Starting phenix.real_space_refine
on Tue Apr 29 22:39:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jun_61831/04_2025/9jun_61831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jun_61831/04_2025/9jun_61831.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/9jun_61831/04_2025/9jun_61831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jun_61831/04_2025/9jun_61831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jun_61831/04_2025/9jun_61831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jun_61831/04_2025/9jun_61831.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=   0.004
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 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.74, per 1000 atoms: 0.64
  Number of scatterers: 8971
  At special positions: 0
  Unit cell: (106.02, 98.58, 125.55, 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: 3.03
  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:
      42 helices and 5 sheets defined
      69.0% alpha, 2.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 34
    Processing helix  chain 'A' and resid 37 through 74
      removed outlier: 4.191A  pdb=" N   LEU A  58 " --> pdb=" O   HIS A  54 " (cutoff:3.500A)
      Proline residue:  A  59  - end of helix
    Processing helix  chain 'A' and resid 78 through 132
    Processing helix  chain 'A' and resid 134 through 141
      removed outlier: 3.679A  pdb=" N   PHE A 138 " --> pdb=" O   ASP A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 164
      removed outlier: 3.953A  pdb=" N   ILE A 151 " --> pdb=" O   VAL A 147 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   ASN A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   GLN A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   ASP A 160 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE A 162 " --> pdb=" O   VAL A 158 " (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
      removed outlier: 3.731A  pdb=" N   GLN A 236 " --> pdb=" O   GLN A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 243
      removed outlier: 3.570A  pdb=" N   VAL A 240 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    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: 3.755A  pdb=" N   HIS A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 406 through 417
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 444 through 446
      No H-bonds generated for 'chain 'A' and resid 444 through 446'
    Processing helix  chain 'A' and resid 459 through 466
    Processing helix  chain 'A' and resid 472 through 482
      removed outlier: 3.990A  pdb=" N   VAL A 482 " --> pdb=" O   GLU A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 498
      removed outlier: 3.672A  pdb=" N   THR A 498 " --> pdb=" O   GLY A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 523
    Processing helix  chain 'A' and resid 538 through 550
      removed outlier: 4.490A  pdb=" N   GLU A 542 " --> pdb=" O   ASP A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 571
    Processing helix  chain 'A' and resid 577 through 581
      removed outlier: 3.561A  pdb=" N   GLY A 580 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
    Processing helix  chain 'A' and resid 696 through 729
    Processing helix  chain 'A' and resid 732 through 786
    Processing helix  chain 'A' and resid 788 through 794
    Processing helix  chain 'A' and resid 798 through 852
      removed outlier: 3.654A  pdb=" N   ALA A 810 " --> pdb=" O   LEU A 806 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASN A 811 " --> pdb=" O   ALA A 807 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   ARG A 844 " --> pdb=" O   VAL A 840 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   LEU A 845 " --> pdb=" O   LEU A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 869
    Processing helix  chain 'A' and resid 873 through 878
      removed outlier: 3.592A  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 898
    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 1065 through 1073
      removed outlier: 4.071A  pdb=" N   ILE A1069 " --> pdb=" O   LYS A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1088
    Processing helix  chain 'A' and resid 1094 through 1100
      removed outlier: 3.680A  pdb=" N   ILE A1098 " --> pdb=" O   ASN A1094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1115 through 1122
      removed outlier: 3.527A  pdb=" N   ASN A1119 " --> pdb=" O   THR A1115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1128 through 1139
    Processing helix  chain 'A' and resid 1141 through 1148
      removed outlier: 3.610A  pdb=" N   ILE A1145 " --> pdb=" O   ALA A1141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1150 through 1154
    Processing helix  chain 'A' and resid 1164 through 1180
    Processing helix  chain 'A' and resid 1194 through 1210
    Processing helix  chain 'A' and resid 1257 through 1264
    Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 370
    Processing sheet with id=AA2, first strand: chain 'A' and resid 529 through 530
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1048 through 1049
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1029 through 1031
      removed outlier: 8.112A  pdb=" N   PHE A1031 " --> pdb=" O   ARG A1043 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ARG A1043 " --> pdb=" O   PHE A1031 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1054 through 1055
      removed outlier: 6.541A  pdb=" N   MET A1184 " --> pdb=" O   ILE A1215 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ALA A1103 " --> pdb=" O   LEU A1185 " (cutoff:3.500A)

    617 hydrogen bonds defined for protein.
