Starting phenix.real_space_refine
on Thu Jul  2 00:18:49 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8cxo_27062/07_2026/8cxo_27062.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cxo_27062/07_2026/8cxo_27062.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8cxo_27062/07_2026/8cxo_27062.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8cxo_27062/07_2026/8cxo_27062.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cxo_27062/07_2026/8cxo_27062.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cxo_27062/07_2026/8cxo_27062.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cxo_27062/07_2026/8cxo_27062.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cxo_27062/07_2026/8cxo_27062.map"
  }
  resolution = 3.7
  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=   0.002
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      30      5.16       5
     C    2863      2.51       5
     N     724      2.21       5
     O     775      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4392
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 551, 4364
          Classifications: {'peptide': 551}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 535}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.83, per 1000 atoms: 0.19
  Number of scatterers: 4392
  At special positions: 0
  Unit cell: (75.985, 65.13, 123.58, 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      30     16.00
     O     775      8.00
     N     724      7.00
     C    2863      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 197 " - pdb=" SG  CYS A 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 221 " - pdb=" SG  CYS A 299 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 318 " - pdb=" SG  CYS A 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 494 " - pdb=" SG  CYS A 511 " distance=2.03

  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: 0.34
  Conformation dependent library (CDL) restraints added in 139.3 milliseconds
  

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1010

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 3 sheets defined
      65.5% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 227 through 259
      removed outlier: 3.998A  pdb=" N   ASP A 259 " --> pdb=" O   THR A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 264
    Processing helix  chain 'A' and resid 265 through 268
    Processing helix  chain 'A' and resid 269 through 287
      removed outlier: 3.595A  pdb=" N   TYR A 273 " --> pdb=" O   VAL A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 290
      No H-bonds generated for 'chain 'A' and resid 288 through 290'
    Processing helix  chain 'A' and resid 292 through 299
    Processing helix  chain 'A' and resid 316 through 347
      removed outlier: 4.079A  pdb=" N   PHE A 347 " --> pdb=" O   TRP A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 359
      No H-bonds generated for 'chain 'A' and resid 357 through 359'
    Processing helix  chain 'A' and resid 360 through 382
      Proline residue:  A 372  - end of helix
      removed outlier: 3.526A  pdb=" N   VAL A 382 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 408
      removed outlier: 3.825A  pdb=" N   ARG A 404 " --> pdb=" O   ASN A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 437
    Processing helix  chain 'A' and resid 1015 through 1027
    Processing helix  chain 'A' and resid 1047 through 1059
    Processing helix  chain 'A' and resid 1060 through 1065
      removed outlier: 6.464A  pdb=" N   GLU A1063 " --> pdb=" O   SER A1060 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLN A1065 " --> pdb=" O   LYS A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1090
    Processing helix  chain 'A' and resid 1101 through 1112
    Processing helix  chain 'A' and resid 1126 through 1134
      removed outlier: 4.036A  pdb=" N   GLU A1130 " --> pdb=" O   LEU A1126 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ALA A1131 " --> pdb=" O   VAL A1127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1149
      removed outlier: 4.029A  pdb=" N   ARG A1147 " --> pdb=" O   GLY A1144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1162 through 1178
    Processing helix  chain 'A' and resid 1181 through 1193
    Processing helix  chain 'A' and resid 1206 through 452
      removed outlier: 3.526A  pdb=" N   GLU A 451 " --> pdb=" O   ALA A1206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 494
      removed outlier: 3.599A  pdb=" N   PHE A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ALA A 482 " --> pdb=" O   PHE A 478 " (cutoff:3.500A)
      removed outlier: 5.444A  pdb=" N   GLU A 483 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   CYS A 494 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 497
      No H-bonds generated for 'chain 'A' and resid 495 through 497'
    Processing helix  chain 'A' and resid 518 through 537
      removed outlier: 3.690A  pdb=" N   GLY A 533 " --> pdb=" O   MET A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 541
    Processing helix  chain 'A' and resid 542 through 554
      removed outlier: 3.682A  pdb=" N   LEU A 546 " --> pdb=" O   THR A 542 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 203
    Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 388
      removed outlier: 3.551A  pdb=" N   ASP A 388 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ILE A 393 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1093 through 1096
      removed outlier: 5.722A  pdb=" N   VAL A1033 " --> pdb=" O   ARG A1068 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   ILE A1070 " --> pdb=" O   VAL A1033 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   PHE A1035 " --> pdb=" O   ILE A1070 " (cutoff:3.500A)
      removed outlier: 8.151A  pdb=" N   ILE A1072 " --> pdb=" O   PHE A1035 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   PHE A1037 " --> pdb=" O   ILE A1072 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   THR A1034 " --> pdb=" O   PHE A1114 " (cutoff:3.500A)
      removed outlier: 7.692A  pdb=" N   ILE A1116 " --> pdb=" O   THR A1034 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   MET A1036 " --> pdb=" O   ILE A1116 " (cutoff:3.500A)

    259 hydrogen bonds defined for protein.
