Starting phenix.real_space_refine
on Wed Sep 17 13:53:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jun_61831/09_2025/9jun_61831.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jun_61831/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jun_61831/09_2025/9jun_61831.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jun_61831/09_2025/9jun_61831.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jun_61831/09_2025/9jun_61831.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jun_61831/09_2025/9jun_61831.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.38, per 1000 atoms: 0.27
  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: 0.97
  Conformation dependent library (CDL) restraints added in 379.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.23
  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: 1.59

  Time building geometry restraints manager: 1.24 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:             0.900
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.400
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.950
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.009   0.001   ARG A1050 
 TYR   0.018   0.001   TYR A1117 
 PHE   0.019   0.001   PHE A 686 
 TRP   0.018   0.001   TRP A 697 
 HIS   0.003   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9137)
  covalent geometry    : angle       0.57301 (12366)
  hydrogen bonds       : bond        0.12679 (  617)
  hydrogen bonds       : angle       5.15009 ( 1806)

*********************** 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  : 0.337 
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: 0.1093
  time to fit residues: 36.0680
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  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.0870
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0470
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.200046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.146646 restraints weight = 11383.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 1.88
r_work: 0.3575 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3461 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9137  Z= 0.132
  Angle     :  0.553   9.492  12366  Z= 0.286
  Chirality :  0.040   0.239   1428
  Planarity :  0.003   0.039   1572
  Dihedral  :  3.762  14.803   1254
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.70 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.26), residues: 1161
  helix:  2.55 (0.19), residues: 745
  sheet: -1.45 (0.87), residues: 34
  loop : -1.61 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 298 
 TYR   0.011   0.001   TYR A1256 
 PHE   0.011   0.001   PHE A 853 
 TRP   0.011   0.001   TRP A 843 
 HIS   0.008   0.001   HIS A1101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9137)
  covalent geometry    : angle       0.55341 (12366)
  hydrogen bonds       : bond        0.05079 (  617)
  hydrogen bonds       : angle       4.13624 ( 1806)

*********************** 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
  161 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 LYS cc_start: 0.7706 (ptmt) cc_final: 0.7175 (ptpp)
REVERT: A  121 LYS cc_start: 0.8533 (mtmt) cc_final: 0.7726 (mptt)
REVERT: A  125 LYS cc_start: 0.7969 (mmmm) cc_final: 0.7490 (mttt)
REVERT: A  157 MET cc_start: 0.8002 (mpp) cc_final: 0.7798 (mpp)
REVERT: A  159 GLN cc_start: 0.8141 (tp40) cc_final: 0.7691 (tt0)
REVERT: A  217 ASN cc_start: 0.7506 (t0) cc_final: 0.7003 (m-40)
REVERT: A  229 ILE cc_start: 0.8132 (mt) cc_final: 0.7879 (mt)
REVERT: A  441 TRP cc_start: 0.8115 (t60) cc_final: 0.7863 (t60)
REVERT: A  491 LYS cc_start: 0.8072 (pttt) cc_final: 0.7497 (ptmt)
REVERT: A  514 ARG cc_start: 0.5324 (mtp-110) cc_final: 0.4391 (mtm-85)
REVERT: A  532 GLU cc_start: 0.4795 (tm-30) cc_final: 0.3879 (tt0)
REVERT: A  553 MET cc_start: 0.6589 (mmp) cc_final: 0.6275 (mmp)
REVERT: A  701 LEU cc_start: 0.8475 (tt) cc_final: 0.8092 (mt)
REVERT: A  738 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8363 (mmmt)
REVERT: A  752 SER cc_start: 0.8992 (m) cc_final: 0.8784 (p)
REVERT: A  997 PHE cc_start: 0.8323 (m-80) cc_final: 0.7955 (m-80)
REVERT: A 1122 TYR cc_start: 0.8107 (t80) cc_final: 0.7799 (t80)
  outliers start: 10
  outliers final: 7
  residues processed: 154
  average time/residue: 0.1000
  time to fit residues: 21.6440
Evaluate side-chains
  141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 ILE
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
Chi-restraints excluded: chain A residue 1177 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 96 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 89 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 56 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.191354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137348 restraints weight = 11108.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.86
r_work: 0.3438 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3320 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3191