    1806 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: 3.13

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2857
        1.34 -     1.46: 1155
        1.46 -     1.57: 5057
        1.57 -     1.69: 0
        1.69 -     1.81: 68
  Bond restraints: 9137
  Sorted by residual:
  bond pdb=" CA  ALA A 983 "
       pdb=" C   ALA A 983 "
    ideal  model  delta    sigma   weight residual
    1.522  1.536 -0.015 1.29e-02 6.01e+03 1.27e+00
  bond pdb=" CA  ALA A 325 "
       pdb=" C   ALA A 325 "
    ideal  model  delta    sigma   weight residual
    1.522  1.536 -0.014 1.29e-02 6.01e+03 1.26e+00
  bond pdb=" CG1 ILE A1120 "
       pdb=" CD1 ILE A1120 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.10e+00
  bond pdb=" C   LEU A 321 "
       pdb=" O   LEU A 321 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.012 1.15e-02 7.56e+03 1.09e+00
  bond pdb=" CG  ARG A 298 "
       pdb=" CD  ARG A 298 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.88e-01
  ... (remaining 9132 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 11950
        1.34 -     2.67: 323
        2.67 -     4.01: 59
        4.01 -     5.35: 26
        5.35 -     6.69: 8
  Bond angle restraints: 12366
  Sorted by residual:
  angle pdb=" N   GLN A 546 "
        pdb=" CA  GLN A 546 "
        pdb=" CB  GLN A 546 "
      ideal   model   delta    sigma   weight residual
     110.16  114.65   -4.49 1.48e+00 4.57e-01 9.20e+00
  angle pdb=" N   GLU A  84 "
        pdb=" CA  GLU A  84 "
        pdb=" CB  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     110.12  114.20   -4.08 1.47e+00 4.63e-01 7.70e+00
  angle pdb=" N   GLY A1052 "
        pdb=" CA  GLY A1052 "
        pdb=" C   GLY A1052 "
      ideal   model   delta    sigma   weight residual
     113.18  118.94   -5.76 2.37e+00 1.78e-01 5.91e+00
  angle pdb=" C   PHE A 243 "
        pdb=" N   VAL A 244 "
        pdb=" CA  VAL A 244 "
      ideal   model   delta    sigma   weight residual
     121.97  126.14   -4.17 1.80e+00 3.09e-01 5.38e+00
  angle pdb=" C   LEU A1057 "
        pdb=" N   VAL A1058 "
        pdb=" CA  VAL A1058 "
      ideal   model   delta    sigma   weight residual
     123.16  120.71    2.45 1.06e+00 8.90e-01 5.32e+00
  ... (remaining 12361 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 4914
       17.95 -    35.90: 451
       35.90 -    53.85: 66
       53.85 -    71.80: 20
       71.80 -    89.74: 12
  Dihedral angle restraints: 5463
    sinusoidal: 2109
      harmonic: 3354
  Sorted by residual:
  dihedral pdb=" CA  ASP A1018 "
           pdb=" CB  ASP A1018 "
           pdb=" CG  ASP A1018 "
           pdb=" OD1 ASP A1018 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.04   59.04     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" CB  GLU A  85 "
           pdb=" CG  GLU A  85 "
           pdb=" CD  GLU A  85 "
           pdb=" OE1 GLU A  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.74  -89.74     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A 164 "
           pdb=" CG  GLU A 164 "
           pdb=" CD  GLU A 164 "
           pdb=" OE1 GLU A 164 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.73  -89.73     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 5460 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1104
       0.045 -    0.090: 272
       0.090 -    0.135: 48
       0.135 -    0.180: 3
       0.180 -    0.226: 1
  Chirality restraints: 1428
  Sorted by residual:
  chirality pdb=" CB  ILE A 527 "
            pdb=" CA  ILE A 527 "
            pdb=" CG1 ILE A 527 "
            pdb=" CG2 ILE A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  MET A 157 "
            pdb=" N   MET A 157 "
            pdb=" C   MET A 157 "
            pdb=" CB  MET A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CA  ILE A1041 "
            pdb=" N   ILE A1041 "
            pdb=" C   ILE A1041 "
            pdb=" CB  ILE A1041 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.76e-01
  ... (remaining 1425 not shown)

  Planarity restraints: 1572
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1084 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   MET A1084 "    0.055 2.00e-02 2.50e+03
        pdb=" O   MET A1084 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ILE A1085 "   -0.018 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   1.65e-02 2.72e+00
        pdb=" C   LEU A 721 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LEU A 721 "    0.011 2.00e-02 2.50e+03
        pdb=" N   SER A 722 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 711 "   -0.007 2.00e-02 2.50e+03   1.47e-02 2.15e+00
        pdb=" C   GLY A 711 "    0.025 2.00e-02 2.50e+03
        pdb=" O   GLY A 711 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   SER A 712 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1569 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1114
        2.75 -     3.29: 9729
        3.29 -     3.82: 15560
        3.82 -     4.36: 17278
        4.36 -     4.90: 29814
  Nonbonded interactions: 73495
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A1170 "