    753 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: 0.51

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1374
        1.34 -     1.46: 1147
        1.46 -     1.58: 1935
        1.58 -     1.70: 0
        1.70 -     1.82: 45
  Bond restraints: 4501
  Sorted by residual:
  bond pdb=" C13 CLR A1301 "
       pdb=" C14 CLR A1301 "
    ideal  model  delta    sigma   weight residual
    1.537  1.504  0.033 2.00e-02 2.50e+03 2.71e+00
  bond pdb=" C1  CLR A1301 "
       pdb=" C10 CLR A1301 "
    ideal  model  delta    sigma   weight residual
    1.544  1.515  0.029 2.00e-02 2.50e+03 2.10e+00
  bond pdb=" C16 CLR A1301 "
       pdb=" C17 CLR A1301 "
    ideal  model  delta    sigma   weight residual
    1.554  1.528  0.026 2.00e-02 2.50e+03 1.67e+00
  bond pdb=" C15 CLR A1301 "
       pdb=" C16 CLR A1301 "
    ideal  model  delta    sigma   weight residual
    1.541  1.517  0.024 2.00e-02 2.50e+03 1.45e+00
  bond pdb=" CA  VAL A 214 "
       pdb=" CB  VAL A 214 "
    ideal  model  delta    sigma   weight residual
    1.527  1.541 -0.014 1.31e-02 5.83e+03 1.19e+00
  ... (remaining 4496 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 5911
        1.39 -     2.77: 145
        2.77 -     4.16: 22
        4.16 -     5.54: 16
        5.54 -     6.93: 2
  Bond angle restraints: 6096
  Sorted by residual:
  angle pdb=" N   CYS A1004 "
        pdb=" CA  CYS A1004 "
        pdb=" C   CYS A1004 "
      ideal   model   delta    sigma   weight residual
     107.20  112.41   -5.21 1.70e+00 3.46e-01 9.41e+00
  angle pdb=" C   TYR A 211 "
        pdb=" N   GLU A 212 "
        pdb=" CA  GLU A 212 "
      ideal   model   delta    sigma   weight residual
     121.19  125.96   -4.77 1.59e+00 3.96e-01 8.98e+00
  angle pdb=" N   TYR A 266 "
        pdb=" CA  TYR A 266 "
        pdb=" C   TYR A 266 "
      ideal   model   delta    sigma   weight residual
     109.81  115.33   -5.52 2.21e+00 2.05e-01 6.24e+00
  angle pdb=" N   GLY A1001 "
        pdb=" CA  GLY A1001 "
        pdb=" C   GLY A1001 "
      ideal   model   delta    sigma   weight residual
     113.99  116.99   -3.00 1.28e+00 6.10e-01 5.50e+00
  angle pdb=" C6  CLR A1301 "
        pdb=" C7  CLR A1301 "
        pdb=" C8  CLR A1301 "
      ideal   model   delta    sigma   weight residual
     113.19  106.26    6.93 3.00e+00 1.11e-01 5.34e+00
  ... (remaining 6091 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 2491
       17.14 -    34.28: 106
       34.28 -    51.42: 18
       51.42 -    68.56: 3
       68.56 -    85.70: 1
  Dihedral angle restraints: 2619
    sinusoidal: 1042
      harmonic: 1577
  Sorted by residual:
  dihedral pdb=" CB  CYS A 494 "
           pdb=" SG  CYS A 494 "
           pdb=" SG  CYS A 511 "
           pdb=" CB  CYS A 511 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.05  -52.05     1      1.00e+01 1.00e-02 3.70e+01
  dihedral pdb=" CA  LEU A 441 "
           pdb=" C   LEU A 441 "
           pdb=" N   GLY A1001 "
           pdb=" CA  GLY A1001 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.34  -29.66     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  TYR A 211 "
           pdb=" C   TYR A 211 "
           pdb=" N   GLU A 212 "
           pdb=" CA  GLU A 212 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.38  -27.62     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 2616 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 553
       0.045 -    0.089: 90
       0.089 -    0.134: 29
       0.134 -    0.178: 4
       0.178 -    0.223: 1
  Chirality restraints: 677
  Sorted by residual:
  chirality pdb=" C10 CLR A1301 "
            pdb=" C1  CLR A1301 "
            pdb=" C5  CLR A1301 "
            pdb=" C9  CLR A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.63   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  ILE A1139 "
            pdb=" N   ILE A1139 "
            pdb=" C   ILE A1139 "
            pdb=" CB  ILE A1139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" CA  ILE A1137 "
            pdb=" N   ILE A1137 "
            pdb=" C   ILE A1137 "
            pdb=" CB  ILE A1137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.17e-01
  ... (remaining 674 not shown)

  Planarity restraints: 759
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1122 "   -0.020 5.00e-02 4.00e+02   3.09e-02 1.53e+00
        pdb=" N   PRO A1123 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A1123 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A1123 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 437 "    0.019 5.00e-02 4.00e+02   2.80e-02 1.25e+00
        pdb=" N   PRO A 438 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A 438 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 438 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A1201 "   -0.005 2.00e-02 2.50e+03   1.05e-02 1.09e+00
        pdb=" C   MET A1201 "    0.018 2.00e-02 2.50e+03
        pdb=" O   MET A1201 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASP A1202 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 756 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1443
        2.84 -     3.36: 4332
        3.36 -     3.87: 7300
        3.87 -     4.39: 8453
        4.39 -     4.90: 13879
  Nonbonded interactions: 35407
  Sorted by model distance:
  nonbonded pdb=" O   MET A1201 "
