Starting phenix.real_space_refine
on Mon May 12 12:01:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9juj_61827/05_2025/9juj_61827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9juj_61827/05_2025/9juj_61827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9juj_61827/05_2025/9juj_61827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9juj_61827/05_2025/9juj_61827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9juj_61827/05_2025/9juj_61827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9juj_61827/05_2025/9juj_61827.cif"
  }
  resolution = 3.4
  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=   0.003
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      41      5.16       5
     C    5736      2.51       5
     N    1543      2.21       5
     O    1651      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8971
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1165, 8971
          Classifications: {'peptide': 1165}
          Link IDs: {'PTRANS': 30, 'TRANS': 1134}
          Chain breaks: 1
  Time building chain proxies: 5.64, per 1000 atoms: 0.63
  Number of scatterers: 8971
  At special positions: 0
  Unit cell: (106.02, 102.3, 123.69, 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      41     16.00
     O    1651      8.00
     N    1543      7.00
     C    5736      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=0, symmetry=0
  Time building additional restraints: 2.43
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2158

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 6 sheets defined
      66.5% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 34
    Processing helix  chain 'A' and resid 37 through 75
      removed outlier: 4.031A  pdb=" N   LEU A  58 " --> pdb=" O   HIS A  54 " (cutoff:3.500A)
      Proline residue:  A  59  - end of helix
      removed outlier: 3.871A  pdb=" N   ASN A  75 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 133
    Processing helix  chain 'A' and resid 134 through 140
      removed outlier: 3.672A  pdb=" N   PHE A 138 " --> pdb=" O   ASP A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 4.921A  pdb=" N   ALA A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   VAL A 156 " --> pdb=" O   ASN A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 187
    Processing helix  chain 'A' and resid 187 through 236
      Proline residue:  A 199  - end of helix
    Processing helix  chain 'A' and resid 236 through 243
    Processing helix  chain 'A' and resid 245 through 299
    Processing helix  chain 'A' and resid 303 through 347
      Proline residue:  A 326  - end of helix
      removed outlier: 3.557A  pdb=" N   HIS A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
      removed outlier: 3.712A  pdb=" N   ARG A 353 " --> pdb=" O   THR A 350 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ASN A 354 " --> pdb=" O   ILE A 351 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 350 through 354'
    Processing helix  chain 'A' and resid 409 through 417
      removed outlier: 3.751A  pdb=" N   VAL A 413 " --> pdb=" O   LYS A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 445
    Processing helix  chain 'A' and resid 459 through 466
    Processing helix  chain 'A' and resid 472 through 483
      removed outlier: 3.711A  pdb=" N   ALA A 480 " --> pdb=" O   ILE A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 491
    Processing helix  chain 'A' and resid 509 through 523
    Processing helix  chain 'A' and resid 540 through 546
    Processing helix  chain 'A' and resid 678 through 693
      removed outlier: 4.240A  pdb=" N   GLN A 682 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 729
      removed outlier: 3.558A  pdb=" N   TYR A 729 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 785
    Processing helix  chain 'A' and resid 788 through 794
      removed outlier: 3.638A  pdb=" N   PHE A 792 " --> pdb=" O   GLU A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 842
    Processing helix  chain 'A' and resid 845 through 852
    Processing helix  chain 'A' and resid 852 through 869
    Processing helix  chain 'A' and resid 873 through 878
      removed outlier: 4.009A  pdb=" N   HIS A 878 " --> pdb=" O   LEU A 874 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 891
    Processing helix  chain 'A' and resid 891 through 899
    Processing helix  chain 'A' and resid 900 through 954
      Proline residue:  A 914  - end of helix
    Processing helix  chain 'A' and resid 958 through 1001
      Proline residue:  A 984  - end of helix
    Processing helix  chain 'A' and resid 1067 through 1073
      removed outlier: 3.634A  pdb=" N   ILE A1072 " --> pdb=" O   VAL A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1095 through 1100
    Processing helix  chain 'A' and resid 1116 through 1124
      removed outlier: 3.523A  pdb=" N   HIS A1124 " --> pdb=" O   ILE A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1139
    Processing helix  chain 'A' and resid 1141 through 1146
    Processing helix  chain 'A' and resid 1164 through 1180
      removed outlier: 3.660A  pdb=" N   LYS A1180 " --> pdb=" O   ALA A1176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1212
      removed outlier: 3.917A  pdb=" N   ARG A1212 " --> pdb=" O   ALA A1208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1255
      removed outlier: 3.613A  pdb=" N   GLY A1254 " --> pdb=" O   ASN A1250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1255 through 1264
      removed outlier: 3.788A  pdb=" N   MET A1259 " --> pdb=" O   ILE A1255 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 368 through 370
    Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 401
      removed outlier: 6.157A  pdb=" N   ILE A 399 " --> pdb=" O   THR A 558 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 446 through 449
      removed outlier: 3.840A  pdb=" N   VAL A 449 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 577 through 578
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1045 through 1048
      removed outlier: 5.435A  pdb=" N   LEU A1045 " --> pdb=" O   HIS A1028 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1102 through 1103
      removed outlier: 5.980A  pdb=" N   ALA A1103 " --> pdb=" O   LEU A1185 " (cutoff:3.500A)

    603 hydrogen bonds defined for protein.
