Starting phenix.real_space_refine
on Mon May 12 12:12:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jun_61831/05_2025/9jun_61831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jun_61831/05_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_61831/05_2025/9jun_61831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jun_61831/05_2025/9jun_61831.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jun_61831/05_2025/9jun_61831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jun_61831/05_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-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: 5.39, per 1000 atoms: 0.60
  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: 2.71
  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: 1.09
  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: 3.09

  Time building geometry restraints manager: 2.98 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:             0.680
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     24.310
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.370
-------------------------------------------------------------------------------
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  : 0.937 
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: 0.2233
  time to fit residues: 73.2019
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  : 0.914 
-------------------------------------------------------------------------------
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 = 0.143111 restraints weight = 11165.205|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 2.12
r_work: 0.3446 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
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  : 0.993 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7795 (ptmt) cc_final: 0.7188 (ptpp)
REVERT: A   41 TYR cc_start: 0.8273 (m-80) cc_final: 0.8060 (m-80)
REVERT: A  121 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8399 (mtmm)
REVERT: A  217 ASN cc_start: 0.7555 (t0) cc_final: 0.6911 (m-40)
REVERT: A  229 ILE cc_start: 0.8343 (mt) cc_final: 0.8109 (mt)
REVERT: A  441 TRP cc_start: 0.8232 (t60) cc_final: 0.8019 (t60)
REVERT: A  491 LYS cc_start: 0.8076 (pttt) cc_final: 0.7344 (tttm)
REVERT: A  514 ARG cc_start: 0.5417 (mtp-110) cc_final: 0.4458 (mtm-85)
REVERT: A  532 GLU cc_start: 0.5127 (tm-30) cc_final: 0.4105 (tt0)
REVERT: A  553 MET cc_start: 0.6605 (mmp) cc_final: 0.6283 (mmp)
REVERT: A  697 TRP cc_start: 0.7600 (m-10) cc_final: 0.7300 (m-10)
REVERT: A  701 LEU cc_start: 0.8377 (tt) cc_final: 0.7908 (mt)
REVERT: A  738 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8391 (mmmt)
REVERT: A  801 ARG cc_start: 0.7274 (mtm-85) cc_final: 0.6914 (mtt180)
REVERT: A 1028 HIS cc_start: 0.7680 (m90) cc_final: 0.7285 (m-70)
REVERT: A 1122 TYR cc_start: 0.8340 (t80) cc_final: 0.8106 (t80)
  outliers start: 12
  outliers final: 5
  residues processed: 152
  average time/residue: 0.2147
  time to fit residues: 45.3732
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  : 1.029 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 41 optimal weight:    6.9990
   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:    0.8380

-------------------------------------------------------------------------------
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 = 0.4183 r_free = 0.4183 target = 0.191484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.136765 restraints weight = 11216.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.89
r_work: 0.3443 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3326 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.3266

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= 0.129
  Angle     :  0.526   8.041  12366  Z= 0.273
  Chirality :  0.039   0.247   1428
  Planarity :  0.003   0.039   1572
  Dihedral  :  3.659  14.553   1254
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.80 %
    Favored  : 84.93 %
  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:  1.62 (0.25), residues: 1161
  helix:  2.37 (0.19), residues: 752
  sheet: -1.16 (0.93), residues: 34
  loop : -1.53 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 791 
 HIS   0.005   0.001   HIS A1101 
 PHE   0.010   0.001   PHE A  72 
 TYR   0.010   0.001   TYR A 729 
 ARG   0.009   0.000   ARG A 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04775 (  617)