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= 0.146
  Angle     :  0.544   7.810  12366  Z= 0.283
  Chirality :  0.040   0.199   1428
  Planarity :  0.004   0.041   1572
  Dihedral  :  3.718  14.583   1254
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.25), residues: 1161
  helix:  2.33 (0.19), residues: 752
  sheet: -1.13 (0.92), residues: 34
  loop : -1.50 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 298 
 TYR   0.011   0.001   TYR A  89 
 PHE   0.021   0.001   PHE A 686 
 TRP   0.007   0.001   TRP A 188 
 HIS   0.007   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9137)
  covalent geometry    : angle       0.54406 (12366)
  hydrogen bonds       : bond        0.04916 (  617)
  hydrogen bonds       : angle       4.11706 ( 1806)

*********************** 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
  155 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8216 (mtmm)
REVERT: A  125 LYS cc_start: 0.8394 (mmmm) cc_final: 0.8175 (tptp)
REVERT: A  217 ASN cc_start: 0.7529 (t0) cc_final: 0.6886 (m-40)
REVERT: A  229 ILE cc_start: 0.8349 (mt) cc_final: 0.8114 (mt)
REVERT: A  441 TRP cc_start: 0.8193 (t60) cc_final: 0.7988 (t60)
REVERT: A  512 LYS cc_start: 0.7718 (mtmm) cc_final: 0.7418 (mtmt)
REVERT: A  514 ARG cc_start: 0.5775 (mtp-110) cc_final: 0.4687 (mtm-85)
REVERT: A  532 GLU cc_start: 0.5243 (tm-30) cc_final: 0.3912 (tt0)
REVERT: A  553 MET cc_start: 0.6592 (mmp) cc_final: 0.6263 (mmp)
REVERT: A  701 LEU cc_start: 0.8512 (tt) cc_final: 0.7954 (mt)
REVERT: A  729 TYR cc_start: 0.8708 (m-80) cc_final: 0.8063 (m-80)
REVERT: A  801 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.7116 (mtt180)
REVERT: A 1028 HIS cc_start: 0.7516 (m90) cc_final: 0.7185 (m-70)
  outliers start: 15
  outliers final: 7
  residues processed: 149
  average time/residue: 0.1014
  time to fit residues: 21.0521
Evaluate side-chains
  129 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 122
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
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 80 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 102 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.190626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.135446 restraints weight = 11340.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 1.92
r_work: 0.3430 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.3615

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     :  0.533   7.530  12366  Z= 0.274
  Chirality :  0.039   0.196   1428
  Planarity :  0.003   0.046   1572
  Dihedral  :  3.682  15.691   1254
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 15.49 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.25), residues: 1161
  helix:  2.29 (0.18), residues: 752
  sheet: -1.12 (0.93), residues: 34
  loop : -1.54 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 298 
 TYR   0.013   0.001   TYR A  41 
 PHE   0.015   0.001   PHE A 686 
 TRP   0.009   0.001   TRP A 791 
 HIS   0.005   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9137)
  covalent geometry    : angle       0.53335 (12366)
  hydrogen bonds       : bond        0.04708 (  617)
  hydrogen bonds       : angle       4.05927 ( 1806)

*********************** 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
  150 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8379 (mtmm)
REVERT: A  217 ASN cc_start: 0.7437 (t0) cc_final: 0.6827 (m-40)
REVERT: A  229 ILE cc_start: 0.8271 (mt) cc_final: 0.7967 (mt)
REVERT: A  361 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6585 (pp)
REVERT: A  426 GLN cc_start: 0.7560 (pt0) cc_final: 0.7231 (pp30)
REVERT: A  477 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6619 (pt0)
REVERT: A  512 LYS cc_start: 0.7928 (mtmm) cc_final: 0.7686 (mtmt)
REVERT: A  514 ARG cc_start: 0.5944 (mtp-110) cc_final: 0.4953 (mtm-85)
REVERT: A  532 GLU cc_start: 0.5372 (tm-30) cc_final: 0.4035 (tt0)
REVERT: A  542 GLU cc_start: 0.6781 (pm20) cc_final: 0.6299 (tt0)
REVERT: A  553 MET cc_start: 0.6517 (mmp) cc_final: 0.6254 (mmp)
REVERT: A  701 LEU cc_start: 0.8463 (tt) cc_final: 0.7884 (mt)
REVERT: A  729 TYR cc_start: 0.8628 (m-80) cc_final: 0.7883 (m-80)
REVERT: A 1028 HIS cc_start: 0.7589 (m90) cc_final: 0.7142 (m-70)
REVERT: A 1122 TYR cc_start: 0.8436 (t80) cc_final: 0.8143 (t80)
  outliers start: 15
  outliers final: 6
  residues processed: 144
  average time/residue: 0.0986
  time to fit residues: 19.8979
Evaluate side-chains
  121 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 114
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 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  802 ILE
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1069 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 38 optimal weight:    0.0770
   chunk 103 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0980
   chunk 56 optimal weight:    8.9990
   chunk 96 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    1.0342