            pdb=" N   ILE A1203 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" N   GLU A1098 "
            pdb=" OE1 GLU A1098 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" NZ  LYS A 434 "
            pdb=" C2  CLR A1301 "
     model   vdw
     2.353 3.520
  nonbonded pdb=" O   ARG A1204 "
            pdb=" ND2 ASN A 450 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" O   GLU A1056 "
            pdb=" OG  SER A1059 "
     model   vdw
     2.420 3.040
  ... (remaining 35402 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.300
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.880
  Find NCS groups from input model:        0.010
  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:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
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   0.033   4505  Z= 0.167
  Angle     :  0.582   6.930   6104  Z= 0.314
  Chirality :  0.040   0.223    677
  Planarity :  0.003   0.031    759
  Dihedral  : 10.024  85.704   1597
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  2.74 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  1.90 (0.36), residues: 547
  helix:  1.91 (0.28), residues: 317
  sheet:  1.64 (0.82), residues: 29
  loop :  0.24 (0.48), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1106 
 TYR   0.008   0.001   TYR A 398 
 PHE   0.015   0.001   PHE A1124 
 TRP   0.010   0.001   TRP A1007 
 HIS   0.003   0.001   HIS A 231 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.17 ( 4501)
  covalent geometry    : angle       0.58140 /  0.31 ( 6096)
  SS BOND              : bond        0.00382 /  0.21 (    4)
  SS BOND              : angle       1.01043 /  0.66 (    8)
  hydrogen bonds       : bond        0.22656 / 14.61 (  259)
  hydrogen bonds       : angle       6.12820 /  4.49 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 TYR cc_start: 0.8547 (t80) cc_final: 0.8130 (t80)
REVERT: A  261 ARG cc_start: 0.8833 (mtt90) cc_final: 0.8621 (ttm110)
REVERT: A  309 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8525 (mp0)
REVERT: A  348 LYS cc_start: 0.8892 (mttt) cc_final: 0.8629 (mtmt)
REVERT: A  384 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8310 (mm-40)
REVERT: A  390 VAL cc_start: 0.9414 (t) cc_final: 0.9179 (p)
REVERT: A 1003 ASP cc_start: 0.6208 (t0) cc_final: 0.5900 (t0)
REVERT: A 1090 HIS cc_start: 0.8396 (m-70) cc_final: 0.7929 (m-70)
REVERT: A 1122 GLU cc_start: 0.7933 (tp30) cc_final: 0.6644 (tp30)
REVERT: A 1123 PRO cc_start: 0.9172 (Cg_exo) cc_final: 0.8716 (Cg_endo)
REVERT: A 1130 GLU cc_start: 0.4917 (tt0) cc_final: 0.4673 (tt0)
REVERT: A 1132 MET cc_start: 0.9281 (mtp) cc_final: 0.8960 (mtp)
REVERT: A 1137 ILE cc_start: 0.8615 (mt) cc_final: 0.8033 (mm)
REVERT: A 1154 THR cc_start: 0.9239 (m) cc_final: 0.8875 (p)
REVERT: A 1172 LYS cc_start: 0.9369 (tptt) cc_final: 0.8892 (mmtt)
REVERT: A  523 LYS cc_start: 0.9276 (mttt) cc_final: 0.9017 (mttt)
REVERT: A  530 PHE cc_start: 0.9295 (m-80) cc_final: 0.9062 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.0660
  time to fit residues: 19.2139
Evaluate side-chains
  153 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:    0.0670
   overall best weight:    2.2924

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 196 GLN
A 222 GLN
** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 288 GLN
A1065 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.107118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.086521 restraints weight = 10305.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.089389 restraints weight = 5129.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.091738 restraints weight = 3293.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.093298 restraints weight = 2323.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.094443 restraints weight = 1815.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4505  Z= 0.241
  Angle     :  0.703   9.213   6104  Z= 0.367
  Chirality :  0.047   0.154    677
  Planarity :  0.005   0.033    759
  Dihedral  :  5.214  26.032    607
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 15.52 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  1.97 (0.35), residues: 547
  helix:  2.25 (0.28), residues: 314
  sheet:  2.13 (1.05), residues: 19
  loop : -0.20 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1102 
 TYR   0.014   0.002   TYR A 363 
 PHE   0.016   0.002   PHE A 322 
 TRP   0.011   0.002   TRP A1007 
 HIS   0.006   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00531 /  0.24 ( 4501)
  covalent geometry    : angle       0.70332 /  0.37 ( 6096)
  SS BOND              : bond        0.00236 /  0.15 (    4)
  SS BOND              : angle       0.70216 /  0.41 (    8)
  hydrogen bonds       : bond        0.06105 /  3.97 (  259)
  hydrogen bonds       : angle       4.67123 /  3.49 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  237 TYR cc_start: 0.8551 (t80) cc_final: 0.8304 (t80)
REVERT: A  253 LEU cc_start: 0.9335 (mp) cc_final: 0.9106 (mp)
REVERT: A  309 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8565 (mp0)
REVERT: A  348 LYS cc_start: 0.9057 (mttt) cc_final: 0.8824 (mtmt)
REVERT: A  384 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8464 (mm-40)
REVERT: A  441 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6544 (mt)