            pdb=" OG  SER A1200 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" OD2 ASP A 793 "
            pdb=" OH  TYR A1076 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OH  TYR A 265 "
            pdb=" OD1 ASN A 771 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" NH2 ARG A 805 "
            pdb=" OE2 GLU A 998 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" NH1 ARG A 418 "
            pdb=" O   LEU A 434 "
     model   vdw
     2.272 3.120
  ... (remaining 73490 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:             1.160
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.070
  Find NCS groups from input model:        0.320
  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:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9137  Z= 0.142
  Angle     :  0.573   6.687  12366  Z= 0.307
  Chirality :  0.039   0.226   1428
  Planarity :  0.004   0.039   1572
  Dihedral  : 14.490  89.744   3305
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  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:  1.31 (0.25), residues: 1161
  helix:  2.14 (0.19), residues: 742
  sheet: -1.53 (1.01), residues: 27
  loop : -1.56 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 697 
 HIS   0.003   0.001   HIS A 171 
 PHE   0.019   0.001   PHE A 686 
 TYR   0.018   0.001   TYR A1117 
 ARG   0.009   0.001   ARG A1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12679 (  617)
  hydrogen bonds       : angle       5.15009 ( 1806)
  covalent geometry    : bond        0.00282 ( 9137)
  covalent geometry    : angle       0.57301 (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
  244 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A  121 LYS cc_start: 0.7987 (mtmt) cc_final: 0.6930 (mptt)
REVERT: A  125 LYS cc_start: 0.7299 (mmmm) cc_final: 0.6650 (mmtm)
REVERT: A  217 ASN cc_start: 0.7422 (t0) cc_final: 0.6693 (m-40)
REVERT: A  228 ASN cc_start: 0.7990 (m-40) cc_final: 0.7600 (m110)
REVERT: A  229 ILE cc_start: 0.7736 (mt) cc_final: 0.7533 (mt)
REVERT: A  236 GLN cc_start: 0.6874 (tt0) cc_final: 0.6649 (tt0)
REVERT: A  440 ARG cc_start: 0.4494 (mtm-85) cc_final: 0.4289 (ttp80)
REVERT: A  441 TRP cc_start: 0.8246 (t60) cc_final: 0.7049 (t60)
REVERT: A  491 LYS cc_start: 0.7889 (pttt) cc_final: 0.7449 (ptmt)
REVERT: A  514 ARG cc_start: 0.5618 (mtp-110) cc_final: 0.4168 (mtm-85)
REVERT: A  532 GLU cc_start: 0.4468 (tm-30) cc_final: 0.3358 (tt0)
REVERT: A  738 LYS cc_start: 0.8390 (mmtp) cc_final: 0.8102 (mmmt)
REVERT: A  752 SER cc_start: 0.8649 (m) cc_final: 0.8406 (p)
REVERT: A  766 ASP cc_start: 0.8062 (m-30) cc_final: 0.7787 (m-30)
REVERT: A  782 SER cc_start: 0.8735 (t) cc_final: 0.8459 (p)
REVERT: A  873 ASP cc_start: 0.7480 (t0) cc_final: 0.7027 (t70)
REVERT: A 1184 MET cc_start: 0.7545 (ttm) cc_final: 0.7297 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.2300
  time to fit residues: 75.8616
Evaluate side-chains
  152 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 59 optimal weight:    0.2980
   chunk 46 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 55 optimal weight:   20.0000
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 299 HIS
A 513 GLN
A 812 ASN
A 842 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.192843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.143110 restraints weight = 11165.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.12
r_work: 0.3446 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3325 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9137  Z= 0.154
  Angle     :  0.575   9.757  12366  Z= 0.300
  Chirality :  0.041   0.188   1428
  Planarity :  0.004   0.037   1572
  Dihedral  :  3.868  16.130   1254
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 11.91 %
    Favored  : 86.83 %
  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:  1.53 (0.25), residues: 1161
  helix:  2.36 (0.19), residues: 745
  sheet: -1.35 (0.88), residues: 34
  loop : -1.59 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 843 
 HIS   0.007   0.001   HIS A1101 
 PHE   0.013   0.001   PHE A 853 
 TYR   0.012   0.002   TYR A  89 
 ARG   0.006   0.001   ARG A 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05165 (  617)
  hydrogen bonds       : angle       4.23224 ( 1806)
  covalent geometry    : bond        0.00330 ( 9137)
  covalent geometry    : angle       0.57548 (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
  158 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 146
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7793 (ptmt) cc_final: 0.7186 (ptpp)
REVERT: A   41 TYR cc_start: 0.8276 (m-80) cc_final: 0.8061 (m-80)
REVERT: A  121 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8400 (mtmm)
REVERT: A  217 ASN cc_start: 0.7556 (t0) cc_final: 0.6913 (m-40)
REVERT: A  229 ILE cc_start: 0.8342 (mt) cc_final: 0.8108 (mt)
REVERT: A  441 TRP cc_start: 0.8233 (t60) cc_final: 0.8021 (t60)
REVERT: A  491 LYS cc_start: 0.8075 (pttt) cc_final: 0.7343 (tttm)
REVERT: A  514 ARG cc_start: 0.5414 (mtp-110) cc_final: 0.4454 (mtm-85)
REVERT: A  532 GLU cc_start: 0.5128 (tm-30) cc_final: 0.4107 (tt0)
