Starting phenix.real_space_refine
on Thu Mar  6 07:17:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d8q_27254/03_2025/8d8q_27254.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d8q_27254/03_2025/8d8q_27254.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d8q_27254/03_2025/8d8q_27254.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d8q_27254/03_2025/8d8q_27254.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d8q_27254/03_2025/8d8q_27254.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d8q_27254/03_2025/8d8q_27254.cif"
  }
  resolution = 4.2
  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=   0.044
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      27      5.16       5
     C    3291      2.51       5
     N     874      2.21       5
     O    1010      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5202
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "H"
      Number of atoms: 996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 996
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 5, 'TRANS': 124}
    Chain: "L"
      Number of atoms: 883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 883
          Classifications: {'peptide': 114}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108}
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 832
          Classifications: {'peptide': 109}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102}
    Chain: "C"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 941
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.49, per 1000 atoms: 1.25
  Number of scatterers: 5202
  At special positions: 0
  Unit cell: (77.996, 94.86, 102.238, 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      27     16.00
     O    1010      8.00
     N     874      7.00
     C    3291      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.12
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.12
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  97 " - pdb=" SG  CYS C 102 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 593.9 milliseconds
  

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 15 sheets defined
      11.4% alpha, 36.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'L' and resid 30B through 30F
      removed outlier: 4.153A  pdb=" N   LYS L  30F" --> pdb=" O   SER L  30C" (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 385 through 390
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.089A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'B' and resid 30 through 31
      No H-bonds generated for 'chain 'B' and resid 30 through 31'
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 3.540A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 64
    Processing helix  chain 'C' and resid 83 through 87
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.826A  pdb=" N   MET H  34 " --> pdb=" O   ARG H  50 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ARG H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.707A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13
    Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.587A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.544A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.551A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.551A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   THR B  97 " --> pdb=" O   HIS B  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 6
    Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.116A  pdb=" N   ARG C  38 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   TRP C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12

    205 hydrogen bonds defined for protein.
    456 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: 1.47

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1000
        1.32 -     1.45: 1457
        1.45 -     1.57: 2834
        1.57 -     1.70: 0
        1.70 -     1.82: 36
  Bond restraints: 5327
  Sorted by residual:
  bond pdb=" CB  TYR L  91 "
       pdb=" CG  TYR L  91 "
    ideal  model  delta    sigma   weight residual
    1.512  1.449  0.063 2.20e-02 2.07e+03 8.16e+00
  bond pdb=" CG  ASP H  58 "
       pdb=" OD1 ASP H  58 "
    ideal  model  delta    sigma   weight residual
    1.249  1.198  0.051 1.90e-02 2.77e+03 7.25e+00
  bond pdb=" CB  ASN A 422 "
       pdb=" CG  ASN A 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.450  0.066 2.50e-02 1.60e+03 7.04e+00
  bond pdb=" CB  LEU A 455 "
       pdb=" CG  LEU A 455 "
    ideal  model  delta    sigma   weight residual
    1.530  1.479  0.051 2.00e-02 2.50e+03 6.51e+00