    1791 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: 3.10

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2945
        1.35 -     1.47: 1984
        1.47 -     1.59: 4140
        1.59 -     1.71: 0
        1.71 -     1.84: 68
  Bond restraints: 9137
  Sorted by residual:
  bond pdb=" N   VAL A 235 "
       pdb=" CA  VAL A 235 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.21e-02 6.83e+03 9.55e+00
  bond pdb=" N   VAL A 239 "
       pdb=" CA  VAL A 239 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.88e+00
  bond pdb=" N   VAL A 203 "
       pdb=" CA  VAL A 203 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.21e-02 6.83e+03 8.79e+00
  bond pdb=" N   VAL A 230 "
       pdb=" CA  VAL A 230 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.036 1.21e-02 6.83e+03 8.75e+00
  bond pdb=" N   ILE A 204 "
       pdb=" CA  ILE A 204 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.033 1.17e-02 7.31e+03 8.05e+00
  ... (remaining 9132 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 11893
        2.07 -     4.13: 437
        4.13 -     6.20: 33
        6.20 -     8.26: 2
        8.26 -    10.33: 1
  Bond angle restraints: 12366
  Sorted by residual:
  angle pdb=" C   THR A1128 "
        pdb=" CA  THR A1128 "
        pdb=" CB  THR A1128 "
      ideal   model   delta    sigma   weight residual
     116.54  112.04    4.50 1.15e+00 7.56e-01 1.53e+01
  angle pdb=" C   ASN A 484 "
        pdb=" CA  ASN A 484 "
        pdb=" CB  ASN A 484 "
      ideal   model   delta    sigma   weight residual
     116.34  110.87    5.47 1.40e+00 5.10e-01 1.53e+01
  angle pdb=" CA  GLU A1150 "
        pdb=" CB  GLU A1150 "
        pdb=" CG  GLU A1150 "
      ideal   model   delta    sigma   weight residual
     114.10  121.27   -7.17 2.00e+00 2.50e-01 1.29e+01
  angle pdb=" CB  MET A 157 "
        pdb=" CG  MET A 157 "
        pdb=" SD  MET A 157 "
      ideal   model   delta    sigma   weight residual
     112.70  102.37   10.33 3.00e+00 1.11e-01 1.18e+01
  angle pdb=" N   ILE A 201 "
        pdb=" CA  ILE A 201 "
        pdb=" C   ILE A 201 "
      ideal   model   delta    sigma   weight residual
     110.62  107.23    3.39 1.02e+00 9.61e-01 1.10e+01
  ... (remaining 12361 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4919
       17.93 -    35.85: 442
       35.85 -    53.78: 69
       53.78 -    71.70: 26
       71.70 -    89.62: 7
  Dihedral angle restraints: 5463
    sinusoidal: 2109
      harmonic: 3354
  Sorted by residual:
  dihedral pdb=" CA  ARG A 844 "
           pdb=" C   ARG A 844 "
           pdb=" N   LEU A 845 "
           pdb=" CA  LEU A 845 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.25   17.75     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  PHE A 552 "
           pdb=" C   PHE A 552 "
           pdb=" N   MET A 553 "
           pdb=" CA  MET A 553 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.24  -16.76     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" C   ILE A 341 "
           pdb=" N   ILE A 341 "
           pdb=" CA  ILE A 341 "
           pdb=" CB  ILE A 341 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.26    8.26     0      2.50e+00 1.60e-01 1.09e+01
  ... (remaining 5460 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1221
       0.069 -    0.138: 172
       0.138 -    0.206: 32
       0.206 -    0.275: 2
       0.275 -    0.344: 1
  Chirality restraints: 1428
  Sorted by residual:
  chirality pdb=" CB  ILE A 341 "
            pdb=" CA  ILE A 341 "
            pdb=" CG1 ILE A 341 "
            pdb=" CG2 ILE A 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.30    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" CB  VAL A 235 "
            pdb=" CA  VAL A 235 "
            pdb=" CG1 VAL A 235 "
            pdb=" CG2 VAL A 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  ILE A 201 "
            pdb=" N   ILE A 201 "
            pdb=" C   ILE A 201 "
            pdb=" CB  ILE A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 1425 not shown)

  Planarity restraints: 1572
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 238 "    0.235 9.50e-02 1.11e+02   1.05e-01 6.79e+00
        pdb=" NE  ARG A 238 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 238 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 238 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 238 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 721 "    0.008 2.00e-02 2.50e+03   1.62e-02 2.62e+00
        pdb=" C   LEU A 721 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   LEU A 721 "    0.011 2.00e-02 2.50e+03
