Starting phenix.real_space_refine
on Fri Jul 25 07:06:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7a8p_11679/07_2025/7a8p_11679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7a8p_11679/07_2025/7a8p_11679.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7a8p_11679/07_2025/7a8p_11679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7a8p_11679/07_2025/7a8p_11679.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7a8p_11679/07_2025/7a8p_11679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7a8p_11679/07_2025/7a8p_11679.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     Cl      1      4.86       5
     C    4669      2.51       5
     N    1304      2.21       5
     O    1284      1.98       5
     F       1      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7305
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 911, 7272
          Classifications: {'peptide': 911}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 59, 'TRANS': 851}
          Chain breaks: 6
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'R4Q': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.68, per 1000 atoms: 0.64
  Number of scatterers: 7305
  At special positions: 0
  Unit cell: (77.562, 97.578, 110.922, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      46     16.00
     F       1      9.00
     O    1284      8.00
     N    1304      7.00
     C    4669      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.79
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1730

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 8 sheets defined
      68.5% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 221 through 237
    Processing helix  chain 'A' and resid 238 through 252
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 3.734A  pdb=" N   LYS A 257 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 275
    Processing helix  chain 'A' and resid 276 through 290
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 312 through 326
    Processing helix  chain 'A' and resid 329 through 337
      removed outlier: 3.681A  pdb=" N   LEU A 333 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   PHE A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   THR A 335 " --> pdb=" O   GLN A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 353
      removed outlier: 3.595A  pdb=" N   LYS A 353 " --> pdb=" O   LYS A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 379
    Processing helix  chain 'A' and resid 392 through 410
    Processing helix  chain 'A' and resid 426 through 463
      removed outlier: 3.719A  pdb=" N   ARG A 447 " --> pdb=" O   LYS A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 474
      removed outlier: 4.174A  pdb=" N   LEU A 474 " --> pdb=" O   PHE A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 490
    Processing helix  chain 'A' and resid 497 through 520
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 3.683A  pdb=" N   LYS A 532 " --> pdb=" O   ASN A 528 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   CYS A 535 " --> pdb=" O   ARG A 531 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   LEU A 536 " --> pdb=" O   LYS A 532 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LEU A 537 " --> pdb=" O   TYR A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 557
    Processing helix  chain 'A' and resid 568 through 587
    Processing helix  chain 'A' and resid 624 through 635
    Processing helix  chain 'A' and resid 676 through 687
    Processing helix  chain 'A' and resid 688 through 704
      removed outlier: 3.849A  pdb=" N   LEU A 692 " --> pdb=" O   PRO A 688 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   GLY A 694 " --> pdb=" O   THR A 690 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   ALA A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 723
    Processing helix  chain 'A' and resid 772 through 789
    Processing helix  chain 'A' and resid 810 through 814
    Processing helix  chain 'A' and resid 818 through 824
    Processing helix  chain 'A' and resid 836 through 850
    Processing helix  chain 'A' and resid 856 through 867
    Processing helix  chain 'A' and resid 867 through 877
    Processing helix  chain 'A' and resid 884 through 888
    Processing helix  chain 'A' and resid 890 through 907
      removed outlier: 3.739A  pdb=" N   ALA A 907 " --> pdb=" O   ASN A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 936
    Processing helix  chain 'A' and resid 937 through 944
    Processing helix  chain 'A' and resid 954 through 974
    Processing helix  chain 'A' and resid 975 through 981
    Processing helix  chain 'A' and resid 986 through 1000
    Processing helix  chain 'A' and resid 1006 through 1017
      removed outlier: 3.586A  pdb=" N   LEU A1017 " --> pdb=" O   ARG A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1021 through 1023
      No H-bonds generated for 'chain 'A' and resid 1021 through 1023'
    Processing helix  chain 'A' and resid 1024 through 1044
    Processing helix  chain 'A' and resid 1044 through 1064
    Processing helix  chain 'A' and resid 1114 through 1142
      Proline residue:  A1120  - end of helix
    Processing helix  chain 'A' and resid 1159 through 1177
      removed outlier: 3.773A  pdb=" N   GLU A1177 " --> pdb=" O   ARG A1173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1192
    Processing helix  chain 'A' and resid 1204 through 1210
    Processing helix  chain 'A' and resid 1220 through 1225
      removed outlier: 4.049A  pdb=" N   ARG A1224 " --> pdb=" O   GLU A1220 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415
    Processing sheet with id=AA2, first strand: chain 'A' and resid 495 through 496
      removed outlier: 3.614A  pdb=" N   LYS A 622 " --> pdb=" O   TYR A 607 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   TYR A 607 " --> pdb=" O   LYS A 622 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 588 through 589
    Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 795
    Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 799
    Processing sheet with id=AA6, first strand: chain 'A' and resid 831 through 832
    Processing sheet with id=AA7, first strand: chain 'A' and resid 919 through 921
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1069 through 1071