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.188024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.133398 restraints weight = 11186.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 1.90
r_work: 0.3406 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4025

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     :  0.543   8.485  12366  Z= 0.279
  Chirality :  0.040   0.234   1428
  Planarity :  0.003   0.042   1572
  Dihedral  :  3.646  15.979   1254
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 16.65 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.25), residues: 1161
  helix:  2.24 (0.18), residues: 752
  sheet: -1.13 (0.93), residues: 34
  loop : -1.60 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 298 
 TYR   0.012   0.001   TYR A  41 
 PHE   0.015   0.001   PHE A 686 
 TRP   0.017   0.001   TRP A 441 
 HIS   0.006   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9137)
  covalent geometry    : angle       0.54349 (12366)
  hydrogen bonds       : bond        0.04705 (  617)
  hydrogen bonds       : angle       4.06378 ( 1806)

*********************** 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
  144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8760 (mtmt) cc_final: 0.7899 (mptt)
REVERT: A  217 ASN cc_start: 0.7509 (t0) cc_final: 0.6942 (m-40)
REVERT: A  229 ILE cc_start: 0.8261 (mt) cc_final: 0.7932 (mt)
REVERT: A  426 GLN cc_start: 0.7647 (pt0) cc_final: 0.7293 (pp30)
REVERT: A  441 TRP cc_start: 0.8251 (t60) cc_final: 0.7764 (t-100)
REVERT: A  477 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6714 (pt0)
REVERT: A  514 ARG cc_start: 0.5923 (mtp-110) cc_final: 0.4940 (mtm-85)
REVERT: A  542 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6284 (tt0)
REVERT: A  553 MET cc_start: 0.6437 (mmp) cc_final: 0.6214 (mmp)
REVERT: A  701 LEU cc_start: 0.8471 (tt) cc_final: 0.7864 (mt)
REVERT: A  729 TYR cc_start: 0.8663 (m-80) cc_final: 0.8003 (m-80)
REVERT: A 1028 HIS cc_start: 0.7598 (m90) cc_final: 0.7036 (m-70)
REVERT: A 1184 MET cc_start: 0.8325 (tpt) cc_final: 0.7798 (tpp)
  outliers start: 19
  outliers final: 9
  residues processed: 139
  average time/residue: 0.0983
  time to fit residues: 19.2320
Evaluate side-chains
  126 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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  542 GLU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 90 optimal weight:    0.4980
   chunk 68 optimal weight:    0.7980
   chunk 112 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.4156 r_free = 0.4156 target = 0.188532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.137997 restraints weight = 11253.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.37
r_work: 0.3414 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.4268

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= 0.125
  Angle     :  0.539   9.872  12366  Z= 0.274
  Chirality :  0.040   0.292   1428
  Planarity :  0.003   0.041   1572
  Dihedral  :  3.625  14.582   1254
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.12 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.25), residues: 1161
  helix:  2.26 (0.18), residues: 753
  sheet: -1.18 (0.93), residues: 34
  loop : -1.66 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 298 
 TYR   0.014   0.001   TYR A  41 
 PHE   0.015   0.001   PHE A 686 
 TRP   0.011   0.001   TRP A 441 
 HIS   0.004   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9137)
  covalent geometry    : angle       0.53918 (12366)
  hydrogen bonds       : bond        0.04538 (  617)
  hydrogen bonds       : angle       4.03860 ( 1806)