REVERT: A  553 MET cc_start: 0.6591 (mmp) cc_final: 0.6269 (mmp)
REVERT: A  697 TRP cc_start: 0.7600 (m-10) cc_final: 0.7301 (m-10)
REVERT: A  701 LEU cc_start: 0.8377 (tt) cc_final: 0.7908 (mt)
REVERT: A  738 LYS cc_start: 0.8648 (mmtp) cc_final: 0.8392 (mmmt)
REVERT: A  801 ARG cc_start: 0.7273 (mtm-85) cc_final: 0.6914 (mtt180)
REVERT: A 1028 HIS cc_start: 0.7680 (m90) cc_final: 0.7284 (m-70)
REVERT: A 1122 TYR cc_start: 0.8338 (t80) cc_final: 0.8103 (t80)
  outliers start: 12
  outliers final: 5
  residues processed: 152
  average time/residue: 0.2128
  time to fit residues: 45.2828
Evaluate side-chains
  133 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  813 VAL
Chi-restraints excluded: chain A residue 1069 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A1169 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.190951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.136599 restraints weight = 11225.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.89
r_work: 0.3438 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3348

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= 0.136
  Angle     :  0.527   7.960  12366  Z= 0.274
  Chirality :  0.040   0.234   1428
  Planarity :  0.003   0.041   1572
  Dihedral  :  3.661  14.183   1254
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.70 %
    Favored  : 84.72 %
  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:  1.60 (0.25), residues: 1161
  helix:  2.35 (0.18), residues: 752
  sheet: -1.17 (0.93), residues: 34
  loop : -1.53 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 791 
 HIS   0.006   0.001   HIS A1101 
 PHE   0.011   0.001   PHE A  72 
 TYR   0.010   0.001   TYR A1155 
 ARG   0.010   0.001   ARG A 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04787 (  617)
  hydrogen bonds       : angle       4.09325 ( 1806)
  covalent geometry    : bond        0.00278 ( 9137)
  covalent geometry    : angle       0.52691 (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
  160 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8320 (m-80) cc_final: 0.7957 (m-80)
REVERT: A  121 LYS cc_start: 0.8744 (mtmt) cc_final: 0.8406 (mtmm)
REVERT: A  157 MET cc_start: 0.8016 (mpp) cc_final: 0.7603 (mtm)
REVERT: A  217 ASN cc_start: 0.7544 (t0) cc_final: 0.6873 (m-40)
REVERT: A  229 ILE cc_start: 0.8291 (mt) cc_final: 0.8010 (mt)
REVERT: A  514 ARG cc_start: 0.5718 (mtp-110) cc_final: 0.4689 (mtm-85)
REVERT: A  532 GLU cc_start: 0.5347 (tm-30) cc_final: 0.3995 (tt0)
REVERT: A  553 MET cc_start: 0.6601 (mmp) cc_final: 0.6290 (mmp)
REVERT: A  701 LEU cc_start: 0.8465 (tt) cc_final: 0.7870 (mt)
REVERT: A  729 TYR cc_start: 0.8677 (m-80) cc_final: 0.7974 (m-80)
REVERT: A  738 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8374 (mmmt)
REVERT: A  801 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.7133 (mtt180)
REVERT: A 1028 HIS cc_start: 0.7553 (m90) cc_final: 0.7192 (m-70)
REVERT: A 1122 TYR cc_start: 0.8382 (t80) cc_final: 0.8126 (t80)
  outliers start: 15
  outliers final: 8
  residues processed: 154
  average time/residue: 0.2147
  time to fit residues: 46.6442
Evaluate side-chains
  126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  780 MET
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1069 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0370
   chunk 102 optimal weight:    9.9990
   chunk 52 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 103 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.1662

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 236 GLN
A 513 GLN
A1169 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.187874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.132747 restraints weight = 11143.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.90
r_work: 0.3397 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9137  Z= 0.144
  Angle     :  0.541   6.786  12366  Z= 0.280
  Chirality :  0.040   0.169   1428
  Planarity :  0.003   0.040   1572
  Dihedral  :  3.683  16.148   1254
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.02 %
    Favored  : 81.88 %
  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:  1.40 (0.25), residues: 1161
  helix:  2.21 (0.18), residues: 752
  sheet: -1.23 (0.91), residues: 34
  loop : -1.62 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 441 
 HIS   0.006   0.001   HIS A 171 
 PHE   0.013   0.001   PHE A  72 
 TYR   0.012   0.001   TYR A 719 
 ARG   0.011   0.000   ARG A 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04854 (  617)
  hydrogen bonds       : angle       4.13022 ( 1806)
  covalent geometry    : bond        0.00311 ( 9137)
  covalent geometry    : angle       0.54056 (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
  153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8359 (m-80) cc_final: 0.7994 (m-80)
REVERT: A  121 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8450 (mtmm)
REVERT: A  157 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7891 (mpp)
REVERT: A  217 ASN cc_start: 0.7474 (t0) cc_final: 0.6907 (m-40)