  hydrogen bonds       : angle       4.08379 ( 1806)
  covalent geometry    : bond        0.00266 ( 9137)
  covalent geometry    : angle       0.52557 (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
  150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8302 (m-80) cc_final: 0.7924 (m-80)
REVERT: A  121 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8405 (mtmm)
REVERT: A  157 MET cc_start: 0.8051 (mpp) cc_final: 0.7617 (mtm)
REVERT: A  217 ASN cc_start: 0.7546 (t0) cc_final: 0.6908 (m-40)
REVERT: A  229 ILE cc_start: 0.8275 (mt) cc_final: 0.7995 (mt)
REVERT: A  514 ARG cc_start: 0.5763 (mtp-110) cc_final: 0.4723 (mtm-85)
REVERT: A  532 GLU cc_start: 0.5279 (tm-30) cc_final: 0.3890 (tt0)
REVERT: A  553 MET cc_start: 0.6580 (mmp) cc_final: 0.6265 (mmp)
REVERT: A  701 LEU cc_start: 0.8472 (tt) cc_final: 0.7887 (mt)
REVERT: A  729 TYR cc_start: 0.8691 (m-80) cc_final: 0.7992 (m-80)
REVERT: A  738 LYS cc_start: 0.8630 (mmtp) cc_final: 0.8362 (mmmt)
REVERT: A  801 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.7100 (mtt180)
REVERT: A 1028 HIS cc_start: 0.7544 (m90) cc_final: 0.7183 (m-70)
REVERT: A 1122 TYR cc_start: 0.8353 (t80) cc_final: 0.8080 (t80)
  outliers start: 12
  outliers final: 7
  residues processed: 145
  average time/residue: 0.2071
  time to fit residues: 41.6380
Evaluate side-chains
  123 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
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  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:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 102 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 103 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 797 ASN
** A1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1169 GLN
** A1228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.178662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.129729 restraints weight = 11326.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 1.99
r_work: 0.3260 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.4874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   9137  Z= 0.276
  Angle     :  0.677   7.888  12366  Z= 0.359
  Chirality :  0.045   0.171   1428
  Planarity :  0.005   0.056   1572
  Dihedral  :  4.309  19.107   1254
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.94 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.91 %
    Favored  : 81.56 %
  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:  0.58 (0.24), residues: 1161
  helix:  1.49 (0.18), residues: 749
  sheet: -1.39 (0.88), residues: 34
  loop : -1.75 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A 441 
 HIS   0.014   0.002   HIS A 171 
 PHE   0.022   0.003   PHE A 375 
 TYR   0.025   0.003   TYR A1155 
 ARG   0.016   0.001   ARG A 298 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06105 (  617)
  hydrogen bonds       : angle       4.61806 ( 1806)
  covalent geometry    : bond        0.00635 ( 9137)
  covalent geometry    : angle       0.67704 (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
  170 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8517 (m-80) cc_final: 0.8202 (m-80)
REVERT: A  157 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7492 (mpt)
REVERT: A  217 ASN cc_start: 0.7696 (t0) cc_final: 0.7246 (m-40)
REVERT: A  440 ARG cc_start: 0.6459 (mtm-85) cc_final: 0.5869 (ttp80)
REVERT: A  441 TRP cc_start: 0.8344 (t60) cc_final: 0.7784 (t-100)
REVERT: A  514 ARG cc_start: 0.6055 (mtp-110) cc_final: 0.5013 (mtm-85)
REVERT: A  542 GLU cc_start: 0.6711 (pm20) cc_final: 0.6178 (tt0)
REVERT: A  684 ASN cc_start: 0.4941 (t0) cc_final: 0.4467 (m110)
REVERT: A  691 LYS cc_start: 0.7059 (ttmt) cc_final: 0.6452 (tptp)
REVERT: A  738 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8547 (mmmt)
REVERT: A  796 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6724 (pt0)
REVERT: A  893 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7948 (mtm-85)
REVERT: A  997 PHE cc_start: 0.8298 (m-80) cc_final: 0.8021 (m-80)
REVERT: A 1069 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8514 (mt)
REVERT: A 1084 MET cc_start: 0.6026 (tpt) cc_final: 0.5303 (tmm)
REVERT: A 1183 ILE cc_start: 0.8593 (mt) cc_final: 0.8233 (tt)
REVERT: A 1187 ASP cc_start: 0.7833 (t70) cc_final: 0.7336 (t70)
  outliers start: 24
  outliers final: 9
  residues processed: 163