        pdb=" N   SER A 722 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 711 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   GLY A 711 "    0.028 2.00e-02 2.50e+03
        pdb=" O   GLY A 711 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   SER A 712 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1569 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1100
        2.75 -     3.29: 9959
        3.29 -     3.83: 15785
        3.83 -     4.36: 18071
        4.36 -     4.90: 30413
  Nonbonded interactions: 75328
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 116 "
            pdb=" NE2 GLN A 159 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" O   TRP A 441 "
            pdb=" NE2 GLN A 445 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" NE2 GLN A 842 "
            pdb=" O   TRP A 843 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" O   GLY A1254 "
            pdb=" NH1 ARG A1258 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" NH2 ARG A 123 "
            pdb=" O   ILE A 151 "
     model   vdw
     2.271 3.120
  ... (remaining 75323 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.790
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6299
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   9137  Z= 0.334
  Angle     :  0.760  10.327  12366  Z= 0.521
  Chirality :  0.051   0.344   1428
  Planarity :  0.005   0.105   1572
  Dihedral  : 14.448  89.625   3305
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.16 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.24), residues: 1161
  helix:  1.17 (0.19), residues: 749
  sheet: -0.22 (1.26), residues: 25
  loop : -2.11 (0.28), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 188 
 HIS   0.009   0.001   HIS A 486 
 PHE   0.024   0.001   PHE A 552 
 TYR   0.016   0.001   TYR A 908 
 ARG   0.007   0.000   ARG A 569 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11949 (  603)
  hydrogen bonds       : angle       5.41510 ( 1791)
  covalent geometry    : bond        0.00473 ( 9137)
  covalent geometry    : angle       0.76043 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ILE cc_start: 0.7108 (mt) cc_final: 0.6565 (mm)
REVERT: A  162 ILE cc_start: 0.7938 (pt) cc_final: 0.7687 (pt)
REVERT: A  273 MET cc_start: 0.6642 (mmm) cc_final: 0.6250 (mtm)
REVERT: A  442 LEU cc_start: 0.6467 (mp) cc_final: 0.5741 (tp)
REVERT: A  511 GLN cc_start: 0.4254 (tp-100) cc_final: 0.3535 (tp-100)
REVERT: A  736 MET cc_start: 0.6061 (ttp) cc_final: 0.5788 (ttp)
REVERT: A 1114 THR cc_start: 0.6996 (t) cc_final: 0.6493 (p)
REVERT: A 1118 GLU cc_start: 0.7115 (pt0) cc_final: 0.6347 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 166
  average time/residue: 0.2614
  time to fit residues: 57.2295
Evaluate side-chains
  95 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.2980
   chunk 87 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 59 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0470
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 67 optimal weight:    0.9990
   chunk 105 optimal weight:   10.0000
   overall best weight:    0.6280

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

Flipped N/Q/H residues before XYZ refinement:
A 388 ASN
A 445 GLN
A 506 GLN
A 682 GLN
A 797 ASN
A 911 ASN
A1073 GLN
A1124 HIS
A1246 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.241046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.182022 restraints weight = 9382.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.4148 rms_B_bonded: 2.37
r_work: 0.4028 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3911 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9137  Z= 0.137
  Angle     :  0.567   7.647  12366  Z= 0.305
  Chirality :  0.040   0.154   1428
  Planarity :  0.004   0.035   1572
  Dihedral  :  4.324  57.319   1256
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  8.85 %
    Favored  : 89.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.82 (0.25), residues: 1161
  helix:  1.71 (0.19), residues: 758
  sheet: -0.50 (1.25), residues: 25
  loop : -1.89 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 188 
 HIS   0.004   0.001   HIS A 588 
 PHE   0.025   0.001   PHE A 552 
 TYR   0.020   0.001   TYR A 295 
 ARG   0.006   0.000   ARG A1199 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04706 (  603)
  hydrogen bonds       : angle       4.15771 ( 1791)
  covalent geometry    : bond        0.00274 ( 9137)
  covalent geometry    : angle       0.56695 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7764 (ptpp) cc_final: 0.7363 (mttp)
REVERT: A  162 ILE cc_start: 0.8460 (pt) cc_final: 0.8254 (pt)
REVERT: A  273 MET cc_start: 0.7715 (mmm) cc_final: 0.7037 (mtp)
REVERT: A  442 LEU cc_start: 0.6709 (mp) cc_final: 0.5924 (tp)
