C 639 "
        pdb=" CB  CYS C 639 "
        pdb=" SG  CYS C 639 "
      ideal   model   delta    sigma   weight residual
     114.40  117.45   -3.05 2.30e+00 1.89e-01 1.76e+00
  angle pdb=" N   VAL C 515 "
        pdb=" CA  VAL C 515 "
        pdb=" C   VAL C 515 "
      ideal   model   delta    sigma   weight residual
     109.34  112.04   -2.70 2.08e+00 2.31e-01 1.68e+00
  angle pdb=" CA  GLU C 586 "
        pdb=" CB  GLU C 586 "
        pdb=" CG  GLU C 586 "
      ideal   model   delta    sigma   weight residual
     114.10  116.34   -2.24 2.00e+00 2.50e-01 1.25e+00
  ... (remaining 6742 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.29: 2740
       13.29 -    26.59: 223
       26.59 -    39.88: 44
       39.88 -    53.17: 9
       53.17 -    66.46: 2
  Dihedral angle restraints: 3018
    sinusoidal: 1254
      harmonic: 1764
  Sorted by residual:
  dihedral pdb=" CA  TYR C 423 "
           pdb=" C   TYR C 423 "
           pdb=" N   LEU C 424 "
           pdb=" CA  LEU C 424 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.48   17.52     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  VAL C 515 "
           pdb=" C   VAL C 515 "
           pdb=" N   THR C 516 "
           pdb=" CA  THR C 516 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.88  -16.12     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  ASP C 357 "
           pdb=" CB  ASP C 357 "
           pdb=" CG  ASP C 357 "
           pdb=" OD1 ASP C 357 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.99   51.99     1      2.00e+01 2.50e-03 9.22e+00
  ... (remaining 3015 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 443
       0.027 -    0.054: 192
       0.054 -    0.081: 59
       0.081 -    0.109: 25
       0.109 -    0.136: 18
  Chirality restraints: 737
  Sorted by residual:
  chirality pdb=" CA  ILE C 645 "
            pdb=" N   ILE C 645 "
            pdb=" C   ILE C 645 "
            pdb=" CB  ILE C 645 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CA  ILE C 533 "
            pdb=" N   ILE C 533 "
            pdb=" C   ILE C 533 "
            pdb=" CB  ILE C 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  VAL A  49 "
            pdb=" N   VAL A  49 "
            pdb=" C   VAL A  49 "
            pdb=" CB  VAL A  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.03e-01
  ... (remaining 734 not shown)

  Planarity restraints: 873
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 430 "    0.020 5.00e-02 4.00e+02   3.04e-02 1.48e+00
        pdb=" N   PRO C 431 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO C 431 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 431 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 114 "    0.018 5.00e-02 4.00e+02   2.78e-02 1.24e+00
        pdb=" N   PRO A 115 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 115 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 115 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  94 "   -0.017 5.00e-02 4.00e+02   2.63e-02 1.10e+00
        pdb=" N   PRO A  95 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A  95 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A  95 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 870 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 16
        2.44 -     3.06: 3199
        3.06 -     3.67: 6746
        3.67 -     4.29: 10189
        4.29 -     4.90: 17722
  Nonbonded interactions: 37872
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C 639 "
            pdb=" C03 A1AIV B 101 "
     model   vdw
     1.831 3.800
  nonbonded pdb=" OE1 GLN B   2 "
            pdb=" OG1 THR B  14 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OD1 ASN C 478 "
            pdb=" OG  SER C 483 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OG  SER C 608 "
            pdb=" OD2 ASP C 612 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OE2 GLU A   9 "
            pdb=" OH  TYR A  60 "
     model   vdw
     2.344 3.040
  ... (remaining 37867 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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=0.37 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:             2.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.580
  Find NCS groups from input model:        0.030
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
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      :  0.003   0.111   4985  Z= 0.199
  Angle     :  0.471   5.255   6747  Z= 0.232
  Chirality :  0.039   0.136    737
  Planarity :  0.003   0.030    873
  Dihedral  : 10.222  66.463   1878
  Min Nonbonded Distance : 1.831

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  6.08 %
    Favored  : 92.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.13 (0.37), residues: 594
  helix:  1.70 (0.34), residues: 250
  sheet:  0.68 (0.61), residues: 82
  loop : -0.09 (0.42), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 422 
 TYR   0.007   0.001   TYR C 367 
 PHE   0.009   0.001   PHE C 522 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.001   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 4983)