  bond pdb=" CD  GLU H   6 "
       pdb=" OE2 GLU H   6 "
    ideal  model  delta    sigma   weight residual
    1.249  1.201  0.048 1.90e-02 2.77e+03 6.40e+00
  ... (remaining 5322 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 6105
        1.55 -     3.10: 917
        3.10 -     4.66: 155
        4.66 -     6.21: 41
        6.21 -     7.76: 10
  Bond angle restraints: 7228
  Sorted by residual:
  angle pdb=" C   GLN L  42 "
        pdb=" N   PRO L  43 "
        pdb=" CA  PRO L  43 "
      ideal   model   delta    sigma   weight residual
     119.66  126.03   -6.37 7.20e-01 1.93e+00 7.82e+01
  angle pdb=" C   GLY C   8 "
        pdb=" N   PRO C   9 "
        pdb=" CA  PRO C   9 "
      ideal   model   delta    sigma   weight residual
     119.78  127.54   -7.76 1.03e+00 9.43e-01 5.68e+01
  angle pdb=" C   GLY H 104 "
        pdb=" N   PRO H 105 "
        pdb=" CA  PRO H 105 "
      ideal   model   delta    sigma   weight residual
     119.56  126.58   -7.02 1.01e+00 9.80e-01 4.83e+01
  angle pdb=" C   ILE B  58 "
        pdb=" N   PRO B  59 "
        pdb=" CA  PRO B  59 "
      ideal   model   delta    sigma   weight residual
     119.78  126.73   -6.95 1.03e+00 9.43e-01 4.55e+01
  angle pdb=" C   SER A 383 "
        pdb=" N   PRO A 384 "
        pdb=" CA  PRO A 384 "
      ideal   model   delta    sigma   weight residual
     119.47  127.11   -7.64 1.16e+00 7.43e-01 4.34e+01
  ... (remaining 7223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 3013
       16.62 -    33.25: 85
       33.25 -    49.87: 24
       49.87 -    66.49: 18
       66.49 -    83.11: 8
  Dihedral angle restraints: 3148
    sinusoidal: 1232
      harmonic: 1916
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.82  -52.82     1      1.00e+01 1.00e-02 3.80e+01
  dihedral pdb=" CB  CYS C  22 "
           pdb=" SG  CYS C  22 "
           pdb=" SG  CYS C  92 "
           pdb=" CB  CYS C  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.71   36.29     1      1.00e+01 1.00e-02 1.86e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  125.01  -32.01     1      1.00e+01 1.00e-02 1.46e+01
  ... (remaining 3145 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 421
       0.037 -    0.075: 238
       0.075 -    0.112: 88
       0.112 -    0.150: 24
       0.150 -    0.187: 9
  Chirality restraints: 780
  Sorted by residual:
  chirality pdb=" CA  VAL C  37 "
            pdb=" N   VAL C  37 "
            pdb=" C   VAL C  37 "
            pdb=" CB  VAL C  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 8.73e-01
  chirality pdb=" CA  ILE L  75 "
            pdb=" N   ILE L  75 "
            pdb=" C   ILE L  75 "
            pdb=" CB  ILE L  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 7.70e-01
  chirality pdb=" CA  TYR A 421 "
            pdb=" N   TYR A 421 "
            pdb=" C   TYR A 421 "
            pdb=" CB  TYR A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.17e-01
  ... (remaining 777 not shown)

  Planarity restraints: 928
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 489 "    0.030 2.00e-02 2.50e+03   1.63e-02 5.34e+00
        pdb=" CG  TYR A 489 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 489 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 489 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 489 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 489 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 489 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 489 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  32 "    0.027 2.00e-02 2.50e+03   1.62e-02 5.27e+00
        pdb=" CG  TYR L  32 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  32 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  32 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  32 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  32 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  32 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR L  32 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 449 "   -0.025 2.00e-02 2.50e+03   1.37e-02 3.74e+00
        pdb=" CG  TYR A 449 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 449 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 449 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 449 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 449 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 449 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 449 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 925 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 157
        2.69 -     3.24: 4892