REVERT: A  470 ASP cc_start: 0.8053 (m-30) cc_final: 0.7811 (m-30)
REVERT: A  521 MET cc_start: 0.6503 (mmm) cc_final: 0.6295 (mmm)
REVERT: A  556 ARG cc_start: 0.4091 (mmt90) cc_final: 0.3785 (mmm-85)
REVERT: A  997 PHE cc_start: 0.6832 (m-10) cc_final: 0.6471 (m-80)
  outliers start: 19
  outliers final: 9
  residues processed: 129
  average time/residue: 0.2127
  time to fit residues: 38.6260
Evaluate side-chains
  94 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  388 ASN
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  921 TRP
Chi-restraints excluded: chain A residue 1054 THR
Chi-restraints excluded: chain A residue 1068 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 52 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 88 optimal weight:    5.9990
   chunk 99 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 445 GLN
** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.236377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.173298 restraints weight = 9497.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.4091 rms_B_bonded: 1.83
r_work: 0.3999 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3885 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6929
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9137  Z= 0.143
  Angle     :  0.551   7.669  12366  Z= 0.293
  Chirality :  0.039   0.159   1428
  Planarity :  0.004   0.039   1572
  Dihedral  :  3.890  17.831   1254
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.64 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.25), residues: 1161
  helix:  1.69 (0.19), residues: 758
  sheet: -0.57 (1.23), residues: 25
  loop : -1.85 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 441 
 HIS   0.003   0.001   HIS A  54 
 PHE   0.024   0.001   PHE A 552 
 TYR   0.019   0.001   TYR A 295 
 ARG   0.005   0.000   ARG A 688 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04619 (  603)
  hydrogen bonds       : angle       4.04541 ( 1791)
  covalent geometry    : bond        0.00286 ( 9137)
  covalent geometry    : angle       0.55072 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7905 (ptpp) cc_final: 0.7625 (mttp)
REVERT: A  273 MET cc_start: 0.7582 (mmm) cc_final: 0.7006 (mtp)
REVERT: A  442 LEU cc_start: 0.6523 (mp) cc_final: 0.5967 (tp)
REVERT: A  470 ASP cc_start: 0.8031 (m-30) cc_final: 0.7790 (m-30)
REVERT: A  556 ARG cc_start: 0.4351 (mmt90) cc_final: 0.4068 (mmm-85)
  outliers start: 19
  outliers final: 13
  residues processed: 121
  average time/residue: 0.1984
  time to fit residues: 34.4908
Evaluate side-chains
  107 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  286 TYR
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue  867 MET
Chi-restraints excluded: chain A residue  921 TRP
Chi-restraints excluded: chain A residue 1054 THR
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1186 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 102 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 85 optimal weight:    0.5980
   chunk 82 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.219481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.165975 restraints weight = 9505.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.75
r_work: 0.3774 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3648 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.4890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9137  Z= 0.210
  Angle     :  0.647   8.707  12366  Z= 0.350
  Chirality :  0.043   0.159   1428
  Planarity :  0.005   0.053   1572
  Dihedral  :  4.307  21.535   1254
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 16.02 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.24), residues: 1161
  helix:  1.12 (0.18), residues: 759
  sheet: -1.06 (1.17), residues: 25
  loop : -1.92 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 441 
 HIS   0.009   0.002   HIS A 347 
 PHE   0.026   0.002   PHE A 552 
 TYR   0.019   0.002   TYR A 279 
 ARG   0.004   0.001   ARG A 468 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05483 (  603)
  hydrogen bonds       : angle       4.38325 ( 1791)
  covalent geometry    : bond        0.00460 ( 9137)
  covalent geometry    : angle       0.64698 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A   83 MET cc_start: 0.8499 (tpp) cc_final: 0.8279 (mmt)
REVERT: A  157 MET cc_start: 0.6009 (ttm) cc_final: 0.5460 (ttm)
REVERT: A  248 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7192 (mtm-85)
REVERT: A  273 MET cc_start: 0.7686 (mmm) cc_final: 0.7039 (mtp)
REVERT: A  341 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8207 (mt)
REVERT: A  399 ILE cc_start: 0.6669 (tt) cc_final: 0.6400 (mm)