REVERT: A  229 ILE cc_start: 0.8311 (mt) cc_final: 0.7990 (mt)
REVERT: A  441 TRP cc_start: 0.8191 (t60) cc_final: 0.7985 (t60)
REVERT: A  477 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6714 (pt0)
REVERT: A  514 ARG cc_start: 0.5914 (mtp-110) cc_final: 0.4913 (mtm-85)
REVERT: A  553 MET cc_start: 0.6450 (mmp) cc_final: 0.6203 (mmp)
REVERT: A  701 LEU cc_start: 0.8395 (tt) cc_final: 0.7833 (mt)
REVERT: A  729 TYR cc_start: 0.8646 (m-80) cc_final: 0.7975 (m-80)
REVERT: A  738 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8399 (mmmt)
REVERT: A  997 PHE cc_start: 0.8236 (m-80) cc_final: 0.7965 (m-80)
REVERT: A 1028 HIS cc_start: 0.7680 (m90) cc_final: 0.7154 (m-70)
  outliers start: 20
  outliers final: 8
  residues processed: 146
  average time/residue: 0.2059
  time to fit residues: 41.9318
Evaluate side-chains
  131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1069 ILE
Chi-restraints excluded: chain A residue 1124 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 43 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0010
   chunk 110 optimal weight:    5.9990
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
A1124 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.188896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.134389 restraints weight = 11182.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.89
r_work: 0.3419 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3299 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9137  Z= 0.121
  Angle     :  0.535   9.323  12366  Z= 0.271
  Chirality :  0.039   0.290   1428
  Planarity :  0.003   0.041   1572
  Dihedral  :  3.591  14.735   1254
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.91 %
    Favored  : 80.51 %
  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:  1.51 (0.25), residues: 1161
  helix:  2.36 (0.19), residues: 747
  sheet: -1.93 (0.95), residues: 27
  loop : -1.63 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 441 
 HIS   0.004   0.001   HIS A 171 
 PHE   0.009   0.001   PHE A  72 
 TYR   0.010   0.001   TYR A1155 
 ARG   0.004   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04558 (  617)
  hydrogen bonds       : angle       4.03473 ( 1806)
  covalent geometry    : bond        0.00246 ( 9137)
  covalent geometry    : angle       0.53467 (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
  139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8325 (m-80) cc_final: 0.7951 (m-80)
REVERT: A  121 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8339 (mtmm)
REVERT: A  157 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7615 (mtm)
REVERT: A  217 ASN cc_start: 0.7553 (t0) cc_final: 0.7197 (m-40)
REVERT: A  229 ILE cc_start: 0.8207 (mt) cc_final: 0.7908 (mt)
REVERT: A  477 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6712 (pt0)
REVERT: A  514 ARG cc_start: 0.5882 (mtp-110) cc_final: 0.4885 (mtm-85)
REVERT: A  542 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6231 (tt0)
REVERT: A  553 MET cc_start: 0.6398 (mmp) cc_final: 0.6180 (mmp)
REVERT: A  701 LEU cc_start: 0.8458 (tt) cc_final: 0.7888 (mt)
REVERT: A  729 TYR cc_start: 0.8609 (m-80) cc_final: 0.7921 (m-80)
REVERT: A  738 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8416 (mmmt)
REVERT: A  997 PHE cc_start: 0.8134 (m-80) cc_final: 0.7760 (m-80)
REVERT: A 1028 HIS cc_start: 0.7715 (m90) cc_final: 0.7277 (m-70)
REVERT: A 1187 ASP cc_start: 0.7645 (t70) cc_final: 0.6959 (t70)
  outliers start: 15
  outliers final: 9
  residues processed: 133
  average time/residue: 0.2158
  time to fit residues: 40.4340
Evaluate side-chains
  127 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  173 MET
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  802 ILE
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1069 ILE
Chi-restraints excluded: chain A residue 1084 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 109 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   chunk 7 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A1169 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.185899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.131129 restraints weight = 11121.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 1.88
r_work: 0.3378 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.4476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9137  Z= 0.137
  Angle     :  0.539   9.645  12366  Z= 0.277
  Chirality :  0.040   0.311   1428
  Planarity :  0.003   0.041   1572
  Dihedral  :  3.628  14.911   1254
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 17.28 %
    Favored  : 80.19 %
  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:  1.37 (0.25), residues: 1161
  helix:  2.23 (0.18), residues: 748
  sheet: -2.04 (0.92), residues: 27
  loop : -1.64 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 791 
 HIS   0.006   0.001   HIS A 171 
 PHE   0.011   0.001   PHE A  72 
 TYR   0.012   0.001   TYR A1155 
 ARG   0.002   0.000   ARG A1179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04742 (  617)
  hydrogen bonds       : angle       4.08948 ( 1806)