  average time/residue: 0.2389
  time to fit residues: 53.7237
Evaluate side-chains
  143 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 131
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
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  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  796 GLU
Chi-restraints excluded: chain A residue  802 ILE
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:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0470
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 110 optimal weight:    8.9990
   overall best weight:    0.7278

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 486 HIS
A 693 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.184467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.133805 restraints weight = 11123.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.11
r_work: 0.3337 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.4854

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= 0.130
  Angle     :  0.554   9.134  12366  Z= 0.284
  Chirality :  0.040   0.166   1428
  Planarity :  0.003   0.039   1572
  Dihedral  :  3.822  15.831   1254
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.00 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 18.02 %
    Favored  : 80.61 %
  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:  1.12 (0.25), residues: 1161
  helix:  1.97 (0.18), residues: 753
  sheet: -2.21 (0.90), residues: 27
  loop : -1.63 (0.31), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 441 
 HIS   0.004   0.001   HIS A1101 
 PHE   0.023   0.001   PHE A 686 
 TYR   0.013   0.001   TYR A1155 
 ARG   0.004   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04821 (  617)
  hydrogen bonds       : angle       4.25175 ( 1806)
  covalent geometry    : bond        0.00263 ( 9137)
  covalent geometry    : angle       0.55387 (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
  146 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 ASP cc_start: 0.8761 (m-30) cc_final: 0.8474 (m-30)
REVERT: A   41 TYR cc_start: 0.8455 (m-80) cc_final: 0.8158 (m-80)
REVERT: A  121 LYS cc_start: 0.8791 (mtmt) cc_final: 0.7932 (mptt)
REVERT: A  157 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7725 (mpp)
REVERT: A  217 ASN cc_start: 0.7561 (t0) cc_final: 0.6916 (m-40)
REVERT: A  440 ARG cc_start: 0.6266 (mtm-85) cc_final: 0.5654 (ttp80)
REVERT: A  441 TRP cc_start: 0.8229 (t60) cc_final: 0.7609 (t-100)
REVERT: A  514 ARG cc_start: 0.5877 (mtp-110) cc_final: 0.4975 (mtm-85)
REVERT: A  542 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6216 (tt0)
REVERT: A  684 ASN cc_start: 0.4928 (t0) cc_final: 0.4393 (m110)
REVERT: A  691 LYS cc_start: 0.7054 (ttmt) cc_final: 0.6624 (mmtt)
REVERT: A  738 LYS cc_start: 0.8742 (mmtp) cc_final: 0.8481 (mmmt)
REVERT: A  796 GLU cc_start: 0.7102 (mp0) cc_final: 0.6702 (pt0)
REVERT: A  853 PHE cc_start: 0.8390 (t80) cc_final: 0.8110 (t80)
REVERT: A  997 PHE cc_start: 0.8225 (m-80) cc_final: 0.7985 (m-80)
REVERT: A 1028 HIS cc_start: 0.7691 (m90) cc_final: 0.7239 (m-70)
REVERT: A 1084 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5141 (tmm)
REVERT: A 1187 ASP cc_start: 0.7654 (t70) cc_final: 0.7055 (t70)
  outliers start: 13
  outliers final: 4
  residues processed: 142
  average time/residue: 0.2115
  time to fit residues: 41.5255
Evaluate side-chains
  131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 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  907 LEU
Chi-restraints excluded: chain A residue  980 LEU
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:    0.9990
   chunk 109 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 18 optimal weight:    8.9990
   chunk 70 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 100 optimal weight:    6.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.184273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.134346 restraints weight = 11029.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 1.71
r_work: 0.3389 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3276 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4925

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= 0.130
  Angle     :  0.543   8.939  12366  Z= 0.279
  Chirality :  0.040   0.258   1428
  Planarity :  0.003   0.040   1572
  Dihedral  :  3.717  15.519   1254