        3.24 -     3.80: 8245
        3.80 -     4.35: 11033
        4.35 -     4.90: 18057
  Nonbonded interactions: 42384
  Sorted by model distance:
  nonbonded pdb=" N   TYR L  49 "
            pdb=" CD1 TYR L  49 "
     model   vdw
     2.139 3.420
  nonbonded pdb=" O   LYS H 111 "
            pdb=" OH  TYR H 114 "
     model   vdw
     2.458 3.040
  nonbonded pdb=" O   TYR L  30A"
            pdb=" N   SER L  30C"
     model   vdw
     2.487 3.120
  nonbonded pdb=" O   SER L  93 "
            pdb=" OG1 THR L  94 "
     model   vdw
     2.490 3.040
  nonbonded pdb=" OE1 GLU A 340 "
            pdb=" NZ  LYS A 356 "
     model   vdw
     2.498 3.120
  ... (remaining 42379 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             7.740
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.440
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
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      :  0.012   0.066   5327  Z= 0.732
  Angle     :  1.230   7.760   7228  Z= 0.851
  Chirality :  0.054   0.187    780
  Planarity :  0.005   0.027    927
  Dihedral  : 11.021  83.112   1917
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 1.66
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  1.52 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  1.06 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.35), residues: 659
  helix: -4.41 (0.31), residues: 33
  sheet:  1.24 (0.31), residues: 256
  loop :  2.53 (0.36), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.005   TRP A 436 
 HIS   0.003   0.001   HIS B  90 
 PHE   0.015   0.004   PHE H  67 
 TYR   0.030   0.005   TYR A 489 
 ARG   0.002   0.000   ARG H  66 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 231
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   67 PHE cc_start: 0.6548 (m-80) cc_final: 0.5847 (m-80)
REVERT: H  120 LEU cc_start: 0.8426 (tp) cc_final: 0.7602 (pp)
REVERT: L    3 VAL cc_start: 0.8346 (t) cc_final: 0.8091 (m)
REVERT: L   46 LEU cc_start: 0.8987 (tp) cc_final: 0.8671 (tp)
REVERT: L   72 THR cc_start: 0.7216 (m) cc_final: 0.6987 (m)
REVERT: L   78 LEU cc_start: 0.8328 (tp) cc_final: 0.7927 (tp)
REVERT: L   85 ILE cc_start: 0.8790 (mm) cc_final: 0.8154 (tp)
REVERT: A  355 ARG cc_start: 0.7939 (ttt90) cc_final: 0.7329 (ttp-170)
REVERT: A  461 LEU cc_start: 0.8715 (mt) cc_final: 0.8506 (mp)
REVERT: B   14 SER cc_start: 0.8112 (m) cc_final: 0.7637 (t)
REVERT: B   36 TYR cc_start: 0.7400 (m-80) cc_final: 0.6903 (m-80)
REVERT: B   46 LEU cc_start: 0.8577 (tp) cc_final: 0.8179 (tp)
REVERT: B   47 LEU cc_start: 0.7761 (mp) cc_final: 0.7494 (mt)
REVERT: C   18 VAL cc_start: 0.8846 (p) cc_final: 0.8563 (p)
REVERT: C   36 TRP cc_start: 0.8957 (m100) cc_final: 0.8585 (m100)
REVERT: C   46 GLU cc_start: 0.8174 (tt0) cc_final: 0.7843 (tp30)
REVERT: C   51 ILE cc_start: 0.8990 (tt) cc_final: 0.8760 (tt)
REVERT: C   70 THR cc_start: 0.8531 (p) cc_final: 0.8182 (t)
REVERT: C   72 ASP cc_start: 0.8597 (t0) cc_final: 0.7883 (t70)
  outliers start: 3
  outliers final: 2
  residues processed: 233
  average time/residue: 0.2214
  time to fit residues: 62.2889
Evaluate side-chains
  121 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 119
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    0.0770
   chunk 49 optimal weight:    5.9990
   chunk 27 optimal weight:    0.4980
   chunk 16 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.096196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.082796 restraints weight = 17831.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.085218 restraints weight = 10198.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.086918 restraints weight = 6848.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   5327  Z= 0.190
  Angle     :  0.643   9.805   7228  Z= 0.348
  Chirality :  0.048   0.293    780
  Planarity :  0.005   0.039    927
  Dihedral  :  4.954  19.009    759
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.12 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.48 %
    Favored  : 97.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  1.20 (0.33), residues: 659
  helix: -3.82 (0.58), residues: 33
  sheet:  0.59 (0.32), residues: 238
  loop :  1.62 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H 115 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.020   0.002   PHE C  29 
 TYR   0.017   0.002   TYR L  49 
 ARG   0.008   0.001   ARG A 403 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.7990 (mmm) cc_final: 0.7692 (mmm)
REVERT: H   39 GLN cc_start: 0.7773 (pp30) cc_final: 0.7322 (pp30)
REVERT: H   43 LYS cc_start: 0.8494 (mptt) cc_final: 0.8259 (mmtm)