  covalent geometry    : bond        0.00291 ( 9137)
  covalent geometry    : angle       0.53875 (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
  150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8374 (m-80) cc_final: 0.8052 (m-80)
REVERT: A  121 LYS cc_start: 0.8680 (mtmt) cc_final: 0.7851 (mptt)
REVERT: A  157 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7780 (mpp)
REVERT: A  217 ASN cc_start: 0.7569 (t0) cc_final: 0.6964 (m-40)
REVERT: A  229 ILE cc_start: 0.8236 (mt) cc_final: 0.7903 (mt)
REVERT: A  440 ARG cc_start: 0.6225 (mtm-85) cc_final: 0.5549 (ttp80)
REVERT: A  514 ARG cc_start: 0.5975 (mtp-110) cc_final: 0.4993 (mtm-85)
REVERT: A  542 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6105 (tt0)
REVERT: A  701 LEU cc_start: 0.8365 (tt) cc_final: 0.7777 (mt)
REVERT: A  729 TYR cc_start: 0.8627 (m-80) cc_final: 0.7988 (m-80)
REVERT: A  738 LYS cc_start: 0.8675 (mmtp) cc_final: 0.8434 (mmmt)
REVERT: A  997 PHE cc_start: 0.8139 (m-80) cc_final: 0.7841 (m-80)
REVERT: A 1028 HIS cc_start: 0.7690 (m90) cc_final: 0.7102 (m-70)
REVERT: A 1069 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8594 (mt)
REVERT: A 1187 ASP cc_start: 0.7769 (t70) cc_final: 0.7126 (t70)
  outliers start: 24
  outliers final: 12
  residues processed: 143
  average time/residue: 0.2223
  time to fit residues: 44.5403
Evaluate side-chains
  135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1066 SER
Chi-restraints excluded: chain A residue 1069 ILE
Chi-restraints excluded: chain A residue 1084 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 96 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0770
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 236 GLN
A 486 HIS
A 797 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.188211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.137895 restraints weight = 11179.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.20
r_work: 0.3388 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.4585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9137  Z= 0.119
  Angle     :  0.537  10.668  12366  Z= 0.273
  Chirality :  0.040   0.304   1428
  Planarity :  0.003   0.042   1572
  Dihedral  :  3.564  14.312   1254
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.65 %
    Favored  : 79.03 %
  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:  1.44 (0.25), residues: 1161
  helix:  2.32 (0.18), residues: 748
  sheet: -1.97 (0.92), residues: 27
  loop : -1.69 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 441 
 HIS   0.004   0.001   HIS A 171 
 PHE   0.010   0.001   PHE A 552 
 TYR   0.010   0.001   TYR A 729 
 ARG   0.002   0.000   ARG A1179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04490 (  617)
  hydrogen bonds       : angle       4.05724 ( 1806)
  covalent geometry    : bond        0.00240 ( 9137)
  covalent geometry    : angle       0.53663 (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
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A   41 TYR cc_start: 0.8402 (m-80) cc_final: 0.8023 (m-80)
REVERT: A  121 LYS cc_start: 0.8667 (mtmt) cc_final: 0.7770 (mptt)
REVERT: A  157 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7649 (mtm)
REVERT: A  217 ASN cc_start: 0.7510 (t0) cc_final: 0.7145 (m-40)
REVERT: A  229 ILE cc_start: 0.8174 (mt) cc_final: 0.7844 (mt)
REVERT: A  440 ARG cc_start: 0.6329 (mtm-85) cc_final: 0.5630 (ttp80)
REVERT: A  477 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6402 (pt0)
REVERT: A  513 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7232 (mp10)
REVERT: A  514 ARG cc_start: 0.5858 (mtp-110) cc_final: 0.4956 (mtm-85)
REVERT: A  542 GLU cc_start: 0.6403 (OUTLIER) cc_final: 0.6108 (tt0)
REVERT: A  701 LEU cc_start: 0.8408 (tt) cc_final: 0.7848 (mt)
REVERT: A  729 TYR cc_start: 0.8623 (m-80) cc_final: 0.8012 (m-80)
REVERT: A  738 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8449 (mmmt)
REVERT: A  853 PHE cc_start: 0.8412 (t80) cc_final: 0.8170 (t80)
REVERT: A  864 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8082 (mtpt)
REVERT: A  997 PHE cc_start: 0.8127 (m-80) cc_final: 0.7844 (m-80)
REVERT: A 1187 ASP cc_start: 0.7656 (t70) cc_final: 0.6991 (t70)
  outliers start: 22
  outliers final: 13
  residues processed: 141
  average time/residue: 0.2398
  time to fit residues: 47.7502
Evaluate side-chains
  134 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue  998 GLU
Chi-restraints excluded: chain A residue 1066 SER
Chi-restraints excluded: chain A residue 1084 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 94 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 18 optimal weight:    8.9990
   chunk 105 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 59 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN
A 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.186300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.135615 restraints weight = 11313.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.42
r_work: 0.3363 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.4746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9137  Z= 0.133