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.51 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 19.70 %
    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:  1.24 (0.25), residues: 1161
  helix:  2.09 (0.18), residues: 754
  sheet: -2.43 (0.73), residues: 37
  loop : -1.58 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 441 
 HIS   0.005   0.001   HIS A 171 
 PHE   0.010   0.001   PHE A 138 
 TYR   0.012   0.001   TYR A1155 
 ARG   0.003   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04746 (  617)
  hydrogen bonds       : angle       4.16780 ( 1806)
  covalent geometry    : bond        0.00270 ( 9137)
  covalent geometry    : angle       0.54250 (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
  137 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8370 (m-80) cc_final: 0.8020 (m-80)
REVERT: A  121 LYS cc_start: 0.8702 (mtmt) cc_final: 0.7832 (mptt)
REVERT: A  122 MET cc_start: 0.8598 (tmm) cc_final: 0.8373 (tmm)
REVERT: A  217 ASN cc_start: 0.7518 (t0) cc_final: 0.7134 (m-40)
REVERT: A  440 ARG cc_start: 0.6356 (mtm-85) cc_final: 0.5741 (ttp80)
REVERT: A  441 TRP cc_start: 0.8253 (t60) cc_final: 0.7679 (t-100)
REVERT: A  514 ARG cc_start: 0.5877 (mtp-110) cc_final: 0.4967 (mtm-85)
REVERT: A  542 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6192 (tt0)
REVERT: A  684 ASN cc_start: 0.4875 (t0) cc_final: 0.4377 (m110)
REVERT: A  691 LYS cc_start: 0.7026 (ttmt) cc_final: 0.6643 (mmtt)
REVERT: A  729 TYR cc_start: 0.8571 (m-80) cc_final: 0.7961 (m-80)
REVERT: A  738 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8429 (mmmt)
REVERT: A  796 GLU cc_start: 0.7158 (mp0) cc_final: 0.6777 (pt0)
REVERT: A  853 PHE cc_start: 0.8329 (t80) cc_final: 0.8065 (t80)
REVERT: A  864 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8114 (mtpt)
REVERT: A  997 PHE cc_start: 0.8179 (m-80) cc_final: 0.7783 (m-80)
REVERT: A 1028 HIS cc_start: 0.7705 (m90) cc_final: 0.7157 (m-70)
REVERT: A 1183 ILE cc_start: 0.8360 (mt) cc_final: 0.8062 (tt)
REVERT: A 1187 ASP cc_start: 0.7560 (t70) cc_final: 0.6654 (t70)
  outliers start: 12
  outliers final: 8
  residues processed: 134
  average time/residue: 0.2271
  time to fit residues: 42.0953
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  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  398 THR
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  907 LEU
Chi-restraints excluded: chain A residue  980 LEU
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:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 96 optimal weight:    9.9990
   chunk 44 optimal weight:    8.9990
   chunk 82 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4115 r_free = 0.4115 target = 0.184643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.135678 restraints weight = 11131.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 1.81
r_work: 0.3381 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.5013

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     :  0.542  10.211  12366  Z= 0.279
  Chirality :  0.040   0.304   1428
  Planarity :  0.003   0.040   1572
  Dihedral  :  3.680  14.973   1254
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.43 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.86 %
    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:  1.26 (0.25), residues: 1161
  helix:  2.14 (0.18), residues: 752
  sheet: -2.49 (0.72), residues: 37
  loop : -1.65 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 441 
 HIS   0.005   0.001   HIS A 171 
 PHE   0.021   0.001   PHE A 686 
 TYR   0.011   0.001   TYR A1155 
 ARG   0.003   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04682 (  617)
  hydrogen bonds       : angle       4.15001 ( 1806)
  covalent geometry    : bond        0.00274 ( 9137)
  covalent geometry    : angle       0.54191 (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
  149 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 129
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ASP cc_start: 0.8696 (m-30) cc_final: 0.8446 (m-30)
REVERT: A   41 TYR cc_start: 0.8349 (m-80) cc_final: 0.7997 (m-80)
REVERT: A  121 LYS cc_start: 0.8713 (mtmt) cc_final: 0.7834 (mptt)
REVERT: A  141 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6439 (mt-10)
REVERT: A  159 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7702 (tt0)