REVERT: H   46 GLU cc_start: 0.8228 (tt0) cc_final: 0.7738 (tt0)
REVERT: H  111 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7696 (mttt)
REVERT: H  113 ASP cc_start: 0.7078 (t70) cc_final: 0.6576 (p0)
REVERT: H  120 LEU cc_start: 0.8510 (tp) cc_final: 0.7732 (pp)
REVERT: L    3 VAL cc_start: 0.8206 (t) cc_final: 0.7980 (m)
REVERT: L   15 LEU cc_start: 0.8278 (mt) cc_final: 0.7642 (mt)
REVERT: L   58 VAL cc_start: 0.8451 (t) cc_final: 0.8232 (p)
REVERT: L   85 ILE cc_start: 0.8678 (mm) cc_final: 0.7870 (tp)
REVERT: L  103 LYS cc_start: 0.8586 (tttt) cc_final: 0.8019 (tptm)
REVERT: A  355 ARG cc_start: 0.7436 (ttt90) cc_final: 0.7158 (ttp-170)
REVERT: A  398 ASP cc_start: 0.8515 (m-30) cc_final: 0.8297 (m-30)
REVERT: A  402 ILE cc_start: 0.8755 (pt) cc_final: 0.8470 (pt)
REVERT: A  422 ASN cc_start: 0.8890 (m-40) cc_final: 0.8108 (m-40)
REVERT: B   14 SER cc_start: 0.7998 (m) cc_final: 0.7648 (t)
REVERT: B   49 TYR cc_start: 0.7439 (p90) cc_final: 0.7223 (p90)
REVERT: B   65 SER cc_start: 0.8298 (t) cc_final: 0.7912 (t)
REVERT: B  105 GLU cc_start: 0.4417 (tp30) cc_final: 0.4181 (tp30)
REVERT: C    4 LEU cc_start: 0.8161 (mt) cc_final: 0.7646 (mt)
REVERT: C   18 VAL cc_start: 0.8805 (p) cc_final: 0.8166 (p)
REVERT: C   46 GLU cc_start: 0.8237 (tt0) cc_final: 0.7805 (tp30)
REVERT: C   70 THR cc_start: 0.8583 (p) cc_final: 0.8282 (t)
REVERT: C   72 ASP cc_start: 0.8539 (t0) cc_final: 0.7849 (t70)
REVERT: C   82 LEU cc_start: 0.7947 (tp) cc_final: 0.7606 (tp)
REVERT: C   85 GLU cc_start: 0.8166 (pm20) cc_final: 0.7850 (pm20)
REVERT: C   91 TYR cc_start: 0.9008 (m-80) cc_final: 0.8760 (m-10)
REVERT: C  104 ASP cc_start: 0.8318 (m-30) cc_final: 0.8102 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1933
  time to fit residues: 44.5748
Evaluate side-chains
  125 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 60 optimal weight:    8.9990
   chunk 54 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
** H  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 ASN
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.094633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.081308 restraints weight = 18198.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.083683 restraints weight = 10440.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.085314 restraints weight = 7055.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.4301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   5327  Z= 0.207
  Angle     :  0.608   8.365   7228  Z= 0.330
  Chirality :  0.046   0.253    780
  Planarity :  0.005   0.040    927
  Dihedral  :  4.682  18.969    759
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  2.43 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.77 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  0.78 (0.33), residues: 659
  helix: -3.65 (0.62), residues: 33
  sheet:  0.55 (0.32), residues: 237
  loop :  1.09 (0.33), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 353 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.031   0.002   PHE H  67 
 TYR   0.021   0.002   TYR L  91 
 ARG   0.006   0.001   ARG A 403 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8093 (mmm) cc_final: 0.7698 (mmm)
REVERT: H   39 GLN cc_start: 0.7896 (pp30) cc_final: 0.7286 (pp30)
REVERT: H   43 LYS cc_start: 0.8518 (mptt) cc_final: 0.8277 (mmtm)
REVERT: H   46 GLU cc_start: 0.8071 (tt0) cc_final: 0.7667 (tt0)
REVERT: H   75 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8471 (mmtt)
REVERT: H  120 LEU cc_start: 0.8636 (tp) cc_final: 0.7915 (pp)
REVERT: L    3 VAL cc_start: 0.8042 (t) cc_final: 0.7815 (m)
REVERT: L   48 MET cc_start: 0.7237 (tpp) cc_final: 0.6604 (mmm)
REVERT: L   58 VAL cc_start: 0.7895 (t) cc_final: 0.7654 (p)
REVERT: L   85 ILE cc_start: 0.8751 (mm) cc_final: 0.8128 (pt)
REVERT: A  355 ARG cc_start: 0.7700 (ttt90) cc_final: 0.7290 (ttp-170)
REVERT: A  357 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7725 (ttm170)
REVERT: A  402 ILE cc_start: 0.8773 (pt) cc_final: 0.8459 (pt)
REVERT: C   46 GLU cc_start: 0.8284 (tt0) cc_final: 0.7987 (tt0)
REVERT: C   47 TRP cc_start: 0.8483 (t60) cc_final: 0.8201 (t60)
REVERT: C   70 THR cc_start: 0.8578 (p) cc_final: 0.8219 (t)
REVERT: C   71 ARG cc_start: 0.7380 (ppt170) cc_final: 0.7094 (ppt170)
REVERT: C   72 ASP cc_start: 0.8620 (t0) cc_final: 0.7888 (t70)
REVERT: C   86 ASP cc_start: 0.7200 (m-30) cc_final: 0.6914 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1902
  time to fit residues: 38.6140
Evaluate side-chains