REVERT: A 1003 ASP cc_start: 0.6658 (t0) cc_final: 0.6103 (t0)
REVERT: A 1041 PHE cc_start: 0.7527 (m-10) cc_final: 0.7064 (m-10)
REVERT: A 1056 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8734 (tm-30)
REVERT: A 1058 LEU cc_start: 0.9544 (tp) cc_final: 0.9272 (tt)
REVERT: A 1090 HIS cc_start: 0.8313 (m-70) cc_final: 0.7996 (m-70)
REVERT: A 1154 THR cc_start: 0.9162 (m) cc_final: 0.8872 (p)
REVERT: A  481 GLN cc_start: 0.9115 (tp40) cc_final: 0.8846 (tt0)
REVERT: A  484 TRP cc_start: 0.9205 (m-10) cc_final: 0.8531 (m-90)
  outliers start: 23
  outliers final: 20
  residues processed: 157
  average time/residue: 0.0623
  time to fit residues: 12.6889
Evaluate side-chains
  158 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  452 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 24 optimal weight:    0.0170
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0870
   chunk 47 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.4796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 275 ASN ** 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 = 0.3631 r_free = 0.3631 target = 0.116156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.096518 restraints weight = 10276.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.099698 restraints weight = 5079.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.102244 restraints weight = 3200.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.103923 restraints weight = 2226.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.104692 restraints weight = 1690.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4505  Z= 0.130
  Angle     :  0.576   9.047   6104  Z= 0.297
  Chirality :  0.042   0.137    677
  Planarity :  0.003   0.027    759
  Dihedral  :  4.741  30.247    607
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 19.40 %
    Favored  : 76.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  1.97 (0.35), residues: 547
  helix:  2.32 (0.27), residues: 314
  sheet:  1.90 (1.07), residues: 19
  loop : -0.28 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1040 
 TYR   0.015   0.001   TYR A 491 
 PHE   0.018   0.002   PHE A1035 
 TRP   0.007   0.001   TRP A 549 
 HIS   0.004   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.13 ( 4501)
  covalent geometry    : angle       0.57598 /  0.30 ( 6096)
  SS BOND              : bond        0.00099 /  0.06 (    4)
  SS BOND              : angle       0.34839 /  0.19 (    8)
  hydrogen bonds       : bond        0.05125 /  3.35 (  259)
  hydrogen bonds       : angle       4.21417 /  3.15 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.8420 (tp30) cc_final: 0.8135 (tm-30)
REVERT: A  232 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8667 (mm-40)
REVERT: A  253 LEU cc_start: 0.9363 (mp) cc_final: 0.9161 (mp)
REVERT: A  309 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8540 (mp0)
REVERT: A  348 LYS cc_start: 0.9061 (mttt) cc_final: 0.8820 (mtmt)
REVERT: A  388 ASP cc_start: 0.9034 (t0) cc_final: 0.8641 (t0)
REVERT: A 1041 PHE cc_start: 0.7400 (m-10) cc_final: 0.7153 (m-80)
REVERT: A 1090 HIS cc_start: 0.8262 (m-70) cc_final: 0.7938 (m-70)
REVERT: A 1113 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7584 (p0)
REVERT: A 1188 CYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9097 (t)
REVERT: A 1193 MET cc_start: 0.5050 (mmt) cc_final: 0.3168 (mmt)
REVERT: A  487 SER cc_start: 0.9522 (t) cc_final: 0.9157 (p)
REVERT: A  540 VAL cc_start: 0.9398 (m) cc_final: 0.9178 (t)
  outliers start: 19
  outliers final: 10
  residues processed: 164
  average time/residue: 0.0507
  time to fit residues: 11.0367
Evaluate side-chains
  150 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  365 HIS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue 1188 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0970
   chunk 24 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.5156

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 275 ASN ** 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 = 0.3614 r_free = 0.3614 target = 0.115554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.095692 restraints weight = 10360.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.099078 restraints weight = 5098.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.101600 restraints weight = 3123.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.102843 restraints weight = 2174.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.104155 restraints weight = 1726.233|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.4860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4505  Z= 0.123
  Angle     :  0.596  12.493   6104  Z= 0.299
  Chirality :  0.042   0.180    677
  Planarity :  0.004   0.066    759
  Dihedral  :  4.542  25.768    607
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.12 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  1.81 (0.35), residues: 547
  helix:  2.30 (0.28), residues: 320
  sheet:  1.32 (1.22), residues: 18
  loop : -0.59 (0.42), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A1178 
 TYR   0.012   0.001   TYR A1011 
 PHE   0.016   0.001   PHE A 322 
 TRP   0.018   0.001   TRP A 484 
 HIS   0.003   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 4501)
  covalent geometry    : angle       0.59620 /  0.30 ( 6096)