REVERT: A  442 LEU cc_start: 0.7037 (mp) cc_final: 0.6523 (tp)
REVERT: A  811 ASN cc_start: 0.7753 (p0) cc_final: 0.7372 (t0)
REVERT: A  893 ARG cc_start: 0.7699 (ptp90) cc_final: 0.6479 (ptm160)
REVERT: A  970 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7311 (mmp)
REVERT: A  993 MET cc_start: 0.6784 (ptt) cc_final: 0.6459 (ppp)
REVERT: A 1100 LYS cc_start: 0.7499 (tttp) cc_final: 0.7175 (mttp)
REVERT: A 1102 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6802 (mt)
REVERT: A 1118 GLU cc_start: 0.6745 (pt0) cc_final: 0.6089 (tm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 146
  average time/residue: 0.2197
  time to fit residues: 44.4376
Evaluate side-chains
  121 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  248 ARG
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  831 MET
Chi-restraints excluded: chain A residue  853 PHE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  905 VAL
Chi-restraints excluded: chain A residue  921 TRP
Chi-restraints excluded: chain A residue  970 MET
Chi-restraints excluded: chain A residue 1054 THR
Chi-restraints excluded: chain A residue 1068 VAL
Chi-restraints excluded: chain A residue 1102 ILE
Chi-restraints excluded: chain A residue 1186 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 7 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    0.4980
   chunk 54 optimal weight:    9.9990
   chunk 69 optimal weight:    0.7980
   chunk 110 optimal weight:    6.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 484 ASN
A 682 GLN
A1073 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.230328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.171248 restraints weight = 9205.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.4048 rms_B_bonded: 1.86
r_work: 0.3909 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3786 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.5118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9137  Z= 0.132
  Angle     :  0.548   9.088  12366  Z= 0.293
  Chirality :  0.039   0.153   1428
  Planarity :  0.004   0.042   1572
  Dihedral  :  3.976  18.870   1254
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.02 %
    Favored  : 79.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.24), residues: 1161
  helix:  1.55 (0.19), residues: 760
  sheet: -0.34 (1.33), residues: 20
  loop : -1.93 (0.28), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 441 
 HIS   0.009   0.001   HIS A 347 
 PHE   0.024   0.001   PHE A 552 
 TYR   0.014   0.001   TYR A1117 
 ARG   0.005   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04657 (  603)
  hydrogen bonds       : angle       4.07736 ( 1791)
  covalent geometry    : bond        0.00266 ( 9137)
  covalent geometry    : angle       0.54804 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  273 MET cc_start: 0.7631 (mmm) cc_final: 0.6873 (mtp)
REVERT: A  341 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7733 (mm)
REVERT: A  442 LEU cc_start: 0.6991 (mp) cc_final: 0.6559 (tp)
REVERT: A  893 ARG cc_start: 0.7743 (ptp90) cc_final: 0.6622 (ptm160)
REVERT: A  993 MET cc_start: 0.6465 (ptt) cc_final: 0.6155 (ppp)
REVERT: A 1100 LYS cc_start: 0.7468 (tttp) cc_final: 0.7189 (mttp)
REVERT: A 1118 GLU cc_start: 0.6532 (pt0) cc_final: 0.5750 (tm-30)
REVERT: A 1153 LYS cc_start: 0.6443 (mtmm) cc_final: 0.6227 (ptpp)
REVERT: A 1187 ASP cc_start: 0.7364 (t0) cc_final: 0.7074 (t70)
  outliers start: 24
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2080
  time to fit residues: 37.5171
Evaluate side-chains
  112 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  853 PHE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue 1054 THR
Chi-restraints excluded: chain A residue 1186 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 70 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 100 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A1142 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.220561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.166296 restraints weight = 9267.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 2.52
r_work: 0.3796 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3677 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.5503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9137  Z= 0.155
  Angle     :  0.568   8.318  12366  Z= 0.302
  Chirality :  0.040   0.154   1428
  Planarity :  0.004   0.043   1572
  Dihedral  :  4.051  20.661   1254
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.86 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.62 (0.25), residues: 1161
  helix:  1.50 (0.19), residues: 762
  sheet: -0.57 (1.32), residues: 21
  loop : -1.86 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 441 