  Angle     :  0.560  11.139  12366  Z= 0.284
  Chirality :  0.041   0.340   1428
  Planarity :  0.003   0.042   1572
  Dihedral  :  3.626  14.418   1254
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.44 %
    Favored  : 79.14 %
  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:  1.37 (0.25), residues: 1161
  helix:  2.26 (0.18), residues: 748
  sheet: -2.09 (0.90), residues: 27
  loop : -1.70 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 441 
 HIS   0.005   0.001   HIS A 171 
 PHE   0.013   0.001   PHE A 138 
 TYR   0.011   0.001   TYR A1155 
 ARG   0.005   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04640 (  617)
  hydrogen bonds       : angle       4.10413 ( 1806)
  covalent geometry    : bond        0.00282 ( 9137)
  covalent geometry    : angle       0.55999 (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
  150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8425 (m-80) cc_final: 0.8049 (m-80)
REVERT: A  121 LYS cc_start: 0.8682 (mtmt) cc_final: 0.7735 (mptt)
REVERT: A  159 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7869 (tt0)
REVERT: A  217 ASN cc_start: 0.7526 (t0) cc_final: 0.7147 (m-40)
REVERT: A  229 ILE cc_start: 0.8176 (mt) cc_final: 0.7839 (mt)
REVERT: A  440 ARG cc_start: 0.6383 (mtm-85) cc_final: 0.5671 (ttp80)
REVERT: A  513 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7162 (mp10)
REVERT: A  514 ARG cc_start: 0.5983 (mtp-110) cc_final: 0.5075 (mtm-85)
REVERT: A  701 LEU cc_start: 0.8421 (tt) cc_final: 0.7816 (mt)
REVERT: A  729 TYR cc_start: 0.8648 (m-80) cc_final: 0.8057 (m-80)
REVERT: A  738 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8458 (mmmt)
REVERT: A  853 PHE cc_start: 0.8416 (t80) cc_final: 0.8170 (t80)
REVERT: A  997 PHE cc_start: 0.8076 (m-80) cc_final: 0.7803 (m-80)
REVERT: A 1028 HIS cc_start: 0.7759 (m90) cc_final: 0.7210 (m-70)
REVERT: A 1187 ASP cc_start: 0.7626 (t70) cc_final: 0.6736 (t70)
  outliers start: 23
  outliers final: 14
  residues processed: 144
  average time/residue: 0.2790
  time to fit residues: 56.9467
Evaluate side-chains
  136 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1066 SER
Chi-restraints excluded: chain A residue 1084 MET
Chi-restraints excluded: chain A residue 1220 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 109 optimal weight:   10.0000
   chunk 56 optimal weight:    8.9990
   chunk 114 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 236 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.180323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.131591 restraints weight = 11227.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.92
r_work: 0.3287 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.5225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9137  Z= 0.192
  Angle     :  0.620  10.871  12366  Z= 0.319
  Chirality :  0.043   0.337   1428
  Planarity :  0.004   0.042   1572
  Dihedral  :  3.918  15.829   1254
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.28 %
    Favored  : 78.50 %
  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:  1.03 (0.25), residues: 1161
  helix:  1.98 (0.18), residues: 743
  sheet: -2.01 (0.85), residues: 34
  loop : -1.76 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 113 
 HIS   0.009   0.002   HIS A 171 
 PHE   0.017   0.002   PHE A  72 
 TYR   0.019   0.002   TYR A1155 
 ARG   0.005   0.001   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05304 (  617)
  hydrogen bonds       : angle       4.32541 ( 1806)
  covalent geometry    : bond        0.00435 ( 9137)
  covalent geometry    : angle       0.62015 (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
  158 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.996 
Fit side-chains
REVERT: A   41 TYR cc_start: 0.8487 (m-80) cc_final: 0.8154 (m-80)
REVERT: A  159 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7856 (tt0)
REVERT: A  217 ASN cc_start: 0.7592 (t0) cc_final: 0.7220 (m-40)
REVERT: A  229 ILE cc_start: 0.8387 (mt) cc_final: 0.8087 (mt)
REVERT: A  440 ARG cc_start: 0.6756 (mtm-85) cc_final: 0.6407 (ttp80)
REVERT: A  441 TRP cc_start: 0.8315 (t60) cc_final: 0.7717 (t-100)
REVERT: A  470 ASP cc_start: 0.8883 (m-30) cc_final: 0.8374 (t0)
REVERT: A  513 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7232 (mp10)
REVERT: A  514 ARG cc_start: 0.6192 (mtp-110) cc_final: 0.5270 (mtm-85)
REVERT: A  684 ASN cc_start: 0.4958 (t0) cc_final: 0.4577 (m110)
REVERT: A  691 LYS cc_start: 0.7253 (ttmt) cc_final: 0.6628 (tptp)
REVERT: A  738 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8479 (mmmt)
REVERT: A  853 PHE cc_start: 0.8480 (t80) cc_final: 0.8253 (t80)
REVERT: A  864 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8207 (mtpt)
REVERT: A  997 PHE cc_start: 0.8344 (m-80) cc_final: 0.8091 (m-80)
REVERT: A 1053 LYS cc_start: 0.7349 (tptt) cc_final: 0.7047 (tmtt)
REVERT: A 1084 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5272 (tmm)
REVERT: A 1183 ILE cc_start: 0.8519 (mt) cc_final: 0.8175 (tt)
REVERT: A 1187 ASP cc_start: 0.7720 (t70) cc_final: 0.6829 (t70)
  outliers start: 21