*********************** 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  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8318 (mtmm)
REVERT: A  159 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7899 (tt0)
REVERT: A  217 ASN cc_start: 0.7516 (t0) cc_final: 0.7166 (m-40)
REVERT: A  229 ILE cc_start: 0.8188 (mt) cc_final: 0.7881 (mt)
REVERT: A  440 ARG cc_start: 0.5911 (mtm-85) cc_final: 0.5364 (ttp80)
REVERT: A  477 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6709 (pt0)
REVERT: A  512 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7686 (mtmt)
REVERT: A  514 ARG cc_start: 0.5905 (mtp-110) cc_final: 0.4959 (mtm-85)
REVERT: A  542 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6152 (tt0)
REVERT: A  701 LEU cc_start: 0.8391 (tt) cc_final: 0.7768 (mt)
REVERT: A  729 TYR cc_start: 0.8638 (m-80) cc_final: 0.7936 (m-80)
REVERT: A 1028 HIS cc_start: 0.7624 (m90) cc_final: 0.7126 (m-70)
REVERT: A 1184 MET cc_start: 0.8331 (tpt) cc_final: 0.7786 (tpp)
  outliers start: 24
  outliers final: 11
  residues processed: 143
  average time/residue: 0.1041
  time to fit residues: 20.6943
Evaluate side-chains
  131 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 THR
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  499 GLN
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  945 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1124 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 112 optimal weight:   20.0000
   chunk 63 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    1.7788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.182327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.133018 restraints weight = 11378.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.89
r_work: 0.3322 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.4778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9137  Z= 0.179
  Angle     :  0.599   9.830  12366  Z= 0.308
  Chirality :  0.042   0.326   1428
  Planarity :  0.004   0.039   1572
  Dihedral  :  3.845  16.152   1254
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.39 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.25), residues: 1161
  helix:  1.99 (0.18), residues: 751
  sheet: -1.77 (0.74), residues: 44
  loop : -1.64 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 801 
 TYR   0.016   0.002   TYR A1155 
 PHE   0.020   0.002   PHE A 138 
 TRP   0.012   0.002   TRP A 791 
 HIS   0.011   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 9137)
  covalent geometry    : angle       0.59885 (12366)
  hydrogen bonds       : bond        0.05198 (  617)
  hydrogen bonds       : angle       4.25681 ( 1806)

*********************** 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
  147 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.9163 (mtm) cc_final: 0.8957 (mtp)
REVERT: A  159 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7765 (tt0)
REVERT: A  217 ASN cc_start: 0.7672 (t0) cc_final: 0.7279 (m-40)
REVERT: A  229 ILE cc_start: 0.8357 (mt) cc_final: 0.8054 (mt)
REVERT: A  440 ARG cc_start: 0.6334 (mtm-85) cc_final: 0.5841 (ttp80)
REVERT: A  441 TRP cc_start: 0.8270 (t60) cc_final: 0.7715 (t-100)
REVERT: A  514 ARG cc_start: 0.6107 (mtp-110) cc_final: 0.5170 (mtm-85)
REVERT: A  691 LYS cc_start: 0.7100 (ttmt) cc_final: 0.6583 (tptp)
REVERT: A  729 TYR cc_start: 0.8681 (m-80) cc_final: 0.8122 (m-80)
REVERT: A 1028 HIS cc_start: 0.7654 (m90) cc_final: 0.7314 (m-70)
REVERT: A 1184 MET cc_start: 0.8384 (tpt) cc_final: 0.7966 (tpp)
REVERT: A 1187 ASP cc_start: 0.7629 (t70) cc_final: 0.6904 (t70)
  outliers start: 19
  outliers final: 10
  residues processed: 142
  average time/residue: 0.1070
  time to fit residues: 20.9589
Evaluate side-chains
  132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  945 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1124 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 91 optimal weight:   10.0000
   chunk 108 optimal weight:    8.9990
   chunk 100 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 486 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.185123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.135940 restraints weight = 11168.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.76
r_work: 0.3382 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.4886

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     :  0.562  10.911  12366  Z= 0.285
  Chirality :  0.040   0.320   1428
  Planarity :  0.003   0.040   1572
  Dihedral  :  3.751  14.698   1254
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.91 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.25), residues: 1161
  helix:  2.11 (0.18), residues: 754
  sheet: -2.41 (0.73), residues: 37
  loop : -1.59 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 801 
 TYR   0.013   0.001   TYR A  41 
 PHE   0.010   0.001   PHE A  72 
 TRP   0.010   0.001   TRP A 791 
 HIS   0.004   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9137)
  covalent geometry    : angle       0.56188 (12366)
  hydrogen bonds       : bond        0.04696 (  617)
  hydrogen bonds       : angle       4.15313 ( 1806)