  covalent geometry    : angle       0.47066 ( 6747)
  hydrogen bonds       : bond        0.14172 (  223)
  hydrogen bonds       : angle       5.67166 (  623)
  Misc. bond           : bond        0.08075 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7525 (mt-10)
REVERT: A   83 SER cc_start: 0.8825 (m) cc_final: 0.8602 (t)
REVERT: B   42 ARG cc_start: 0.6175 (ttt90) cc_final: 0.5960 (ttt90)
REVERT: C  613 MET cc_start: 0.8614 (ttt) cc_final: 0.8319 (ttt)
  outliers start: 7
  outliers final: 5
  residues processed: 98
  average time/residue: 0.1171
  time to fit residues: 13.6946
Evaluate side-chains
  61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain C residue  387 ASP
Chi-restraints excluded: chain C residue  463 ASN
Chi-restraints excluded: chain C residue  487 ASP
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.1980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3849 r_free = 0.3849 target = 0.135599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.086151 restraints weight = 17259.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 5.50
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4985  Z= 0.150
  Angle     :  0.540   6.160   6747  Z= 0.275
  Chirality :  0.042   0.164    737
  Planarity :  0.004   0.034    873
  Dihedral  :  4.892  41.497    670
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.05 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.06 (0.37), residues: 594
  helix:  1.68 (0.34), residues: 259
  sheet:  0.64 (0.62), residues: 81
  loop : -0.24 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 139 
 TYR   0.010   0.001   TYR C 419 
 PHE   0.020   0.001   PHE C 480 
 TRP   0.008   0.001   TRP C 581 
 HIS   0.002   0.000   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 4983)
  covalent geometry    : angle       0.53967 ( 6747)
  hydrogen bonds       : bond        0.03919 (  223)
  hydrogen bonds       : angle       4.78740 (  623)
  Misc. bond           : bond        0.00248 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.7728 (mtp85) cc_final: 0.7419 (ttm-80)
REVERT: A   83 SER cc_start: 0.8823 (m) cc_final: 0.8539 (t)
REVERT: A   92 GLN cc_start: 0.7480 (mt0) cc_final: 0.6737 (mt0)
REVERT: A  114 ASN cc_start: 0.6944 (t0) cc_final: 0.6612 (t0)
REVERT: A  140 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8828 (mm-30)
REVERT: A  143 ARG cc_start: 0.8327 (tpm170) cc_final: 0.8026 (tpm170)
REVERT: C  613 MET cc_start: 0.8566 (ttt) cc_final: 0.8272 (ttt)
  outliers start: 10
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0986
  time to fit residues: 8.5810
Evaluate side-chains
  66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0770
   chunk 6 optimal weight:    0.0980
   chunk 56 optimal weight:    0.2980
   overall best weight:    0.3738

-------------------------------------------------------------------------------
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 = 0.3866 r_free = 0.3866 target = 0.136796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.087850 restraints weight = 15895.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 5.27
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4985  Z= 0.119
  Angle     :  0.516   6.932   6747  Z= 0.262
  Chirality :  0.042   0.295    737
  Planarity :  0.004   0.061    873
  Dihedral  :  4.377  38.538    664
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.71 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.16 (0.37), residues: 594
  helix:  1.82 (0.34), residues: 259
  sheet:  0.74 (0.61), residues: 81
  loop : -0.26 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 133 
 TYR   0.023   0.001   TYR A 145 
 PHE   0.011   0.001   PHE C 480 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4983)
  covalent geometry    : angle       0.51626 ( 6747)
  hydrogen bonds       : bond        0.03412 (  223)
  hydrogen bonds       : angle       4.72022 (  623)
  Misc. bond           : bond        0.00046 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.8908 (m) cc_final: 0.8584 (t)
REVERT: A   92 GLN cc_start: 0.7483 (mt0) cc_final: 0.6843 (mt0)
REVERT: A  114 ASN cc_start: 0.6946 (t0) cc_final: 0.6475 (t0)
REVERT: C  349 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6923 (mtm-85)
REVERT: C  613 MET cc_start: 0.8643 (ttt) cc_final: 0.8385 (ttt)
  outliers start: 9
  outliers final: 7
  residues processed: 69
  average time/residue: 0.1043
  time to fit residues: 8.8692
Evaluate side-chains
  63 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0470
   chunk 29 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    0.2980
   chunk 22 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   overall best weight:    0.4678

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.142316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.093450 restraints weight = 17404.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 4.99
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3351
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4985  Z= 0.130
  Angle     :  0.506   7.118   6747  Z= 0.255
  Chirality :  0.041   0.126    737
  Planarity :  0.004   0.045    873