REVERT: A  217 ASN cc_start: 0.7532 (t0) cc_final: 0.7141 (m-40)
REVERT: A  384 LYS cc_start: 0.2477 (tptt) cc_final: 0.2211 (tppt)
REVERT: A  440 ARG cc_start: 0.6430 (mtm-85) cc_final: 0.5813 (ttp80)
REVERT: A  441 TRP cc_start: 0.8264 (t60) cc_final: 0.7712 (t-100)
REVERT: A  514 ARG cc_start: 0.5952 (mtp-110) cc_final: 0.5198 (mtm-85)
REVERT: A  542 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6199 (tt0)
REVERT: A  684 ASN cc_start: 0.4879 (t0) cc_final: 0.4375 (m110)
REVERT: A  691 LYS cc_start: 0.7084 (ttmt) cc_final: 0.6767 (mmtt)
REVERT: A  729 TYR cc_start: 0.8543 (m-80) cc_final: 0.7997 (m-80)
REVERT: A  738 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8439 (mmmt)
REVERT: A  796 GLU cc_start: 0.7270 (mp0) cc_final: 0.6880 (pt0)
REVERT: A  853 PHE cc_start: 0.8348 (t80) cc_final: 0.8093 (t80)
REVERT: A  997 PHE cc_start: 0.8038 (m-80) cc_final: 0.7806 (m-80)
REVERT: A 1028 HIS cc_start: 0.7671 (m90) cc_final: 0.7152 (m-70)
REVERT: A 1187 ASP cc_start: 0.7622 (t70) cc_final: 0.6775 (t70)
  outliers start: 20
  outliers final: 13
  residues processed: 144
  average time/residue: 0.2186
  time to fit residues: 43.4481
Evaluate side-chains
  142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
Chi-restraints excluded: chain A residue  145 SER
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  398 THR
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  823 VAL
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 1084 MET
Chi-restraints excluded: chain A residue 1184 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 94 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 18 optimal weight:    8.9990
   chunk 105 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0070
   chunk 93 optimal weight:    0.4980
   overall best weight:    0.7800

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

Flipped N/Q/H residues before XYZ refinement:
A 347 HIS
** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.185094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.137505 restraints weight = 11250.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.00
r_work: 0.3361 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.5104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9137  Z= 0.127
  Angle     :  0.558  11.485  12366  Z= 0.283
  Chirality :  0.040   0.356   1428
  Planarity :  0.004   0.056   1572
  Dihedral  :  3.664  14.587   1254
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.43 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.39 %
    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:  1.33 (0.25), residues: 1161
  helix:  2.15 (0.18), residues: 755
  sheet: -2.12 (0.99), residues: 20
  loop : -1.64 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 441 
 HIS   0.004   0.001   HIS A 171 
 PHE   0.011   0.001   PHE A 138 
 TYR   0.011   0.001   TYR A 729 
 ARG   0.004   0.000   ARG A1220 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04600 (  617)
  hydrogen bonds       : angle       4.13274 ( 1806)
  covalent geometry    : bond        0.00264 ( 9137)
  covalent geometry    : angle       0.55788 (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
  153 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 132
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ASP cc_start: 0.8755 (m-30) cc_final: 0.8479 (m-30)
REVERT: A   41 TYR cc_start: 0.8407 (m-80) cc_final: 0.8041 (m-80)
REVERT: A  121 LYS cc_start: 0.8668 (mtmt) cc_final: 0.7788 (mptt)
REVERT: A  141 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6479 (mt-10)
REVERT: A  159 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7900 (tt0)
REVERT: A  217 ASN cc_start: 0.7526 (t0) cc_final: 0.7031 (m-40)
REVERT: A  384 LYS cc_start: 0.2606 (tptt) cc_final: 0.2150 (tptp)
REVERT: A  440 ARG cc_start: 0.6485 (mtm-85) cc_final: 0.5860 (ttp80)
REVERT: A  470 ASP cc_start: 0.8854 (m-30) cc_final: 0.8439 (t0)
REVERT: A  514 ARG cc_start: 0.5986 (mtp-110) cc_final: 0.5244 (mtm-85)
REVERT: A  684 ASN cc_start: 0.4826 (t0) cc_final: 0.4309 (m110)
REVERT: A  691 LYS cc_start: 0.7086 (ttmt) cc_final: 0.6740 (mmtt)
REVERT: A  729 TYR cc_start: 0.8599 (m-80) cc_final: 0.8054 (m-80)
REVERT: A  738 LYS cc_start: 0.8740 (mmtp) cc_final: 0.8460 (mmmt)
REVERT: A  796 GLU cc_start: 0.7310 (mp0) cc_final: 0.7003 (pt0)
REVERT: A  853 PHE cc_start: 0.8402 (t80) cc_final: 0.8168 (t80)
