Starting phenix.real_space_refine
on Thu Mar  6 04:34:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b57_44202/03_2025/9b57_44202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b57_44202/03_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_44202/03_2025/9b57_44202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b57_44202/03_2025/9b57_44202.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b57_44202/03_2025/9b57_44202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b57_44202/03_2025/9b57_44202.cif"
  }
  resolution = 3.37
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.039
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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.93, per 1000 atoms: 1.01
  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: 1.14
  Conformation dependent library (CDL) restraints added in 831.6 milliseconds
  

  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: 0.50
  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: 1.20

  Time building geometry restraints manager: 1.37 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:             2.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.160
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.110
-------------------------------------------------------------------------------
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   0.073   4983  Z= 0.176
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (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
 TRP   0.006   0.001   TRP C 581 
 HIS   0.001   0.000   HIS A  75 
 PHE   0.009   0.001   PHE C 522 
 TYR   0.007   0.001   TYR C 367 
 ARG   0.002   0.000   ARG C 422 

*********************** 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  : 0.539 
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: 0.2392
  time to fit residues: 28.3777
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  : 0.560 
-------------------------------------------------------------------------------
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 48 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.135530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.087598 restraints weight = 12761.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 4.82
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3175
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3175 r_free = 0.3175    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3175
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4983  Z= 0.309
  Angle     :  0.569   6.620   6747  Z= 0.290
  Chirality :  0.043   0.163    737
  Planarity :  0.004   0.034    873
  Dihedral  :  4.933  41.141    670
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.13 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.37), residues: 594
  helix:  1.58 (0.34), residues: 259
  sheet:  0.46 (0.61), residues: 83
  loop : -0.30 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 581 
 HIS   0.002   0.000   HIS A  55 
 PHE   0.019   0.002   PHE C 480 
 TYR   0.012   0.002   TYR C 419 
 ARG   0.006   0.001   ARG A 139 

*********************** 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
  76 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.551 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.7724 (mtp85) cc_final: 0.7395 (ttm-80)
REVERT: A   83 SER cc_start: 0.8894 (m) cc_final: 0.8599 (t)
REVERT: A   92 GLN cc_start: 0.7439 (mt0) cc_final: 0.6730 (mt0)
REVERT: A  114 ASN cc_start: 0.6963 (t0) cc_final: 0.6644 (t0)
REVERT: A  140 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8881 (mm-30)
REVERT: A  143 ARG cc_start: 0.8366 (tpm170) cc_final: 0.8067 (tpm170)
REVERT: C  587 TRP cc_start: 0.8463 (OUTLIER) cc_final: 0.8006 (m-10)
REVERT: C  613 MET cc_start: 0.8566 (ttt) cc_final: 0.8278 (ttt)
  outliers start: 13
  outliers final: 10
  residues processed: 73
  average time/residue: 0.2945
  time to fit residues: 26.5529
Evaluate side-chains
  68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
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  516 THR
Chi-restraints excluded: chain C residue  570 TYR
Chi-restraints excluded: chain C residue  584 LEU
Chi-restraints excluded: chain C residue  587 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0470
   chunk 0 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0070
   chunk 24 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.3696

-------------------------------------------------------------------------------
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 = 0.3874 r_free = 0.3874 target = 0.137877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.091532 restraints weight = 10347.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 4.32
r_work: 0.3039 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3046 r_free = 0.3046    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4983  Z= 0.178
  Angle     :  0.525   7.106   6747  Z= 0.266
  Chirality :  0.042   0.266    737
  Planarity :  0.004   0.064    873
  Dihedral  :  4.445  38.384    664
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.15 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.37), residues: 594
  helix:  1.74 (0.34), residues: 259
  sheet:  0.70 (0.61), residues: 81
  loop : -0.33 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS C 293 
 PHE   0.012   0.001   PHE C 480 
 TYR   0.023   0.001   TYR A 145 
 ARG   0.007   0.001   ARG B  54 