  outliers final: 15
  residues processed: 153
  average time/residue: 0.2730
  time to fit residues: 59.6595
Evaluate side-chains
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue  998 GLU
Chi-restraints excluded: chain A residue 1066 SER
Chi-restraints excluded: chain A residue 1084 MET
Chi-restraints excluded: chain A residue 1115 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   chunk 34 optimal weight:    0.0060
   chunk 15 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0050
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:    5.9990
   chunk 91 optimal weight:    9.9990
   chunk 106 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.9412

-------------------------------------------------------------------------------
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 = 0.4109 r_free = 0.4109 target = 0.183978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.136306 restraints weight = 11252.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.89
r_work: 0.3345 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.5276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9137  Z= 0.136
  Angle     :  0.590  11.574  12366  Z= 0.298
  Chirality :  0.041   0.359   1428
  Planarity :  0.004   0.056   1572
  Dihedral  :  3.802  14.449   1254
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 19.92 %
    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:  1.22 (0.25), residues: 1161
  helix:  2.09 (0.18), residues: 754
  sheet: -2.56 (0.91), residues: 20
  loop : -1.70 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 791 
 HIS   0.005   0.001   HIS A 171 
 PHE   0.011   0.001   PHE A 792 
 TYR   0.014   0.001   TYR A1155 
 ARG   0.005   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04791 (  617)
  hydrogen bonds       : angle       4.17839 ( 1806)
  covalent geometry    : bond        0.00287 ( 9137)
  covalent geometry    : angle       0.58992 (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
  150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A   41 TYR cc_start: 0.8457 (m-80) cc_final: 0.8067 (m-80)
REVERT: A  217 ASN cc_start: 0.7514 (t0) cc_final: 0.7157 (m-40)
REVERT: A  229 ILE cc_start: 0.8125 (mt) cc_final: 0.7809 (mt)
REVERT: A  384 LYS cc_start: 0.2537 (tptt) cc_final: 0.2015 (tptp)
REVERT: A  440 ARG cc_start: 0.6774 (mtm-85) cc_final: 0.6343 (ttp80)
REVERT: A  470 ASP cc_start: 0.8840 (m-30) cc_final: 0.8361 (t0)
REVERT: A  513 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7194 (mp10)
REVERT: A  514 ARG cc_start: 0.5918 (mtp-110) cc_final: 0.5114 (mtm-85)
REVERT: A  684 ASN cc_start: 0.4978 (t0) cc_final: 0.4507 (m110)
REVERT: A  691 LYS cc_start: 0.7081 (ttmt) cc_final: 0.6519 (tptp)
REVERT: A  701 LEU cc_start: 0.8414 (tt) cc_final: 0.7774 (mt)
REVERT: A  738 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8454 (mmmt)
REVERT: A  853 PHE cc_start: 0.8383 (t80) cc_final: 0.8151 (t80)
REVERT: A  864 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8141 (mtpt)
REVERT: A  997 PHE cc_start: 0.8190 (m-80) cc_final: 0.7930 (m-80)
REVERT: A 1053 LYS cc_start: 0.7530 (tptt) cc_final: 0.7278 (tmtt)
REVERT: A 1183 ILE cc_start: 0.8436 (mt) cc_final: 0.8095 (tt)
REVERT: A 1187 ASP cc_start: 0.7698 (t70) cc_final: 0.6793 (t70)
  outliers start: 19
  outliers final: 15
  residues processed: 144
  average time/residue: 0.2151
  time to fit residues: 43.1014
Evaluate side-chains
  141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  528 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  722 SER
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  907 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1066 SER
Chi-restraints excluded: chain A residue 1184 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 41 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.4102 r_free = 0.4102 target = 0.183396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135599 restraints weight = 11216.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.89
r_work: 0.3344 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.5374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9137  Z= 0.145
  Angle     :  0.602  11.670  12366  Z= 0.304
  Chirality :  0.041   0.337   1428
  Planarity :  0.004   0.061   1572
  Dihedral  :  3.775  14.357   1254
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 20.65 %
    Favored  : 77.66 %
  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:  1.18 (0.25), residues: 1161
  helix:  2.15 (0.18), residues: 747
  sheet: -3.17 (0.74), residues: 27
  loop : -1.78 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 791 
 HIS   0.006   0.001   HIS A 171 
 PHE   0.022   0.001   PHE A1144 
 TYR   0.014   0.001   TYR A1155 
 ARG   0.004   0.000   ARG A1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04824 (  617)
  hydrogen bonds       : angle       4.16293 ( 1806)
  covalent geometry    : bond        0.00314 ( 9137)
  covalent geometry    : angle       0.60153 (12366)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5635.36 seconds
wall clock time: 98 minutes 51.07 seconds (5931.07 seconds total)