  Dihedral  :  4.395  38.510    664
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 11.60 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.15 (0.37), residues: 594
  helix:  1.77 (0.34), residues: 260
  sheet:  0.72 (0.62), residues: 81
  loop : -0.23 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  72 
 TYR   0.009   0.001   TYR C 419 
 PHE   0.009   0.001   PHE C 522 
 TRP   0.006   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4983)
  covalent geometry    : angle       0.50560 ( 6747)
  hydrogen bonds       : bond        0.03435 (  223)
  hydrogen bonds       : angle       4.69383 (  623)
  Misc. bond           : bond        0.00070 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.8878 (m) cc_final: 0.8574 (t)
REVERT: A   92 GLN cc_start: 0.7569 (mt0) cc_final: 0.6993 (mt0)
REVERT: A   99 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7136 (tp)
REVERT: A  140 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8656 (mm-30)
REVERT: B   43 LEU cc_start: 0.8137 (tt) cc_final: 0.7889 (mm)
REVERT: B   54 ARG cc_start: 0.8738 (mtp180) cc_final: 0.8531 (mtp180)
REVERT: C  310 MET cc_start: 0.8372 (mtp) cc_final: 0.8167 (ttt)
REVERT: C  613 MET cc_start: 0.8749 (ttt) cc_final: 0.8527 (ttt)
  outliers start: 13
  outliers final: 11
  residues processed: 67
  average time/residue: 0.0921
  time to fit residues: 7.6874
Evaluate side-chains
  67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0170
   chunk 15 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 42 optimal weight:    0.1980
   chunk 47 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.6218

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.139557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.092264 restraints weight = 12526.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 4.53
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4985  Z= 0.156
  Angle     :  0.532   7.306   6747  Z= 0.268
  Chirality :  0.041   0.143    737
  Planarity :  0.004   0.040    873
  Dihedral  :  4.445  38.499    664
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 11.79 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.05 (0.37), residues: 594
  helix:  1.72 (0.34), residues: 260
  sheet:  0.75 (0.62), residues: 81
  loop : -0.36 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 133 
 TYR   0.027   0.001   TYR A 145 
 PHE   0.010   0.001   PHE C 522 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.001   0.000   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 4983)
  covalent geometry    : angle       0.53182 ( 6747)
  hydrogen bonds       : bond        0.03476 (  223)
  hydrogen bonds       : angle       4.75330 (  623)
  Misc. bond           : bond        0.00036 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.8941 (m) cc_final: 0.8622 (t)
REVERT: A   92 GLN cc_start: 0.7550 (mt0) cc_final: 0.6976 (mt0)
REVERT: A   99 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7141 (tp)
REVERT: A  145 TYR cc_start: 0.7639 (m-10) cc_final: 0.7390 (m-10)
REVERT: B   43 LEU cc_start: 0.8140 (tt) cc_final: 0.7692 (mm)
REVERT: C  294 MET cc_start: 0.7194 (mmm) cc_final: 0.6871 (mmm)
  outliers start: 16
  outliers final: 12
  residues processed: 70
  average time/residue: 0.1005
  time to fit residues: 8.6506
Evaluate side-chains
  69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  516 THR
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 35 optimal weight:    0.0980
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 37 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3998 r_free = 0.3998 target = 0.146132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.101245 restraints weight = 16171.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 4.31
r_work: 0.3204 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4985  Z= 0.128
  Angle     :  0.513   7.359   6747  Z= 0.258
  Chirality :  0.041   0.129    737
  Planarity :  0.004   0.045    873
  Dihedral  :  4.432  38.476    664
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 12.71 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.11 (0.37), residues: 594
  helix:  1.76 (0.34), residues: 260
  sheet:  0.82 (0.63), residues: 81
  loop : -0.34 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 143 
 TYR   0.016   0.001   TYR A 145 
 PHE   0.008   0.001   PHE C 522 
 TRP   0.006   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 4983)
  covalent geometry    : angle       0.51297 ( 6747)
  hydrogen bonds       : bond        0.03338 (  223)
  hydrogen bonds       : angle       4.72700 (  623)
  Misc. bond           : bond        0.00048 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.9071 (m) cc_final: 0.8736 (t)
REVERT: A   92 GLN cc_start: 0.7435 (mt0) cc_final: 0.7001 (mt0)
REVERT: A   99 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7436 (tp)
REVERT: A  114 ASN cc_start: 0.7829 (t0) cc_final: 0.6996 (t0)
  outliers start: 15
  outliers final: 10
  residues processed: 68
  average time/residue: 0.1005
  time to fit residues: 8.3707
Evaluate side-chains
  66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   32 ASP