  SS BOND              : bond        0.00090 /  0.06 (    4)
  SS BOND              : angle       0.35904 /  0.20 (    8)
  hydrogen bonds       : bond        0.04696 /  3.05 (  259)
  hydrogen bonds       : angle       4.13639 /  3.08 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.9362 (mp) cc_final: 0.9120 (mp)
REVERT: A  309 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8541 (mp0)
REVERT: A  388 ASP cc_start: 0.8978 (t0) cc_final: 0.8377 (t0)
REVERT: A 1002 ILE cc_start: 0.8507 (mm) cc_final: 0.7808 (mm)
REVERT: A 1056 GLU cc_start: 0.9255 (tt0) cc_final: 0.8942 (pt0)
REVERT: A 1090 HIS cc_start: 0.8329 (m-70) cc_final: 0.7986 (m-70)
REVERT: A 1113 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7280 (p0)
REVERT: A 1124 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6984 (p90)
REVERT: A 1132 MET cc_start: 0.9287 (mtp) cc_final: 0.8906 (mmm)
REVERT: A 1193 MET cc_start: 0.4873 (mmt) cc_final: 0.3289 (mmt)
REVERT: A  541 TRP cc_start: 0.9004 (m-10) cc_final: 0.8537 (m100)
  outliers start: 18
  outliers final: 10
  residues processed: 155
  average time/residue: 0.0558
  time to fit residues: 11.4518
Evaluate side-chains
  148 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  354 TYR
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1188 CYS
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN
A 515 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.115739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.096447 restraints weight = 10596.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.099703 restraints weight = 5282.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.101724 restraints weight = 3233.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.103426 restraints weight = 2317.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.104794 restraints weight = 1757.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.5117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   4505  Z= 0.141
  Angle     :  0.622   9.962   6104  Z= 0.307
  Chirality :  0.043   0.165    677
  Planarity :  0.004   0.059    759
  Dihedral  :  4.492  23.860    607
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 20.69 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  2.03 (0.36), residues: 547
  helix:  2.58 (0.28), residues: 314
  sheet:  1.13 (1.24), residues: 18
  loop : -0.55 (0.41), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1178 
 TYR   0.009   0.001   TYR A 237 
 PHE   0.013   0.001   PHE A 322 
 TRP   0.030   0.002   TRP A 484 
 HIS   0.003   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 ( 4501)
  covalent geometry    : angle       0.62198 /  0.31 ( 6096)
  SS BOND              : bond        0.00093 /  0.06 (    4)
  SS BOND              : angle       0.33507 /  0.19 (    8)
  hydrogen bonds       : bond        0.04788 /  3.15 (  259)
  hydrogen bonds       : angle       4.12633 /  3.05 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: A  220 GLN cc_start: 0.8695 (pt0) cc_final: 0.8123 (tm-30)
REVERT: A  253 LEU cc_start: 0.9349 (mp) cc_final: 0.9101 (mp)
REVERT: A  309 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8511 (mp0)
REVERT: A 1002 ILE cc_start: 0.8556 (mm) cc_final: 0.7898 (mm)
REVERT: A 1040 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6813 (tpt-90)
REVERT: A 1056 GLU cc_start: 0.9260 (tt0) cc_final: 0.8929 (pt0)
REVERT: A 1058 LEU cc_start: 0.9452 (tp) cc_final: 0.9090 (tt)
REVERT: A 1090 HIS cc_start: 0.8302 (m-70) cc_final: 0.7951 (m-70)
REVERT: A 1113 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7318 (p0)
REVERT: A 1124 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7033 (p90)
REVERT: A 1130 GLU cc_start: 0.4300 (OUTLIER) cc_final: 0.2816 (mt-10)
REVERT: A 1132 MET cc_start: 0.9284 (mtp) cc_final: 0.8919 (mmm)
REVERT: A 1193 MET cc_start: 0.4843 (mmt) cc_final: 0.3341 (mmt)
REVERT: A  481 GLN cc_start: 0.9047 (tt0) cc_final: 0.8823 (tt0)
REVERT: A  487 SER cc_start: 0.9488 (t) cc_final: 0.9126 (p)
REVERT: A  530 PHE cc_start: 0.9303 (m-80) cc_final: 0.9073 (m-10)
REVERT: A  541 TRP cc_start: 0.9106 (m-10) cc_final: 0.8558 (m100)
  outliers start: 24
  outliers final: 15
  residues processed: 158
  average time/residue: 0.0576
  time to fit residues: 12.1281
Evaluate side-chains
  152 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1130 GLU
Chi-restraints excluded: chain A residue 1188 CYS
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 10 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1065 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.112389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.091884 restraints weight = 10501.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.094899 restraints weight = 5109.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.097275 restraints weight = 3215.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.098819 restraints weight = 2239.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.099905 restraints weight = 1744.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.5345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4505  Z= 0.151
  Angle     :  0.641   9.779   6104  Z= 0.317
  Chirality :  0.043   0.162    677
  Planarity :  0.004   0.058    759
  Dihedral  :  4.498  23.901    607