 HIS   0.006   0.001   HIS A 347 
 PHE   0.022   0.002   PHE A 552 
 TYR   0.010   0.001   TYR A 279 
 ARG   0.003   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04850 (  603)
  hydrogen bonds       : angle       4.17932 ( 1791)
  covalent geometry    : bond        0.00332 ( 9137)
  covalent geometry    : angle       0.56829 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  121 LYS cc_start: 0.8552 (tttt) cc_final: 0.7762 (mttp)
REVERT: A  273 MET cc_start: 0.7662 (mmm) cc_final: 0.6944 (mtp)
REVERT: A  893 ARG cc_start: 0.7857 (ptp90) cc_final: 0.6829 (ptm160)
REVERT: A  993 MET cc_start: 0.6741 (ptt) cc_final: 0.6529 (ppp)
REVERT: A 1118 GLU cc_start: 0.6471 (pt0) cc_final: 0.5627 (tm-30)
REVERT: A 1129 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7879 (tm-30)
REVERT: A 1153 LYS cc_start: 0.6441 (mtmm) cc_final: 0.6233 (ptpp)
  outliers start: 26
  outliers final: 15
  residues processed: 128
  average time/residue: 0.1808
  time to fit residues: 33.6904
Evaluate side-chains
  115 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  853 PHE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain A residue  921 TRP
Chi-restraints excluded: chain A residue 1054 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 96 optimal weight:    9.9990
   chunk 44 optimal weight:    8.9990
   chunk 82 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 354 ASN
A1162 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.223013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.164955 restraints weight = 9313.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 2.02
r_work: 0.3829 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3702 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.6013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9137  Z= 0.167
  Angle     :  0.591  10.785  12366  Z= 0.314
  Chirality :  0.041   0.153   1428
  Planarity :  0.004   0.048   1572
  Dihedral  :  4.152  22.111   1254
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.39 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.24), residues: 1161
  helix:  1.41 (0.19), residues: 761
  sheet: -1.59 (1.15), residues: 27
  loop : -1.86 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 946 
 HIS   0.005   0.001   HIS A 171 
 PHE   0.022   0.002   PHE A 552 
 TYR   0.012   0.002   TYR A 279 
 ARG   0.004   0.000   ARG A 443 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04995 (  603)
  hydrogen bonds       : angle       4.23621 ( 1791)
  covalent geometry    : bond        0.00365 ( 9137)
  covalent geometry    : angle       0.59121 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8542 (tttt) cc_final: 0.7840 (mttp)
REVERT: A  213 SER cc_start: 0.6098 (OUTLIER) cc_final: 0.5782 (t)
REVERT: A  273 MET cc_start: 0.7639 (mmm) cc_final: 0.6880 (mtp)
REVERT: A  295 TYR cc_start: 0.8351 (t80) cc_final: 0.8081 (t80)
REVERT: A  416 ILE cc_start: 0.7892 (tt) cc_final: 0.7465 (mt)
REVERT: A  440 ARG cc_start: 0.6977 (mpt180) cc_final: 0.6705 (mpt180)
REVERT: A  444 GLN cc_start: 0.7256 (mt0) cc_final: 0.6580 (mm-40)
REVERT: A  521 MET cc_start: 0.6452 (mmm) cc_final: 0.6086 (mmm)
REVERT: A  811 ASN cc_start: 0.7726 (p0) cc_final: 0.7430 (t0)
REVERT: A  893 ARG cc_start: 0.7994 (ptp90) cc_final: 0.7018 (ptm160)
REVERT: A  970 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7188 (mmp)
REVERT: A  993 MET cc_start: 0.6581 (ptt) cc_final: 0.6225 (ppp)
REVERT: A 1118 GLU cc_start: 0.6155 (pt0) cc_final: 0.5277 (tm-30)
REVERT: A 1129 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7888 (tm-30)
  outliers start: 24
  outliers final: 18
  residues processed: 126
  average time/residue: 0.1959
  time to fit residues: 36.3447
Evaluate side-chains
  120 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 100
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  727 VAL
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  853 PHE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  970 MET
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1054 THR
Chi-restraints excluded: chain A residue 1186 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 74 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
A 693 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4591 r_free = 0.4591 target = 0.227677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.165625 restraints weight = 9396.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 1.83
r_work: 0.3889 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.6136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9137  Z= 0.131
  Angle     :  0.558  10.406  12366  Z= 0.294
  Chirality :  0.040   0.196   1428