  110 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 52 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 39 optimal weight:    0.0870
   chunk 13 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 HIS
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.089228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.075985 restraints weight = 18759.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.078158 restraints weight = 10871.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.079708 restraints weight = 7501.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   5327  Z= 0.328
  Angle     :  0.679   8.180   7228  Z= 0.371
  Chirality :  0.049   0.302    780
  Planarity :  0.005   0.047    927
  Dihedral  :  5.062  17.687    759
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.19 %
    Favored  : 96.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  0.26 (0.33), residues: 659
  helix: -3.78 (0.73), residues: 27
  sheet:  0.26 (0.31), residues: 255
  loop :  0.59 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP B  96 
 HIS   0.004   0.002   HIS B  90 
 PHE   0.025   0.002   PHE A 374 
 TYR   0.039   0.002   TYR H  99 
 ARG   0.005   0.001   ARG H  19 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   39 GLN cc_start: 0.8004 (pp30) cc_final: 0.7406 (pp30)
REVERT: L    3 VAL cc_start: 0.8144 (t) cc_final: 0.7930 (m)
REVERT: L   30 LEU cc_start: 0.8557 (tp) cc_final: 0.8236 (tp)
REVERT: L   30 TYR cc_start: 0.7996 (t80) cc_final: 0.7633 (t80)
REVERT: L   85 ILE cc_start: 0.8734 (mm) cc_final: 0.8109 (pt)
REVERT: L  103 LYS cc_start: 0.8669 (tttt) cc_final: 0.8296 (ttpt)
REVERT: A  355 ARG cc_start: 0.7620 (ttt90) cc_final: 0.7195 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8978 (pt) cc_final: 0.8709 (pt)
REVERT: A  455 LEU cc_start: 0.8413 (tp) cc_final: 0.8134 (tp)
REVERT: B   46 LEU cc_start: 0.8474 (tp) cc_final: 0.8238 (tp)
REVERT: B   95 ARG cc_start: 0.8338 (mpt-90) cc_final: 0.8101 (mtt-85)
REVERT: C   46 GLU cc_start: 0.8157 (tt0) cc_final: 0.7782 (tt0)
REVERT: C   47 TRP cc_start: 0.8833 (t60) cc_final: 0.8592 (t60)
REVERT: C   72 ASP cc_start: 0.8593 (t0) cc_final: 0.7699 (t70)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1912
  time to fit residues: 34.7274
Evaluate side-chains
  106 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 47 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 7 optimal weight:    8.9990
   chunk 61 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 49 optimal weight:    0.5980
   chunk 13 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 14 optimal weight:   20.0000
   overall best weight:    3.2986

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

Flipped N/Q/H residues before XYZ refinement:
L  30EASN
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 HIS
C  56 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.088605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.075445 restraints weight = 18472.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.077663 restraints weight = 10791.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.079166 restraints weight = 7413.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.5382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   5327  Z= 0.325
  Angle     :  0.675  11.191   7228  Z= 0.367
  Chirality :  0.048   0.338    780
  Planarity :  0.005   0.043    927
  Dihedral  :  5.228  17.556    759
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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:  0.02 (0.32), residues: 659
  helix: -3.87 (0.64), residues: 27
  sheet:  0.34 (0.32), residues: 253
  loop :  0.21 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  96 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.020   0.002   PHE A 374 
 TYR   0.033   0.002   TYR H  99 
 ARG   0.007   0.001   ARG B  24 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   32 VAL cc_start: 0.8945 (t) cc_final: 0.8736 (t)
REVERT: H   34 MET cc_start: 0.7903 (mmm) cc_final: 0.7645 (mmm)
REVERT: H   39 GLN cc_start: 0.7795 (pp30) cc_final: 0.6943 (pp30)
REVERT: H   46 GLU cc_start: 0.8145 (tt0) cc_final: 0.7576 (tt0)
REVERT: H   67 PHE cc_start: 0.7163 (m-80) cc_final: 0.6537 (m-80)
REVERT: H  114 TYR cc_start: 0.7520 (m-10) cc_final: 0.7252 (m-10)
REVERT: L   30 TYR cc_start: 0.8333 (t80) cc_final: 0.8003 (t80)
REVERT: L   33 LEU cc_start: 0.9152 (tp) cc_final: 0.8901 (tp)
REVERT: L   85 ILE cc_start: 0.8781 (mm) cc_final: 0.8016 (tp)
REVERT: A  355 ARG cc_start: 0.7582 (ttt90) cc_final: 0.7218 (ttp-170)
REVERT: A  402 ILE cc_start: 0.8951 (pt) cc_final: 0.8678 (pt)
REVERT: A  455 LEU cc_start: 0.8445 (tp) cc_final: 0.8178 (tp)