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 20.69 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  2.03 (0.35), residues: 547
  helix:  2.62 (0.28), residues: 314
  sheet:  1.07 (1.26), residues: 18
  loop : -0.62 (0.40), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A1178 
 TYR   0.012   0.001   TYR A 403 
 PHE   0.013   0.001   PHE A 322 
 TRP   0.022   0.001   TRP A 484 
 HIS   0.003   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.15 ( 4501)
  covalent geometry    : angle       0.64175 /  0.32 ( 6096)
  SS BOND              : bond        0.00128 /  0.08 (    4)
  SS BOND              : angle       0.36140 /  0.20 (    8)
  hydrogen bonds       : bond        0.04676 /  3.07 (  259)
  hydrogen bonds       : angle       4.07744 /  3.03 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.9333 (mp) cc_final: 0.9114 (mp)
REVERT: A  309 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8603 (mm-30)
REVERT: A 1040 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6781 (tpt-90)
REVERT: A 1056 GLU cc_start: 0.9244 (tt0) cc_final: 0.8985 (pt0)
REVERT: A 1090 HIS cc_start: 0.8348 (m-70) cc_final: 0.8030 (m-70)
REVERT: A 1113 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7493 (p0)
REVERT: A 1124 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7371 (p90)
REVERT: A 1130 GLU cc_start: 0.4073 (OUTLIER) cc_final: 0.2525 (mt-10)
REVERT: A 1132 MET cc_start: 0.9260 (mtp) cc_final: 0.8948 (mmm)
REVERT: A  487 SER cc_start: 0.9474 (t) cc_final: 0.9050 (p)
REVERT: A  530 PHE cc_start: 0.9309 (m-80) cc_final: 0.9082 (m-80)
REVERT: A  541 TRP cc_start: 0.9091 (m-10) cc_final: 0.8568 (m100)
  outliers start: 27
  outliers final: 19
  residues processed: 152
  average time/residue: 0.0530
  time to fit residues: 10.7046
Evaluate side-chains
  155 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  241 PHE
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1113 ASP
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1130 GLU
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue 1188 CYS
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 2 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   chunk 50 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 GLN
A 515 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.116693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.097700 restraints weight = 10472.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.100894 restraints weight = 5136.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.103299 restraints weight = 3181.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.104886 restraints weight = 2211.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.105841 restraints weight = 1687.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.5563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4505  Z= 0.126
  Angle     :  0.627  10.675   6104  Z= 0.310
  Chirality :  0.043   0.213    677
  Planarity :  0.004   0.055    759
  Dihedral  :  4.395  24.293    607
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 23.49 %
    Favored  : 71.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  1.99 (0.36), residues: 547
  helix:  2.61 (0.28), residues: 315
  sheet:  0.30 (0.85), residues: 36
  loop : -0.69 (0.42), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A1178 
 TYR   0.016   0.001   TYR A 363 
 PHE   0.013   0.001   PHE A 322 
 TRP   0.038   0.002   TRP A 484 
 HIS   0.003   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.13 ( 4501)
  covalent geometry    : angle       0.62694 /  0.31 ( 6096)
  SS BOND              : bond        0.00112 /  0.07 (    4)
  SS BOND              : angle       0.32471 /  0.18 (    8)
  hydrogen bonds       : bond        0.04507 /  2.95 (  259)
  hydrogen bonds       : angle       4.02387 /  3.00 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.9299 (mp) cc_final: 0.9072 (mp)
REVERT: A  309 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8519 (mp0)
REVERT: A 1040 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6789 (tpt-90)
REVERT: A 1056 GLU cc_start: 0.9192 (tt0) cc_final: 0.8953 (pt0)
REVERT: A 1058 LEU cc_start: 0.9490 (tp) cc_final: 0.9215 (tt)
REVERT: A 1090 HIS cc_start: 0.8194 (m-70) cc_final: 0.7842 (m-70)
REVERT: A 1124 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7116 (p90)
REVERT: A 1129 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8350 (mm)
REVERT: A 1130 GLU cc_start: 0.4466 (OUTLIER) cc_final: 0.3016 (mt-10)
REVERT: A 1132 MET cc_start: 0.9185 (mtp) cc_final: 0.8916 (mmm)
REVERT: A  481 GLN cc_start: 0.9057 (tt0) cc_final: 0.8687 (tt0)
REVERT: A  541 TRP cc_start: 0.9079 (m-10) cc_final: 0.8471 (m100)
  outliers start: 24
  outliers final: 13
  residues processed: 148
  average time/residue: 0.0504
  time to fit residues: 9.9120
Evaluate side-chains
  143 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1071 ILE
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1130 GLU
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue 1188 CYS
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0270
   chunk 7 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.4956