  Planarity :  0.004   0.044   1572
  Dihedral  :  4.003  18.850   1254
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.44 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1161
  helix:  1.61 (0.19), residues: 757
  sheet: -1.45 (1.17), residues: 27
  loop : -1.82 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 950 
 HIS   0.010   0.001   HIS A 347 
 PHE   0.025   0.001   PHE A 552 
 TYR   0.008   0.001   TYR A 699 
 ARG   0.002   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04597 (  603)
  hydrogen bonds       : angle       4.14646 ( 1791)
  covalent geometry    : bond        0.00269 ( 9137)
  covalent geometry    : angle       0.55772 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.8428 (tpp) cc_final: 0.8190 (mmm)
REVERT: A  121 LYS cc_start: 0.8558 (tttt) cc_final: 0.7920 (mttp)
REVERT: A  273 MET cc_start: 0.7702 (mmm) cc_final: 0.6953 (mtp)
REVERT: A  416 ILE cc_start: 0.7814 (tt) cc_final: 0.7390 (mt)
REVERT: A  440 ARG cc_start: 0.7108 (mpt180) cc_final: 0.6869 (mpt180)
REVERT: A  444 GLN cc_start: 0.7126 (mt0) cc_final: 0.6440 (mm-40)
REVERT: A  893 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7050 (ptm160)
REVERT: A  970 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.7069 (mmp)
REVERT: A  993 MET cc_start: 0.6715 (ptt) cc_final: 0.6428 (ppp)
REVERT: A 1054 THR cc_start: 0.5229 (OUTLIER) cc_final: 0.4869 (m)
REVERT: A 1118 GLU cc_start: 0.6334 (pt0) cc_final: 0.5328 (tm-30)
REVERT: A 1129 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7909 (tm-30)
REVERT: A 1153 LYS cc_start: 0.5884 (ptpp) cc_final: 0.5637 (ptpp)
  outliers start: 20
  outliers final: 15
  residues processed: 128
  average time/residue: 0.2088
  time to fit residues: 37.8257
Evaluate side-chains
  115 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  546 GLN
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  693 ASN
Chi-restraints excluded: chain A residue  853 PHE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  970 MET
Chi-restraints excluded: chain A residue 1054 THR
Chi-restraints excluded: chain A residue 1095 LEU
Chi-restraints excluded: chain A residue 1186 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 104 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 60 optimal weight:    6.9990
   chunk 109 optimal weight:    0.3980
   chunk 56 optimal weight:    8.9990
   chunk 114 optimal weight:   10.0000
   chunk 107 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.4543 r_free = 0.4543 target = 0.221915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.165834 restraints weight = 9360.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 2.22
r_work: 0.3834 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3704 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.6335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9137  Z= 0.148
  Angle     :  0.578  10.494  12366  Z= 0.306
  Chirality :  0.040   0.151   1428
  Planarity :  0.004   0.044   1572
  Dihedral  :  4.049  21.356   1254
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.86 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.25), residues: 1161
  helix:  1.55 (0.19), residues: 751
  sheet: -1.51 (1.16), residues: 27
  loop : -1.74 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 946 
 HIS   0.010   0.001   HIS A 347 
 PHE   0.022   0.002   PHE A 552 
 TYR   0.009   0.001   TYR A 279 
 ARG   0.003   0.000   ARG A 777 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04747 (  603)
  hydrogen bonds       : angle       4.17794 ( 1791)
  covalent geometry    : bond        0.00315 ( 9137)
  covalent geometry    : angle       0.57790 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.8673 (tpp) cc_final: 0.8457 (mmt)
REVERT: A  121 LYS cc_start: 0.8604 (tttt) cc_final: 0.7937 (mttp)
REVERT: A  273 MET cc_start: 0.7719 (mmm) cc_final: 0.6906 (mtp)
REVERT: A  342 PHE cc_start: 0.8159 (m-10) cc_final: 0.7946 (m-10)
REVERT: A  416 ILE cc_start: 0.7897 (tt) cc_final: 0.7574 (mt)
REVERT: A  440 ARG cc_start: 0.7275 (mpt180) cc_final: 0.7028 (mpt180)
REVERT: A  444 GLN cc_start: 0.7109 (mt0) cc_final: 0.6446 (mm-40)
REVERT: A  811 ASN cc_start: 0.7741 (p0) cc_final: 0.7430 (t0)
REVERT: A  893 ARG cc_start: 0.8064 (ptp90) cc_final: 0.7179 (ptm160)
REVERT: A  970 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7155 (mmp)
REVERT: A  993 MET cc_start: 0.6618 (ptt) cc_final: 0.6309 (ppp)
REVERT: A 1054 THR cc_start: 0.5133 (OUTLIER) cc_final: 0.4899 (m)
REVERT: A 1118 GLU cc_start: 0.6251 (pt0) cc_final: 0.5270 (tm-30)
  outliers start: 20
  outliers final: 14
  residues processed: 117
  average time/residue: 0.1985
  time to fit residues: 33.5047
Evaluate side-chains