*********************** 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: 11
    poor density    : 61
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.9061 (m) cc_final: 0.8703 (t)
REVERT: A   92 GLN cc_start: 0.7375 (mt0) cc_final: 0.6846 (mt0)
REVERT: A  114 ASN cc_start: 0.7110 (t0) cc_final: 0.6587 (t0)
REVERT: B   43 LEU cc_start: 0.8078 (tt) cc_final: 0.7763 (mm)
REVERT: C  349 ARG cc_start: 0.7604 (mtt180) cc_final: 0.7314 (mtm-85)
REVERT: C  613 MET cc_start: 0.8788 (ttt) cc_final: 0.8556 (ttt)
  outliers start: 11
  outliers final: 8
  residues processed: 68
  average time/residue: 0.2643
  time to fit residues: 22.2266
Evaluate side-chains
  64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
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  317 LEU
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 12 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0980
   chunk 27 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0670
   chunk 19 optimal weight:    8.9990
   overall best weight:    0.3918

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.142474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.094152 restraints weight = 16146.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 4.80
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3366
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4983  Z= 0.180
  Angle     :  0.502   7.126   6747  Z= 0.255
  Chirality :  0.040   0.128    737
  Planarity :  0.004   0.051    873
  Dihedral  :  4.398  38.436    664
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 11.60 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.37), residues: 594
  helix:  1.77 (0.34), residues: 259
  sheet:  0.73 (0.62), residues: 81
  loop : -0.31 (0.42), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  55 
 PHE   0.008   0.001   PHE C 480 
 TYR   0.024   0.001   TYR A 145 
 ARG   0.008   0.001   ARG A  72 

*********************** 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: 11
    poor density    : 59
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7332 (ttm-80)
REVERT: A   83 SER cc_start: 0.8867 (m) cc_final: 0.8564 (t)
REVERT: A   92 GLN cc_start: 0.7583 (mt0) cc_final: 0.7017 (mt0)
REVERT: A   99 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7102 (tp)
REVERT: A  114 ASN cc_start: 0.6872 (t0) cc_final: 0.6401 (t0)
REVERT: A  140 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8655 (mm-30)
REVERT: A  145 TYR cc_start: 0.7758 (m-10) cc_final: 0.7471 (m-80)
REVERT: C  613 MET cc_start: 0.8782 (ttt) cc_final: 0.8544 (ttt)
  outliers start: 11
  outliers final: 9
  residues processed: 68
  average time/residue: 0.2829
  time to fit residues: 24.0513
Evaluate side-chains
  67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
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  120 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0170
   chunk 40 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.6618

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.139133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.093493 restraints weight = 21815.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 5.43
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4983  Z= 0.260
  Angle     :  0.545   8.781   6747  Z= 0.272
  Chirality :  0.042   0.137    737
  Planarity :  0.004   0.055    873
  Dihedral  :  4.505  38.494    664
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 12.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.37), residues: 594
  helix:  1.68 (0.34), residues: 260
  sheet:  0.76 (0.62), residues: 81
  loop : -0.37 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 581 
 HIS   0.001   0.000   HIS A  55 
 PHE   0.011   0.001   PHE C 522 
 TYR   0.013   0.001   TYR A 145 
 ARG   0.005   0.001   ARG A  72 

*********************** 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
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 56
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7442 (ttm-80)
REVERT: A   83 SER cc_start: 0.9024 (m) cc_final: 0.8696 (t)
REVERT: A   92 GLN cc_start: 0.7436 (mt0) cc_final: 0.6812 (mt0)
REVERT: A   99 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7223 (tp)
REVERT: A  140 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8795 (mm-30)
REVERT: B   43 LEU cc_start: 0.8193 (tt) cc_final: 0.7808 (mm)
  outliers start: 16
  outliers final: 11
  residues processed: 69
  average time/residue: 0.2797
  time to fit residues: 23.7420
Evaluate side-chains
  65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
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 A residue  144 LYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 28 optimal weight:    0.1980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.142793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.097010 restraints weight = 10602.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 3.85
r_work: 0.3217 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
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      :  0.004   0.036   4983  Z= 0.267
  Angle     :  0.561   8.438   6747  Z= 0.278
  Chirality :  0.042   0.126    737
  Planarity :  0.004   0.043    873
  Dihedral  :  4.551  38.283    664
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 12.71 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.37), residues: 594
  helix:  1.68 (0.34), residues: 260
  sheet:  0.78 (0.63), residues: 81
  loop : -0.44 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 581 
 HIS   0.002   0.000   HIS A  55 
 PHE   0.011   0.001   PHE C 522 
 TYR   0.010   0.001   TYR C 419 
 ARG   0.010   0.001   ARG A 143 