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 275 ASN ** 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 = 0.3637 r_free = 0.3637 target = 0.118264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.099193 restraints weight = 10534.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.102571 restraints weight = 5236.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.105074 restraints weight = 3208.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.106739 restraints weight = 2224.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.107824 restraints weight = 1683.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.5818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4505  Z= 0.126
  Angle     :  0.650  12.961   6104  Z= 0.317
  Chirality :  0.043   0.224    677
  Planarity :  0.004   0.053    759
  Dihedral  :  4.343  23.516    607
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 23.49 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  2.00 (0.36), residues: 547
  helix:  2.65 (0.29), residues: 314
  sheet:  0.36 (0.87), residues: 36
  loop : -0.73 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A1178 
 TYR   0.011   0.001   TYR A 237 
 PHE   0.013   0.001   PHE A 322 
 TRP   0.077   0.002   TRP A 484 
 HIS   0.003   0.000   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.13 ( 4501)
  covalent geometry    : angle       0.65036 /  0.32 ( 6096)
  SS BOND              : bond        0.00120 /  0.08 (    4)
  SS BOND              : angle       0.31769 /  0.17 (    8)
  hydrogen bonds       : bond        0.04438 /  2.90 (  259)
  hydrogen bonds       : angle       4.07138 /  3.00 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 LEU cc_start: 0.9553 (mt) cc_final: 0.9311 (mp)
REVERT: A  253 LEU cc_start: 0.9255 (mp) cc_final: 0.9024 (mp)
REVERT: A  309 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8556 (mm-30)
REVERT: A 1040 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6770 (tpt-90)
REVERT: A 1056 GLU cc_start: 0.9211 (tt0) cc_final: 0.8904 (pt0)
REVERT: A 1058 LEU cc_start: 0.9486 (tp) cc_final: 0.9126 (tt)
REVERT: A 1090 HIS cc_start: 0.8283 (m-70) cc_final: 0.7909 (m-70)
REVERT: A 1124 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7112 (p90)
REVERT: A 1129 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8156 (mm)
REVERT: A 1130 GLU cc_start: 0.4408 (OUTLIER) cc_final: 0.3917 (mm-30)
REVERT: A 1132 MET cc_start: 0.9182 (mtp) cc_final: 0.8887 (mmm)
REVERT: A  517 PRO cc_start: 0.9077 (Cg_exo) cc_final: 0.8588 (Cg_endo)
REVERT: A  541 TRP cc_start: 0.8988 (m-10) cc_final: 0.8763 (m100)
  outliers start: 18
  outliers final: 11
  residues processed: 145
  average time/residue: 0.0516
  time to fit residues: 9.9209
Evaluate side-chains
  148 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1124 PHE
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1130 GLU
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue 1188 CYS
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 44 optimal weight:    0.0870
   chunk 27 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0370
   chunk 2 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.5638

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.117614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.096974 restraints weight = 10256.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.100498 restraints weight = 4928.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.102857 restraints weight = 2997.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.104579 restraints weight = 2096.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.105962 restraints weight = 1599.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.5966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4505  Z= 0.125
  Angle     :  0.649  12.521   6104  Z= 0.317
  Chirality :  0.043   0.207    677
  Planarity :  0.004   0.053    759
  Dihedral  :  4.305  22.999    607
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 24.14 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  1.99 (0.36), residues: 547
  helix:  2.62 (0.29), residues: 314
  sheet:  0.46 (0.86), residues: 36
  loop : -0.72 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG A1178 
 TYR   0.008   0.001   TYR A 237 
 PHE   0.012   0.001   PHE A 322 
 TRP   0.060   0.002   TRP A 484 
 HIS   0.002   0.000   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.13 ( 4501)
  covalent geometry    : angle       0.64953 /  0.32 ( 6096)
  SS BOND              : bond        0.00112 /  0.07 (    4)
  SS BOND              : angle       0.30846 /  0.17 (    8)
  hydrogen bonds       : bond        0.04367 /  2.88 (  259)
  hydrogen bonds       : angle       4.04450 /  2.98 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.9226 (mp) cc_final: 0.9020 (mp)
REVERT: A 1040 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6724 (tpt-90)
REVERT: A 1056 GLU cc_start: 0.9222 (tt0) cc_final: 0.8976 (pt0)
REVERT: A 1058 LEU cc_start: 0.9485 (tp) cc_final: 0.9130 (tt)
REVERT: A 1090 HIS cc_start: 0.8379 (m-70) cc_final: 0.8021 (m-70)
REVERT: A 1129 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8119 (mm)
REVERT: A 1130 GLU cc_start: 0.4505 (OUTLIER) cc_final: 0.4069 (mm-30)
REVERT: A  481 GLN cc_start: 0.9099 (tt0) cc_final: 0.8738 (tt0)
REVERT: A  541 TRP cc_start: 0.8967 (m-10) cc_final: 0.8755 (m100)
  outliers start: 18
  outliers final: 12
  residues processed: 148
  average time/residue: 0.0478
  time to fit residues: 9.4044