REVERT: B   46 LEU cc_start: 0.8406 (tp) cc_final: 0.8112 (tp)
REVERT: B  100 GLN cc_start: 0.8047 (pp30) cc_final: 0.7841 (pm20)
REVERT: C   46 GLU cc_start: 0.8195 (tt0) cc_final: 0.7887 (tt0)
REVERT: C   72 ASP cc_start: 0.8690 (t0) cc_final: 0.7723 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1879
  time to fit residues: 31.7691
Evaluate side-chains
  97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 4 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
L  30DASN
L  37 GLN
L  89 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.091222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.077973 restraints weight = 18212.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.080257 restraints weight = 10523.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.081825 restraints weight = 7146.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.5548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5327  Z= 0.172
  Angle     :  0.599   9.520   7228  Z= 0.324
  Chirality :  0.046   0.224    780
  Planarity :  0.004   0.045    927
  Dihedral  :  4.848  21.753    759
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.32), residues: 659
  helix: -3.87 (0.62), residues: 27
  sheet:  0.39 (0.33), residues: 244
  loop :  0.11 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  50 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.016   0.001   PHE A 374 
 TYR   0.024   0.001   TYR H  99 
 ARG   0.006   0.001   ARG H  30 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8139 (mmm) cc_final: 0.7760 (mmm)
REVERT: H   39 GLN cc_start: 0.7985 (pp30) cc_final: 0.7192 (pp30)
REVERT: H   46 GLU cc_start: 0.8103 (tt0) cc_final: 0.7500 (tt0)
REVERT: H   82 MET cc_start: 0.8243 (mmm) cc_final: 0.7905 (mmm)
REVERT: H   82 ASN cc_start: 0.8458 (m-40) cc_final: 0.8251 (p0)
REVERT: L   30 TYR cc_start: 0.8275 (t80) cc_final: 0.7858 (t80)
REVERT: A  355 ARG cc_start: 0.7455 (ttt90) cc_final: 0.7202 (ttp-170)
REVERT: A  378 LYS cc_start: 0.8703 (tptp) cc_final: 0.8175 (tptp)
REVERT: A  402 ILE cc_start: 0.8829 (pt) cc_final: 0.8599 (pt)
REVERT: A  455 LEU cc_start: 0.8334 (tp) cc_final: 0.8133 (tp)
REVERT: A  468 ILE cc_start: 0.9051 (pt) cc_final: 0.8508 (mm)
REVERT: B   46 LEU cc_start: 0.8281 (tp) cc_final: 0.8053 (tp)
REVERT: C   10 GLU cc_start: 0.7340 (pp20) cc_final: 0.7133 (pp20)
REVERT: C   44 ARG cc_start: 0.8523 (ptt90) cc_final: 0.8299 (mtm110)
REVERT: C   46 GLU cc_start: 0.8302 (tt0) cc_final: 0.8012 (tt0)
REVERT: C   72 ASP cc_start: 0.8550 (t0) cc_final: 0.7494 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1818
  time to fit residues: 31.2755
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    0.4980
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0170
   chunk 15 optimal weight:   10.0000
   chunk 1 optimal weight:    0.6980
   chunk 14 optimal weight:    8.9990
   chunk 56 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 43 optimal weight:    9.9990
   overall best weight:    0.5620

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

Flipped N/Q/H residues before XYZ refinement:
** L  30DASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.092551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.079410 restraints weight = 18008.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.081661 restraints weight = 10504.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.083269 restraints weight = 7118.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.5777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5327  Z= 0.167
  Angle     :  0.567   7.447   7228  Z= 0.309
  Chirality :  0.045   0.166    780
  Planarity :  0.004   0.043    927
  Dihedral  :  4.648  22.280    759
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.32), residues: 659
  helix: -3.93 (0.63), residues: 27
  sheet:  0.40 (0.33), residues: 240
  loop :  0.07 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 353 
 HIS   0.000   0.000   HIS B  90 
 PHE   0.010   0.001   PHE A 400 
 TYR   0.023   0.002   TYR C  59 
 ARG   0.007   0.001   ARG A 357 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8188 (mmm) cc_final: 0.7771 (mmm)
REVERT: H   39 GLN cc_start: 0.7934 (pp30) cc_final: 0.7041 (pp30)
REVERT: H   46 GLU cc_start: 0.8039 (tt0) cc_final: 0.7517 (tt0)
REVERT: H   82 ASN cc_start: 0.8490 (m-40) cc_final: 0.8104 (p0)
REVERT: L   30 TYR cc_start: 0.8245 (t80) cc_final: 0.7739 (t80)
REVERT: L   33 LEU cc_start: 0.9110 (tp) cc_final: 0.8848 (tp)
REVERT: L   85 ILE cc_start: 0.8591 (mm) cc_final: 0.7650 (tt)
REVERT: L  103 LYS cc_start: 0.8528 (tttt) cc_final: 0.8023 (tptt)