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   chunk 6 optimal weight:    0.0770
   chunk 23 optimal weight:    0.0970
   overall best weight:    0.3736

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.140896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.092084 restraints weight = 16422.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 5.13
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4985  Z= 0.117
  Angle     :  0.533   8.404   6747  Z= 0.264
  Chirality :  0.040   0.136    737
  Planarity :  0.004   0.047    873
  Dihedral  :  4.519  38.415    664
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 14.00 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.22 (0.37), residues: 594
  helix:  1.87 (0.34), residues: 258
  sheet:  0.96 (0.63), residues: 81
  loop : -0.31 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  72 
 TYR   0.012   0.001   TYR A 145 
 PHE   0.008   0.001   PHE C 522 
 TRP   0.007   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4983)
  covalent geometry    : angle       0.53270 ( 6747)
  hydrogen bonds       : bond        0.03191 (  223)
  hydrogen bonds       : angle       4.70049 (  623)
  Misc. bond           : bond        0.00026 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.8959 (m) cc_final: 0.8628 (t)
REVERT: A   92 GLN cc_start: 0.7444 (mt0) cc_final: 0.6914 (mt0)
REVERT: A  114 ASN cc_start: 0.7662 (t0) cc_final: 0.6757 (t0)
REVERT: B   43 LEU cc_start: 0.8407 (tt) cc_final: 0.8066 (mm)
REVERT: B   54 ARG cc_start: 0.8803 (mtp180) cc_final: 0.8573 (mtp180)
REVERT: B   67 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6318 (tp)
  outliers start: 10
  outliers final: 8
  residues processed: 61
  average time/residue: 0.1039
  time to fit residues: 7.8582
Evaluate side-chains
  64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 23 optimal weight:    0.3980
   chunk 38 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3995 r_free = 0.3995 target = 0.145828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.101779 restraints weight = 8066.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3359 rms_B_bonded: 3.48
r_work: 0.3149 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4985  Z= 0.147
  Angle     :  0.538   8.195   6747  Z= 0.266
  Chirality :  0.041   0.130    737
  Planarity :  0.004   0.050    873
  Dihedral  :  4.458  38.474    664
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 13.44 %
    Favored  : 83.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.20 (0.37), residues: 594
  helix:  1.84 (0.34), residues: 258
  sheet:  1.02 (0.65), residues: 81
  loop : -0.33 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 143 
 TYR   0.027   0.001   TYR A 145 
 PHE   0.010   0.001   PHE C 522 
 TRP   0.006   0.001   TRP C 581 
 HIS   0.001   0.000   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 4983)
  covalent geometry    : angle       0.53804 ( 6747)
  hydrogen bonds       : bond        0.03325 (  223)
  hydrogen bonds       : angle       4.74822 (  623)
  Misc. bond           : bond        0.00022 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.9066 (m) cc_final: 0.8712 (t)
REVERT: A   92 GLN cc_start: 0.7414 (mt0) cc_final: 0.7039 (mt0)
REVERT: A   99 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7397 (tp)
REVERT: A  114 ASN cc_start: 0.7873 (t0) cc_final: 0.6979 (t0)
REVERT: A  145 TYR cc_start: 0.7837 (m-10) cc_final: 0.7537 (m-80)
REVERT: B   43 LEU cc_start: 0.8544 (tt) cc_final: 0.8172 (mm)
REVERT: B   67 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.6064 (tp)
REVERT: C  349 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7600 (mtm180)
  outliers start: 16
  outliers final: 11
  residues processed: 64
  average time/residue: 0.0951
  time to fit residues: 7.5319
Evaluate side-chains
  67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  516 THR
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0570
   chunk 37 optimal weight:    0.5980
   chunk 41 optimal weight:    0.3980
   chunk 38 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 56 optimal weight:    0.1980
   chunk 51 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0570
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.2616

-------------------------------------------------------------------------------
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 = 0.4014 r_free = 0.4014 target = 0.146644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.099688 restraints weight = 12927.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 4.52
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4985  Z= 0.103
  Angle     :  0.527   8.345   6747  Z= 0.258
  Chirality :  0.040   0.131    737
  Planarity :  0.004   0.051    873
  Dihedral  :  4.393  38.482    664
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.55 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.28 (0.37), residues: 594
  helix:  1.95 (0.34), residues: 257
  sheet:  0.96 (0.64), residues: 81
  loop : -0.31 (0.42), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  72 
 TYR   0.015   0.001   TYR A 145 