Evaluate side-chains
  143 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1121 PHE
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1130 GLU
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0060
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0970
   chunk 36 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5596

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 481 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.119921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.101158 restraints weight = 10384.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.104631 restraints weight = 5129.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.107052 restraints weight = 3116.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.108876 restraints weight = 2138.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.109828 restraints weight = 1593.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.6076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4505  Z= 0.129
  Angle     :  0.669  12.723   6104  Z= 0.328
  Chirality :  0.043   0.175    677
  Planarity :  0.004   0.054    759
  Dihedral  :  4.338  23.311    607
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.22 %
    Favored  : 70.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  1.99 (0.36), residues: 547
  helix:  2.57 (0.29), residues: 314
  sheet:  0.52 (0.87), residues: 36
  loop : -0.64 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A1178 
 TYR   0.009   0.001   TYR A 476 
 PHE   0.012   0.001   PHE A 322 
 TRP   0.129   0.003   TRP A 484 
 HIS   0.002   0.000   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 4501)
  covalent geometry    : angle       0.66893 /  0.33 ( 6096)
  SS BOND              : bond        0.00107 /  0.07 (    4)
  SS BOND              : angle       0.29465 /  0.17 (    8)
  hydrogen bonds       : bond        0.04513 /  2.99 (  259)
  hydrogen bonds       : angle       4.06924 /  3.00 (  753)

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

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

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1094 Ramachandran restraints generated.
    547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: A 1040 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6748 (tpt-90)
REVERT: A 1052 LEU cc_start: 0.8727 (mt) cc_final: 0.8300 (tt)
REVERT: A 1056 GLU cc_start: 0.9197 (tt0) cc_final: 0.8842 (pt0)
REVERT: A 1058 LEU cc_start: 0.9464 (tp) cc_final: 0.9119 (tt)
REVERT: A 1090 HIS cc_start: 0.8271 (m-70) cc_final: 0.7902 (m-70)
REVERT: A 1129 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8194 (mm)
REVERT: A 1130 GLU cc_start: 0.4492 (OUTLIER) cc_final: 0.3054 (mt-10)
REVERT: A 1132 MET cc_start: 0.9263 (mmm) cc_final: 0.8893 (mmm)
REVERT: A 1191 ARG cc_start: 0.8527 (tpt-90) cc_final: 0.8307 (tpt-90)
  outliers start: 18
  outliers final: 13
  residues processed: 147
  average time/residue: 0.0625
  time to fit residues: 12.0526
Evaluate side-chains
  149 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  233 ASP
Chi-restraints excluded: chain A residue  277 CYS
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1040 ARG
Chi-restraints excluded: chain A residue 1070 ILE
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1130 GLU
Chi-restraints excluded: chain A residue 1179 SER
Chi-restraints excluded: chain A residue  538 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 18 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.4184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.113502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.092960 restraints weight = 10365.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.096051 restraints weight = 5080.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.098389 restraints weight = 3212.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.099954 restraints weight = 2253.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.101244 restraints weight = 1752.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.6133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4505  Z= 0.177
  Angle     :  0.727  12.358   6104  Z= 0.356
  Chirality :  0.045   0.153    677
  Planarity :  0.005   0.058    759
  Dihedral  :  4.517  23.231    607
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 25.65 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.33 %
    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 are not related in a simple way.
  whole:  1.81 (0.36), residues: 547
  helix:  2.40 (0.29), residues: 313
  sheet:  0.96 (1.40), residues: 18
  loop : -0.63 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A1178 
 TYR   0.008   0.001   TYR A 476 
 PHE   0.010   0.001   PHE A 322 
 TRP   0.140   0.004   TRP A 484 
 HIS   0.002   0.001   HIS A 344 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.18 ( 4501)
  covalent geometry    : angle       0.72759 /  0.36 ( 6096)
  SS BOND              : bond        0.00161 /  0.11 (    4)
  SS BOND              : angle       0.40576 /  0.22 (    8)
  hydrogen bonds       : bond        0.05144 /  3.39 (  259)
  hydrogen bonds       : angle       4.22365 /  3.12 (  753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 907.86 seconds
wall clock time: 16 minutes 18.18 seconds (978.18 seconds total)