*********************** 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
  70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.9104 (m) cc_final: 0.8747 (t)
REVERT: A   92 GLN cc_start: 0.7453 (mt0) cc_final: 0.7016 (mt0)
REVERT: A   99 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7438 (tp)
REVERT: B   54 ARG cc_start: 0.8726 (mtp180) cc_final: 0.8240 (mtp180)
  outliers start: 16
  outliers final: 12
  residues processed: 66
  average time/residue: 0.2025
  time to fit residues: 16.8641
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  : 0.561 
-------------------------------------------------------------------------------
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   32 ASP
Chi-restraints excluded: chain C residue  389 TYR
Chi-restraints excluded: chain C residue  413 VAL
Chi-restraints excluded: chain C residue  486 VAL
Chi-restraints excluded: chain C residue  516 THR
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 11 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 56 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 55 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.138734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.092335 restraints weight = 21824.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 5.63
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4983  Z= 0.282
  Angle     :  0.570   9.165   6747  Z= 0.285
  Chirality :  0.042   0.135    737
  Planarity :  0.004   0.046    873
  Dihedral  :  4.636  38.174    664
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 12.52 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.37), residues: 594
  helix:  1.63 (0.34), residues: 260
  sheet:  0.84 (0.63), residues: 81
  loop : -0.45 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 581 
 HIS   0.002   0.000   HIS A  55 
 PHE   0.011   0.001   PHE C 522 
 TYR   0.010   0.001   TYR C 419 
 ARG   0.008   0.001   ARG A  72 

*********************** 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
  71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.9133 (m) cc_final: 0.8783 (t)
REVERT: A   92 GLN cc_start: 0.7464 (mt0) cc_final: 0.6825 (mt0)
REVERT: A   99 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7260 (tp)
REVERT: A  104 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7052 (tt)
REVERT: A  114 ASN cc_start: 0.7655 (t0) cc_final: 0.6846 (t0)
REVERT: B   43 LEU cc_start: 0.8332 (tt) cc_final: 0.7997 (mm)
REVERT: B   67 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5627 (tp)
  outliers start: 17
  outliers final: 12
  residues processed: 66
  average time/residue: 0.2145
  time to fit residues: 17.7632
Evaluate side-chains
  66 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
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  104 LEU
Chi-restraints excluded: chain B residue   14 THR
Chi-restraints excluded: chain B residue   32 ASP
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  486 VAL
Chi-restraints excluded: chain C residue  516 THR
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 40 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 55 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 44 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0060
   chunk 24 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 33 optimal weight:    0.4980
   chunk 49 optimal weight:    0.3980
   overall best weight:    0.3996

-------------------------------------------------------------------------------
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 = 0.145289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.097746 restraints weight = 12713.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 4.36
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4983  Z= 0.186
  Angle     :  0.551   8.580   6747  Z= 0.272
  Chirality :  0.041   0.128    737
  Planarity :  0.004   0.049    873
  Dihedral  :  4.630  38.160    664
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.08 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.37), residues: 594
  helix:  1.78 (0.34), residues: 258
  sheet:  0.94 (0.64), residues: 81
  loop : -0.35 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  55 
 PHE   0.008   0.001   PHE C 522 
 TYR   0.020   0.001   TYR A 145 
 ARG   0.006   0.001   ARG A  72 

*********************** 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: 14
    poor density    : 56
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.9024 (m) cc_final: 0.8677 (t)
REVERT: A   92 GLN cc_start: 0.7575 (mt0) cc_final: 0.7109 (mt0)
REVERT: A   99 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7120 (tp)
REVERT: A  104 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6883 (tt)
REVERT: A  114 ASN cc_start: 0.7860 (t0) cc_final: 0.7113 (t0)
REVERT: B   43 LEU cc_start: 0.8352 (tt) cc_final: 0.7983 (mm)
REVERT: B   67 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5714 (tp)
REVERT: C  294 MET cc_start: 0.7095 (mmm) cc_final: 0.6717 (mmm)
  outliers start: 14
  outliers final: 9
  residues processed: 66
  average time/residue: 0.2449
  time to fit residues: 20.2553
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  : 0.700 
-------------------------------------------------------------------------------
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  104 LEU
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  486 VAL
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 7 optimal weight:    0.0980
   chunk 45 optimal weight:    0.0570
   chunk 18 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.144459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.097538 restraints weight = 12641.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 4.32
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3309
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3309 r_free = 0.3309    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3309
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4983  Z= 0.241
  Angle     :  0.589   9.468   6747  Z= 0.290
  Chirality :  0.041   0.144    737
  Planarity :  0.004   0.051    873
  Dihedral  :  4.638  38.174    664
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.18 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.37), residues: 594
  helix:  1.70 (0.34), residues: 258
  sheet:  1.01 (0.64), residues: 81
  loop : -0.37 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  93 
 HIS   0.001   0.000   HIS C 420 
 PHE   0.009   0.001   PHE C 522 
 TYR   0.025   0.001   TYR A 145 
 ARG   0.011   0.001   ARG A 143 