 PHE   0.006   0.001   PHE C 428 
 TRP   0.007   0.001   TRP A  93 
 HIS   0.001   0.000   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4983)
  covalent geometry    : angle       0.52697 ( 6747)
  hydrogen bonds       : bond        0.03027 (  223)
  hydrogen bonds       : angle       4.68175 (  623)
  Misc. bond           : bond        0.00033 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.8916 (m) cc_final: 0.8565 (t)
REVERT: A   92 GLN cc_start: 0.7403 (mt0) cc_final: 0.6956 (mt0)
REVERT: A   99 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7141 (tp)
REVERT: A  114 ASN cc_start: 0.7739 (t0) cc_final: 0.6909 (t0)
REVERT: B   43 LEU cc_start: 0.8455 (tt) cc_final: 0.8085 (mm)
REVERT: B   67 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.6028 (tp)
REVERT: C  294 MET cc_start: 0.7072 (mmm) cc_final: 0.6676 (mmm)
  outliers start: 11
  outliers final: 9
  residues processed: 63
  average time/residue: 0.0915
  time to fit residues: 7.1422
Evaluate side-chains
  66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 52 optimal weight:    0.0770
   chunk 16 optimal weight:    6.9990
   chunk 8 optimal weight:    0.0670
   chunk 57 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.4076

-------------------------------------------------------------------------------
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 = 0.4006 r_free = 0.4006 target = 0.146084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.098832 restraints weight = 13373.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 4.58
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3376
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3376 r_free = 0.3376    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3376
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4985  Z= 0.120
  Angle     :  0.540   8.563   6747  Z= 0.266
  Chirality :  0.040   0.127    737
  Planarity :  0.004   0.053    873
  Dihedral  :  4.417  38.484    664
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 14.73 %
    Favored  : 83.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.22 (0.37), residues: 594
  helix:  1.84 (0.34), residues: 258
  sheet:  0.97 (0.64), residues: 81
  loop : -0.28 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 143 
 TYR   0.017   0.001   TYR A 145 
 PHE   0.008   0.001   PHE C 522 
 TRP   0.006   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4983)
  covalent geometry    : angle       0.54015 ( 6747)
  hydrogen bonds       : bond        0.03127 (  223)
  hydrogen bonds       : angle       4.67991 (  623)
  Misc. bond           : bond        0.00016 (    2)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.8924 (m) cc_final: 0.8569 (t)
REVERT: A   92 GLN cc_start: 0.7381 (mt0) cc_final: 0.6943 (mt0)
REVERT: A   99 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7181 (tp)
REVERT: A  114 ASN cc_start: 0.7712 (t0) cc_final: 0.6900 (t0)
REVERT: B   43 LEU cc_start: 0.8469 (tt) cc_final: 0.8097 (mm)
REVERT: B   67 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5833 (tp)
REVERT: C  294 MET cc_start: 0.7037 (mmm) cc_final: 0.6687 (mmm)
REVERT: C  349 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6958 (mtm-85)
  outliers start: 10
  outliers final: 8
  residues processed: 64
  average time/residue: 0.1043
  time to fit residues: 8.2685
Evaluate side-chains
  65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LEU
Chi-restraints excluded: chain A residue   43 SER
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  144 LYS
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  570 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 51 optimal weight:    0.3980
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3993 r_free = 0.3993 target = 0.145102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.099032 restraints weight = 11102.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 4.14
r_work: 0.3196 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3189 r_free = 0.3189    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3190 r_free = 0.3190    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4985  Z= 0.147
  Angle     :  0.554   8.398   6747  Z= 0.274
  Chirality :  0.041   0.124    737
  Planarity :  0.004   0.052    873
  Dihedral  :  4.533  38.424    664
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 14.92 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.17 (0.37), residues: 594
  helix:  1.79 (0.34), residues: 258
  sheet:  0.92 (0.64), residues: 81
  loop : -0.29 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  72 
 TYR   0.013   0.001   TYR A 127 
 PHE   0.011   0.001   PHE C 522 
 TRP   0.007   0.001   TRP C 581 
 HIS   0.001   0.000   HIS C 420 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 4983)
  covalent geometry    : angle       0.55409 ( 6747)
  hydrogen bonds       : bond        0.03339 (  223)
  hydrogen bonds       : angle       4.75774 (  623)
  Misc. bond           : bond        0.00015 (    2)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 1281.92 seconds
wall clock time: 22 minutes 23.81 seconds (1343.81 seconds total)