REVERT: A  402 ILE cc_start: 0.8879 (pt) cc_final: 0.8611 (pt)
REVERT: A  455 LEU cc_start: 0.8431 (tp) cc_final: 0.8222 (tp)
REVERT: A  468 ILE cc_start: 0.9087 (pt) cc_final: 0.8522 (mm)
REVERT: B   46 LEU cc_start: 0.8342 (tp) cc_final: 0.7927 (pt)
REVERT: C   44 ARG cc_start: 0.8452 (ptt90) cc_final: 0.8241 (ptt90)
REVERT: C   46 GLU cc_start: 0.8298 (tt0) cc_final: 0.7835 (tt0)
REVERT: C   58 ASN cc_start: 0.7443 (m-40) cc_final: 0.7076 (t0)
REVERT: C   70 THR cc_start: 0.8240 (p) cc_final: 0.7880 (t)
REVERT: C   72 ASP cc_start: 0.8594 (t0) cc_final: 0.7736 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 137
  average time/residue: 0.1800
  time to fit residues: 31.5270
Evaluate side-chains
  102 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 15 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
L  30DASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.090037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.076830 restraints weight = 18461.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.078995 restraints weight = 10820.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.080484 restraints weight = 7453.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.6005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5327  Z= 0.227
  Angle     :  0.605   6.946   7228  Z= 0.330
  Chirality :  0.047   0.284    780
  Planarity :  0.004   0.042    927
  Dihedral  :  4.779  22.263    759
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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: -0.16 (0.32), residues: 659
  helix: -3.95 (0.65), residues: 27
  sheet:  0.49 (0.34), residues: 230
  loop : -0.11 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP H 115 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.018   0.002   PHE B  71 
 TYR   0.020   0.002   TYR H  99 
 ARG   0.009   0.001   ARG B  61 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.8082 (tt0) cc_final: 0.7483 (tt0)
REVERT: L   30 TYR cc_start: 0.8288 (t80) cc_final: 0.7841 (t80)
REVERT: L   33 LEU cc_start: 0.9195 (tp) cc_final: 0.8957 (tp)
REVERT: L  103 LYS cc_start: 0.8533 (tttt) cc_final: 0.7951 (tptt)
REVERT: A  402 ILE cc_start: 0.8955 (pt) cc_final: 0.8688 (pt)
REVERT: A  455 LEU cc_start: 0.8425 (tp) cc_final: 0.8180 (tp)
REVERT: B   36 TYR cc_start: 0.8526 (m-80) cc_final: 0.8301 (m-10)
REVERT: B   71 PHE cc_start: 0.7716 (m-10) cc_final: 0.7378 (m-80)
REVERT: B   77 ARG cc_start: 0.6242 (ptm-80) cc_final: 0.5814 (ptm-80)
REVERT: B   87 TYR cc_start: 0.8260 (m-80) cc_final: 0.7989 (m-10)
REVERT: C   10 GLU cc_start: 0.7762 (pp20) cc_final: 0.7177 (pp20)
REVERT: C   46 GLU cc_start: 0.8137 (tt0) cc_final: 0.7614 (tt0)
REVERT: C   70 THR cc_start: 0.8268 (p) cc_final: 0.7790 (t)
REVERT: C   72 ASP cc_start: 0.8515 (t0) cc_final: 0.7610 (t70)
REVERT: C   73 MET cc_start: 0.7051 (pmm) cc_final: 0.6710 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1755
  time to fit residues: 27.7130
Evaluate side-chains
  92 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 22 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
** L  30DASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.091485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.078037 restraints weight = 18507.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.080277 restraints weight = 11005.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.081869 restraints weight = 7571.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.6129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5327  Z= 0.179
  Angle     :  0.583   6.890   7228  Z= 0.317
  Chirality :  0.044   0.165    780
  Planarity :  0.005   0.074    927
  Dihedral  :  4.832  25.259    759
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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: -0.13 (0.33), residues: 659
  helix: -3.91 (0.66), residues: 27
  sheet:  0.52 (0.34), residues: 231
  loop : -0.10 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H 115 
 HIS   0.001   0.000   HIS B  90 
 PHE   0.015   0.001   PHE B  71 
 TYR   0.018   0.001   TYR H  99 
 ARG   0.008   0.001   ARG A 357 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   19 ARG cc_start: 0.6183 (ttp80) cc_final: 0.5763 (ttp80)
REVERT: H   46 GLU cc_start: 0.7924 (tt0) cc_final: 0.7392 (tt0)
REVERT: H   82 ASN cc_start: 0.8440 (m-40) cc_final: 0.8130 (p0)
REVERT: H  120 LEU cc_start: 0.8895 (tp) cc_final: 0.8050 (pp)
REVERT: L   30 TYR cc_start: 0.8321 (t80) cc_final: 0.7828 (t80)
REVERT: L   33 LEU cc_start: 0.9160 (tp) cc_final: 0.8937 (tp)