*********************** 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
  68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.9029 (m) cc_final: 0.8677 (t)
REVERT: A   92 GLN cc_start: 0.7530 (mt0) cc_final: 0.7077 (mt0)
REVERT: A   99 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7158 (tp)
REVERT: A  104 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6900 (tt)
REVERT: A  114 ASN cc_start: 0.7856 (t0) cc_final: 0.7132 (t0)
REVERT: A  144 LYS cc_start: 0.8282 (pptt) cc_final: 0.7998 (tmmt)
REVERT: B   43 LEU cc_start: 0.8365 (tt) cc_final: 0.7987 (mm)
REVERT: B   67 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5717 (tp)
REVERT: C  294 MET cc_start: 0.7085 (mmm) cc_final: 0.6729 (mmm)
  outliers start: 14
  outliers final: 10
  residues processed: 63
  average time/residue: 0.2177
  time to fit residues: 17.2566
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  : 0.536 
-------------------------------------------------------------------------------
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  104 LEU
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  486 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 14 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0570
   chunk 53 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3914 r_free = 0.3914 target = 0.139865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.093386 restraints weight = 11009.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 4.24
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3247
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4983  Z= 0.232
  Angle     :  0.574   8.350   6747  Z= 0.283
  Chirality :  0.041   0.129    737
  Planarity :  0.004   0.053    873
  Dihedral  :  4.707  38.155    664
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 14.00 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.37), residues: 594
  helix:  1.73 (0.34), residues: 258
  sheet:  0.98 (0.64), residues: 81
  loop : -0.38 (0.42), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  93 
 HIS   0.001   0.000   HIS A  55 
 PHE   0.009   0.001   PHE C 522 
 TYR   0.028   0.001   TYR A 145 
 ARG   0.008   0.001   ARG A  72 

********************** 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
  68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 SER cc_start: 0.9089 (m) cc_final: 0.8736 (t)
REVERT: A   92 GLN cc_start: 0.7433 (mt0) cc_final: 0.6956 (mt0)
REVERT: A   99 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7140 (tp)
REVERT: A  104 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6835 (tt)
REVERT: A  114 ASN cc_start: 0.7859 (t0) cc_final: 0.7134 (t0)
REVERT: B   43 LEU cc_start: 0.8351 (tt) cc_final: 0.7972 (mm)
REVERT: B   67 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5595 (tp)
REVERT: C  294 MET cc_start: 0.7102 (mmm) cc_final: 0.6735 (mmm)
  outliers start: 13
  outliers final: 10
  residues processed: 64
  average time/residue: 0.2388
  time to fit residues: 19.3605
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  : 0.627 
-------------------------------------------------------------------------------
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  104 LEU
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  486 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 21 optimal weight:    0.0770
   chunk 53 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0870
   chunk 23 optimal weight:    0.0970
   chunk 32 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.1914

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.145762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.097998 restraints weight = 18072.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 5.70
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3402
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3402 r_free = 0.3402    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3402 r_free = 0.3402    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3402
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4983  Z= 0.132
  Angle     :  0.529   8.486   6747  Z= 0.260
  Chirality :  0.040   0.132    737
  Planarity :  0.004   0.053    873
  Dihedral  :  4.555  38.397    664
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 15.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.37), residues: 594
  helix:  1.92 (0.34), residues: 257
  sheet:  1.00 (0.65), residues: 80
  loop : -0.30 (0.42), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  93 
 HIS   0.001   0.000   HIS C 371 
 PHE   0.006   0.001   PHE C 428 
 TYR   0.022   0.001   TYR A 145 
 ARG   0.008   0.001   ARG A  72 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 2701.70 seconds
wall clock time: 49 minutes 2.54 seconds (2942.54 seconds total)