  115 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  853 PHE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  970 MET
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1054 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 47 optimal weight:    7.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 693 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.226155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.164650 restraints weight = 9413.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 1.82
r_work: 0.3876 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.6474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9137  Z= 0.135
  Angle     :  0.576   9.778  12366  Z= 0.302
  Chirality :  0.040   0.149   1428
  Planarity :  0.004   0.044   1572
  Dihedral  :  4.056  19.744   1254
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.55 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1161
  helix:  1.58 (0.19), residues: 759
  sheet: -1.43 (1.16), residues: 27
  loop : -1.78 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 946 
 HIS   0.010   0.001   HIS A 347 
 PHE   0.021   0.001   PHE A 552 
 TYR   0.007   0.001   TYR A 699 
 ARG   0.003   0.000   ARG A1175 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04578 (  603)
  hydrogen bonds       : angle       4.14693 ( 1791)
  covalent geometry    : bond        0.00281 ( 9137)
  covalent geometry    : angle       0.57563 (12366)

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

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

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2322 Ramachandran restraints generated.
    1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.931 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8639 (tttt) cc_final: 0.8061 (mttp)
REVERT: A  273 MET cc_start: 0.7718 (mmm) cc_final: 0.6944 (mtp)
REVERT: A  416 ILE cc_start: 0.7806 (tt) cc_final: 0.7335 (mt)
REVERT: A  440 ARG cc_start: 0.7308 (mpt180) cc_final: 0.7074 (mpt180)
REVERT: A  444 GLN cc_start: 0.7048 (mt0) cc_final: 0.6454 (mm-40)
REVERT: A  893 ARG cc_start: 0.8023 (ptp90) cc_final: 0.7254 (ptm160)
REVERT: A  970 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7080 (mmp)
REVERT: A  993 MET cc_start: 0.6688 (ptt) cc_final: 0.6395 (ppp)
REVERT: A 1036 ARG cc_start: 0.5909 (mmm-85) cc_final: 0.5455 (mtm180)
REVERT: A 1054 THR cc_start: 0.5165 (OUTLIER) cc_final: 0.4962 (m)
REVERT: A 1100 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7487 (mttp)
REVERT: A 1118 GLU cc_start: 0.6250 (pt0) cc_final: 0.5209 (tm-30)
  outliers start: 20
  outliers final: 15
  residues processed: 125
  average time/residue: 0.2167
  time to fit residues: 38.2507
Evaluate side-chains
  120 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLU
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  219 SER
Chi-restraints excluded: chain A residue  224 SER
Chi-restraints excluded: chain A residue  303 ASN
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  462 GLU
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  853 PHE
Chi-restraints excluded: chain A residue  860 THR
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  970 MET
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1054 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 347 HIS
** A1219 HIS ** 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 = 0.4460 r_free = 0.4460 target = 0.212488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.158765 restraints weight = 9552.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.32
r_work: 0.3690 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3562 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.6990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9137  Z= 0.234
  Angle     :  0.683  11.020  12366  Z= 0.364
  Chirality :  0.045   0.164   1428
  Planarity :  0.005   0.044   1572
  Dihedral  :  4.484  22.961   1254
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 20.86 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.24), residues: 1161
  helix:  1.05 (0.18), residues: 757
  sheet: -1.64 (1.15), residues: 27
  loop : -1.86 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 946 
 HIS   0.009   0.002   HIS A 347 
 PHE   0.029   0.003   PHE A 552 
 TYR   0.020   0.002   TYR A 279 
 ARG   0.008   0.001   ARG A1082 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05558 (  603)
  hydrogen bonds       : angle       4.50265 ( 1791)
  covalent geometry    : bond        0.00529 ( 9137)
  covalent geometry    : angle       0.68265 (12366)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5253.19 seconds
wall clock time: 91 minutes 27.47 seconds (5487.47 seconds total)