*********************** 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
  148 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8206 (m-80) cc_final: 0.7973 (m-80)
REVERT: A  159 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7900 (tt0)
REVERT: A  217 ASN cc_start: 0.7555 (t0) cc_final: 0.7196 (m-40)
REVERT: A  229 ILE cc_start: 0.8174 (mt) cc_final: 0.7859 (mt)
REVERT: A  440 ARG cc_start: 0.6408 (mtm-85) cc_final: 0.5893 (ttp80)
REVERT: A  477 GLU cc_start: 0.7582 (mm-30) cc_final: 0.6498 (pt0)
REVERT: A  514 ARG cc_start: 0.5916 (mtp-110) cc_final: 0.5121 (mtm-85)
REVERT: A  691 LYS cc_start: 0.6941 (ttmt) cc_final: 0.6594 (mmtt)
REVERT: A  701 LEU cc_start: 0.8393 (tt) cc_final: 0.7762 (mt)
REVERT: A  729 TYR cc_start: 0.8605 (m-80) cc_final: 0.7975 (m-80)
REVERT: A  853 PHE cc_start: 0.8354 (t80) cc_final: 0.8099 (t80)
REVERT: A 1028 HIS cc_start: 0.7719 (m90) cc_final: 0.7327 (m-70)
REVERT: A 1088 LYS cc_start: 0.5755 (ttpt) cc_final: 0.5517 (ttpt)
REVERT: A 1187 ASP cc_start: 0.7631 (t70) cc_final: 0.6944 (t70)
  outliers start: 19
  outliers final: 11
  residues processed: 142
  average time/residue: 0.1009
  time to fit residues: 20.0974
Evaluate side-chains
  132 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  945 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1124 HIS
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 64 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 70 optimal weight:   10.0000
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 100 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.4120 r_free = 0.4120 target = 0.184885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.136973 restraints weight = 11254.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.91
r_work: 0.3365 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4993

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= 0.134
  Angle     :  0.574  11.658  12366  Z= 0.292
  Chirality :  0.040   0.351   1428
  Planarity :  0.003   0.040   1572
  Dihedral  :  3.750  14.339   1254
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.97 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.25), residues: 1161
  helix:  2.16 (0.18), residues: 752
  sheet: -1.80 (0.85), residues: 34
  loop : -1.72 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 801 
 TYR   0.013   0.001   TYR A  41 
 PHE   0.011   0.001   PHE A  72 
 TRP   0.010   0.001   TRP A 791 
 HIS   0.005   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9137)
  covalent geometry    : angle       0.57374 (12366)
  hydrogen bonds       : bond        0.04726 (  617)
  hydrogen bonds       : angle       4.13380 ( 1806)

*********************** 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
  141 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8276 (m-80) cc_final: 0.7985 (m-80)
REVERT: A  159 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7824 (tt0)
REVERT: A  217 ASN cc_start: 0.7577 (t0) cc_final: 0.6953 (m-40)
REVERT: A  229 ILE cc_start: 0.8195 (mt) cc_final: 0.7857 (mt)
REVERT: A  384 LYS cc_start: 0.2602 (tptt) cc_final: 0.2199 (tptp)
REVERT: A  440 ARG cc_start: 0.6530 (mtm-85) cc_final: 0.5988 (ttp80)
REVERT: A  514 ARG cc_start: 0.5985 (mtp-110) cc_final: 0.5160 (mtm-85)
REVERT: A  691 LYS cc_start: 0.7026 (ttmt) cc_final: 0.6610 (mmtt)
REVERT: A  701 LEU cc_start: 0.8405 (tt) cc_final: 0.7805 (mt)
REVERT: A  729 TYR cc_start: 0.8635 (m-80) cc_final: 0.8065 (m-80)
REVERT: A  853 PHE cc_start: 0.8373 (t80) cc_final: 0.8116 (t80)
REVERT: A  864 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8178 (mtpt)
REVERT: A 1028 HIS cc_start: 0.7656 (m90) cc_final: 0.7261 (m-70)
REVERT: A 1184 MET cc_start: 0.8308 (tpt) cc_final: 0.7774 (tpp)
REVERT: A 1187 ASP cc_start: 0.7582 (t70) cc_final: 0.6838 (t70)
  outliers start: 14
  outliers final: 12
  residues processed: 138
  average time/residue: 0.1036
  time to fit residues: 19.6757
Evaluate side-chains
  135 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  945 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1124 HIS
Chi-restraints excluded: chain A residue 1220 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 112 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 11 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.184916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.134920 restraints weight = 11221.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.72
r_work: 0.3396 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.5115