REVERT: L   70 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: L   85 ILE cc_start: 0.8562 (mm) cc_final: 0.7867 (tp)
REVERT: L  103 LYS cc_start: 0.8538 (tttt) cc_final: 0.8009 (tptt)
REVERT: A  402 ILE cc_start: 0.8947 (pt) cc_final: 0.8675 (pt)
REVERT: A  455 LEU cc_start: 0.8455 (tp) cc_final: 0.8183 (tp)
REVERT: B   36 TYR cc_start: 0.8561 (m-80) cc_final: 0.8283 (m-10)
REVERT: B   46 LEU cc_start: 0.8138 (tp) cc_final: 0.7916 (tp)
REVERT: C   10 GLU cc_start: 0.7767 (pp20) cc_final: 0.7097 (pp20)
REVERT: C   46 GLU cc_start: 0.8207 (tt0) cc_final: 0.7520 (tt0)
REVERT: C   70 THR cc_start: 0.8423 (p) cc_final: 0.7930 (t)
REVERT: C   72 ASP cc_start: 0.8746 (t0) cc_final: 0.7773 (t70)
REVERT: C   73 MET cc_start: 0.7100 (pmm) cc_final: 0.6826 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1801
  time to fit residues: 28.6542
Evaluate side-chains
  97 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 24 optimal weight:    0.4980
   chunk 20 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0570
   chunk 30 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    2.5104

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

Flipped N/Q/H residues before XYZ refinement:
** L  30DASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.088345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.074917 restraints weight = 19138.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.076999 restraints weight = 11532.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.078415 restraints weight = 8113.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.6359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5327  Z= 0.270
  Angle     :  0.642   5.738   7228  Z= 0.345
  Chirality :  0.046   0.150    780
  Planarity :  0.005   0.058    927
  Dihedral  :  5.092  24.839    759
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    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: -0.37 (0.32), residues: 659
  helix: -3.98 (0.64), residues: 27
  sheet:  0.46 (0.34), residues: 231
  loop : -0.35 (0.31), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP C  50 
 HIS   0.004   0.002   HIS B  90 
 PHE   0.023   0.002   PHE H  67 
 TYR   0.027   0.002   TYR H  99 
 ARG   0.016   0.001   ARG A 357 

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

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

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1318 Ramachandran restraints generated.
    659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   46 GLU cc_start: 0.7940 (tt0) cc_final: 0.7305 (tt0)
REVERT: H   79 TYR cc_start: 0.7219 (m-80) cc_final: 0.7016 (m-80)
REVERT: L   30 TYR cc_start: 0.8362 (t80) cc_final: 0.7907 (t80)
REVERT: L   33 LEU cc_start: 0.9246 (tp) cc_final: 0.9013 (tp)
REVERT: L  103 LYS cc_start: 0.8502 (tttt) cc_final: 0.7942 (tptt)
REVERT: A  402 ILE cc_start: 0.8997 (pt) cc_final: 0.8736 (pt)
REVERT: A  455 LEU cc_start: 0.8497 (tp) cc_final: 0.8217 (tp)
REVERT: C   10 GLU cc_start: 0.7834 (pp20) cc_final: 0.7083 (pp20)
REVERT: C   46 GLU cc_start: 0.8088 (tt0) cc_final: 0.7521 (tt0)
REVERT: C   70 THR cc_start: 0.8239 (p) cc_final: 0.7778 (t)
REVERT: C   71 ARG cc_start: 0.7635 (ppt170) cc_final: 0.7353 (ppt170)
REVERT: C   72 ASP cc_start: 0.8673 (t0) cc_final: 0.7800 (t70)
REVERT: C   73 MET cc_start: 0.7119 (pmm) cc_final: 0.6838 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1949
  time to fit residues: 27.9212
Evaluate side-chains
  90 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** L  30DASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.089688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.076285 restraints weight = 18814.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.078461 restraints weight = 11056.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.079995 restraints weight = 7619.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.6433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5327  Z= 0.198
  Angle     :  0.613   8.388   7228  Z= 0.329
  Chirality :  0.045   0.155    780
  Planarity :  0.005   0.057    927
  Dihedral  :  4.990  24.212    759
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.33), residues: 659
  helix: -3.94 (0.65), residues: 27
  sheet:  0.50 (0.35), residues: 232
  loop : -0.35 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C  50 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.019   0.001   PHE B  71 
 TYR   0.017   0.001   TYR B  87 
 ARG   0.014   0.001   ARG A 357 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2241.96 seconds
wall clock time: 39 minutes 45.10 seconds (2385.10 seconds total)