REVERT: A  864 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8138 (mtpt)
REVERT: A  997 PHE cc_start: 0.8061 (m-80) cc_final: 0.7830 (m-80)
REVERT: A 1183 ILE cc_start: 0.8468 (mt) cc_final: 0.8149 (tt)
REVERT: A 1187 ASP cc_start: 0.7673 (t70) cc_final: 0.6806 (t70)
  outliers start: 21
  outliers final: 15
  residues processed: 147
  average time/residue: 0.2092
  time to fit residues: 42.6200
Evaluate side-chains
  143 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
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  229 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  398 THR
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 1084 MET
Chi-restraints excluded: chain A residue 1184 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 104 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 60 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0670
   chunk 114 optimal weight:   20.0000
   chunk 107 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.0122

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

Flipped N/Q/H residues before XYZ refinement:
A 546 GLN
** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.184032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.135115 restraints weight = 11134.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.79
r_work: 0.3375 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3261 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.5230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9137  Z= 0.137
  Angle     :  0.577  12.031  12366  Z= 0.292
  Chirality :  0.041   0.369   1428
  Planarity :  0.004   0.058   1572
  Dihedral  :  3.696  14.411   1254
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.60 %
    Favored  : 78.29 %
  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:  1.27 (0.25), residues: 1161
  helix:  2.09 (0.18), residues: 755
  sheet: -2.05 (1.07), residues: 20
  loop : -1.64 (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   0.021   0.001   PHE A 686 
 TYR   0.012   0.001   TYR A1155 
 ARG   0.003   0.000   ARG A1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04730 (  617)
  hydrogen bonds       : angle       4.16480 ( 1806)
  covalent geometry    : bond        0.00296 ( 9137)
  covalent geometry    : angle       0.57666 (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
  154 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.912 
Fit side-chains
REVERT: A   40 ASP cc_start: 0.8715 (m-30) cc_final: 0.8459 (m-30)
REVERT: A   41 TYR cc_start: 0.8339 (m-80) cc_final: 0.7971 (m-80)
REVERT: A  121 LYS cc_start: 0.8642 (mtmt) cc_final: 0.7725 (mptt)
REVERT: A  141 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6357 (mt-10)
REVERT: A  217 ASN cc_start: 0.7509 (t0) cc_final: 0.7120 (m-40)
REVERT: A  220 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7977 (mm-40)
REVERT: A  384 LYS cc_start: 0.2556 (tptt) cc_final: 0.2082 (tptp)
REVERT: A  440 ARG cc_start: 0.6700 (mtm-85) cc_final: 0.6194 (ttp80)
REVERT: A  470 ASP cc_start: 0.8816 (m-30) cc_final: 0.8402 (t0)
REVERT: A  514 ARG cc_start: 0.5876 (mtp-110) cc_final: 0.5166 (mtm-85)
REVERT: A  684 ASN cc_start: 0.4866 (t0) cc_final: 0.4388 (m110)
REVERT: A  691 LYS cc_start: 0.7109 (ttmt) cc_final: 0.6662 (mmtt)
REVERT: A  701 LEU cc_start: 0.8300 (tt) cc_final: 0.7752 (mt)
REVERT: A  729 TYR cc_start: 0.8538 (m-80) cc_final: 0.7994 (m-80)
REVERT: A  738 LYS cc_start: 0.8718 (mmtp) cc_final: 0.8440 (mmmt)
REVERT: A  796 GLU cc_start: 0.7330 (mp0) cc_final: 0.7037 (pt0)
REVERT: A  853 PHE cc_start: 0.8354 (t80) cc_final: 0.8114 (t80)
REVERT: A  997 PHE cc_start: 0.8075 (m-80) cc_final: 0.7829 (m-80)
REVERT: A 1183 ILE cc_start: 0.8443 (mt) cc_final: 0.8105 (tt)
REVERT: A 1187 ASP cc_start: 0.7641 (t70) cc_final: 0.6799 (t70)
  outliers start: 20
  outliers final: 17
  residues processed: 149
  average time/residue: 0.2216
  time to fit residues: 46.7677
Evaluate side-chains
  149 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
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  229 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  398 THR
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  998 GLU
Chi-restraints excluded: chain A residue 1084 MET