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= 0.135
  Angle     :  0.586  11.910  12366  Z= 0.297
  Chirality :  0.041   0.352   1428
  Planarity :  0.003   0.040   1572
  Dihedral  :  3.763  14.937   1254
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 18.86 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.25), residues: 1161
  helix:  2.17 (0.18), residues: 752
  sheet: -2.06 (0.82), residues: 34
  loop : -1.72 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 801 
 TYR   0.013   0.001   TYR A  41 
 PHE   0.011   0.001   PHE A  72 
 TRP   0.010   0.001   TRP A 791 
 HIS   0.005   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9137)
  covalent geometry    : angle       0.58588 (12366)
  hydrogen bonds       : bond        0.04676 (  617)
  hydrogen bonds       : angle       4.14544 ( 1806)

********************** 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
  144 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
REVERT: A   41 TYR cc_start: 0.8224 (m-80) cc_final: 0.7884 (m-80)
REVERT: A  159 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7741 (tt0)
REVERT: A  217 ASN cc_start: 0.7488 (t0) cc_final: 0.7110 (m-40)
REVERT: A  229 ILE cc_start: 0.8134 (mt) cc_final: 0.7805 (mt)
REVERT: A  384 LYS cc_start: 0.2473 (tptt) cc_final: 0.2078 (tptp)
REVERT: A  440 ARG cc_start: 0.6593 (mtm-85) cc_final: 0.6097 (ttp80)
REVERT: A  470 ASP cc_start: 0.8773 (m-30) cc_final: 0.8344 (t0)
REVERT: A  514 ARG cc_start: 0.5929 (mtp-110) cc_final: 0.5122 (mtm-85)
REVERT: A  691 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6627 (mmtt)
REVERT: A  701 LEU cc_start: 0.8317 (tt) cc_final: 0.7709 (mt)
REVERT: A  729 TYR cc_start: 0.8547 (m-80) cc_final: 0.7981 (m-80)
REVERT: A  853 PHE cc_start: 0.8316 (t80) cc_final: 0.8073 (t80)
REVERT: A  864 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8156 (mtpt)
REVERT: A 1028 HIS cc_start: 0.7694 (m90) cc_final: 0.7276 (m-70)
REVERT: A 1088 LYS cc_start: 0.5657 (ttpt) cc_final: 0.5357 (ttpt)
REVERT: A 1187 ASP cc_start: 0.7531 (t70) cc_final: 0.6742 (t70)
  outliers start: 14
  outliers final: 12
  residues processed: 140
  average time/residue: 0.1026
  time to fit residues: 20.0778
Evaluate side-chains
  139 residues out of total 949 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  945 LEU
Chi-restraints excluded: chain A residue  980 LEU
Chi-restraints excluded: chain A residue 1124 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 78 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   chunk 99 optimal weight:    6.9990
   chunk 102 optimal weight:    0.8980
   chunk 47 optimal weight:    0.0670
   chunk 48 optimal weight:    0.6980
   chunk 18 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    1.2920

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.183316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.134097 restraints weight = 11141.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.79
r_work: 0.3359 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3243 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.5266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9137  Z= 0.151
  Angle     :  0.593  11.981  12366  Z= 0.301
  Chirality :  0.041   0.366   1428
  Planarity :  0.004   0.060   1572
  Dihedral  :  3.811  14.875   1254
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 19.07 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.25), residues: 1161
  helix:  2.11 (0.18), residues: 752
  sheet: -1.53 (0.95), residues: 27
  loop : -1.71 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 801 
 TYR   0.013   0.002   TYR A1155 
 PHE   0.012   0.001   PHE A  72 
 TRP   0.010   0.001   TRP A 791 
 HIS   0.006   0.001   HIS A 171 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9137)
  covalent geometry    : angle       0.59271 (12366)
  hydrogen bonds       : bond        0.04846 (  617)
  hydrogen bonds       : angle       4.15820 ( 1806)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2771.19 seconds
wall clock time: 48 minutes 10.70 seconds (2890.70 seconds total)