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 75 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 44 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 106 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.184869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137123 restraints weight = 11196.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.97
r_work: 0.3358 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.5305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   9137  Z= 0.133
  Angle     :  0.600  14.631  12366  Z= 0.299
  Chirality :  0.041   0.345   1428
  Planarity :  0.004   0.055   1572
  Dihedral  :  3.724  14.623   1254
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.02 %
    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:  1.28 (0.25), residues: 1161
  helix:  2.12 (0.18), residues: 753
  sheet: -2.00 (1.10), residues: 20
  loop : -1.67 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 188 
 HIS   0.004   0.001   HIS A 171 
 PHE   0.018   0.001   PHE A1144 
 TYR   0.011   0.001   TYR A 729 
 ARG   0.005   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04676 (  617)
  hydrogen bonds       : angle       4.17480 ( 1806)
  covalent geometry    : bond        0.00283 ( 9137)
  covalent geometry    : angle       0.60047 (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
  148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 ASP cc_start: 0.8771 (m-30) cc_final: 0.8441 (m-30)
REVERT: A   41 TYR cc_start: 0.8395 (m-80) cc_final: 0.8008 (m-80)
REVERT: A  141 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6427 (mt-10)
REVERT: A  151 ILE cc_start: 0.7376 (mm) cc_final: 0.6845 (mt)
REVERT: A  217 ASN cc_start: 0.7486 (t0) cc_final: 0.7124 (m-40)
REVERT: A  384 LYS cc_start: 0.2647 (tptt) cc_final: 0.2186 (tptp)
REVERT: A  440 ARG cc_start: 0.6722 (mtm-85) cc_final: 0.6238 (ttp80)
REVERT: A  470 ASP cc_start: 0.8850 (m-30) cc_final: 0.8413 (t0)
REVERT: A  514 ARG cc_start: 0.5936 (mtp-110) cc_final: 0.5241 (mtm-85)
REVERT: A  684 ASN cc_start: 0.4896 (t0) cc_final: 0.4399 (m110)
REVERT: A  691 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6747 (mmtt)
REVERT: A  729 TYR cc_start: 0.8563 (m-80) cc_final: 0.8027 (m-80)
REVERT: A  738 LYS cc_start: 0.8750 (mmtp) cc_final: 0.8469 (mmmt)
REVERT: A  796 GLU cc_start: 0.7333 (mp0) cc_final: 0.7020 (pt0)
REVERT: A  853 PHE cc_start: 0.8374 (t80) cc_final: 0.8142 (t80)
REVERT: A  864 LYS cc_start: 0.8413 (mtpt) cc_final: 0.8154 (mtpt)
REVERT: A  997 PHE cc_start: 0.8072 (m-80) cc_final: 0.7839 (m-80)
REVERT: A 1183 ILE cc_start: 0.8492 (mt) cc_final: 0.8127 (tt)
REVERT: A 1187 ASP cc_start: 0.7599 (t70) cc_final: 0.6730 (t70)
  outliers start: 18
  outliers final: 15
  residues processed: 142
  average time/residue: 0.2198
  time to fit residues: 43.1053
Evaluate side-chains
  142 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 126
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 GLU
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  229 ILE
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 1084 MET
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:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 63 optimal weight:    0.4980
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.184596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.136679 restraints weight = 11195.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.90
r_work: 0.3359 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9137  Z= 0.134
  Angle     :  0.599  15.007  12366  Z= 0.298
  Chirality :  0.041   0.356   1428
  Planarity :  0.004   0.054   1572
  Dihedral  :  3.697  14.769   1254
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 20.23 %
    Favored  : 77.87 %
  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:  1.29 (0.25), residues: 1161
  helix:  2.14 (0.18), residues: 752
  sheet: -2.16 (1.10), residues: 20
  loop : -1.67 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 188 
 HIS   0.004   0.001   HIS A 171 
 PHE   0.021   0.001   PHE A 686 
 TYR   0.011   0.001   TYR A1155 
 ARG   0.005   0.000   ARG A 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04672 (  617)
  hydrogen bonds       : angle       4.13506 ( 1806)
  covalent geometry    : bond        0.00288 ( 9137)
  covalent geometry    : angle       0.59888 (12366)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4910.45 seconds
wall clock time: 85 minutes 54.89 seconds (5154.89 seconds total)