    456 hydrogen bonds defined for protein.
    1332 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: 2.19

  Time building geometry restraints manager: 2.06 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1746
        1.33 -     1.45: 1433
        1.45 -     1.57: 4230
        1.57 -     1.69: 2
        1.69 -     1.81: 71
  Bond restraints: 7482
  Sorted by residual:
  bond pdb=" C02 R4Q A1301 "
       pdb=" C23 R4Q A1301 "
    ideal  model  delta    sigma   weight residual
    1.537  1.642 -0.105 2.00e-02 2.50e+03 2.73e+01
  bond pdb=" C23 R4Q A1301 "
       pdb=" N25 R4Q A1301 "
    ideal  model  delta    sigma   weight residual
    1.342  1.434 -0.092 2.00e-02 2.50e+03 2.10e+01
  bond pdb=" C04 R4Q A1301 "
       pdb=" O03 R4Q A1301 "
    ideal  model  delta    sigma   weight residual
    1.336  1.413 -0.077 2.00e-02 2.50e+03 1.48e+01
  bond pdb=" C02 R4Q A1301 "
       pdb=" O03 R4Q A1301 "
    ideal  model  delta    sigma   weight residual
    1.414  1.483 -0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" C12 R4Q A1301 "
       pdb=" F13 R4Q A1301 "
    ideal  model  delta    sigma   weight residual
    1.337  1.281  0.056 2.00e-02 2.50e+03 7.85e+00
  ... (remaining 7477 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 10002
        1.64 -     3.28: 104
        3.28 -     4.93: 41
        4.93 -     6.57: 3
        6.57 -     8.21: 3
  Bond angle restraints: 10153
  Sorted by residual:
  angle pdb=" C23 R4Q A1301 "
        pdb=" C02 R4Q A1301 "
        pdb=" O03 R4Q A1301 "
      ideal   model   delta    sigma   weight residual
     109.33  117.54   -8.21 3.00e+00 1.11e-01 7.49e+00
  angle pdb=" CA  PRO A 423 "
        pdb=" C   PRO A 423 "
        pdb=" N   SER A 424 "
      ideal   model   delta    sigma   weight residual
     114.74  117.22   -2.48 1.03e+00 9.43e-01 5.79e+00
  angle pdb=" C29 R4Q A1301 "
        pdb=" C33 R4Q A1301 "
        pdb=" N25 R4Q A1301 "
      ideal   model   delta    sigma   weight residual
     110.08  116.89   -6.81 3.00e+00 1.11e-01 5.15e+00
  angle pdb=" C28 R4Q A1301 "
        pdb=" C29 R4Q A1301 "
        pdb=" C30 R4Q A1301 "
      ideal   model   delta    sigma   weight residual
     113.19  106.52    6.67 3.00e+00 1.11e-01 4.95e+00
  angle pdb=" C02 R4Q A1301 "
        pdb=" C23 R4Q A1301 "
        pdb=" N25 R4Q A1301 "
      ideal   model   delta    sigma   weight residual
     117.72  123.04   -5.32 3.00e+00 1.11e-01 3.14e+00
  ... (remaining 10148 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 3993
       18.00 -    35.99: 439
       35.99 -    53.99: 97
       53.99 -    71.98: 14
       71.98 -    89.98: 9
  Dihedral angle restraints: 4552
    sinusoidal: 1894
      harmonic: 2658
  Sorted by residual:
  dihedral pdb=" CB  GLU A 495 "
           pdb=" CG  GLU A 495 "
           pdb=" CD  GLU A 495 "
           pdb=" OE1 GLU A 495 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.71  -89.71     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" N   LEU A 785 "
           pdb=" CA  LEU A 785 "
           pdb=" CB  LEU A 785 "
           pdb=" CG  LEU A 785 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.55  -57.45     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" N   LEU A 838 "
           pdb=" CA  LEU A 838 "
           pdb=" CB  LEU A 838 "
           pdb=" CG  LEU A 838 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.54   56.54     3      1.50e+01 4.44e-03 9.40e+00
  ... (remaining 4549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1075
       0.074 -    0.147: 53
       0.147 -    0.221: 0
       0.221 -    0.294: 0
       0.294 -    0.368: 1
  Chirality restraints: 1129
  Sorted by residual:
  chirality pdb=" C29 R4Q A1301 "
            pdb=" C28 R4Q A1301 "
            pdb=" C30 R4Q A1301 "
            pdb=" C33 R4Q A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.84    0.37 2.00e-01 2.50e+01 3.38e+00
  chirality pdb=" CA  VAL A1211 "
            pdb=" N   VAL A1211 "
            pdb=" C   VAL A1211 "
            pdb=" CB  VAL A1211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.23e-01
  chirality pdb=" CA  VAL A 646 "
            pdb=" N   VAL A 646 "
            pdb=" C   VAL A 646 "
            pdb=" CB  VAL A 646 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 1126 not shown)

  Planarity restraints: 1305
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 624 "   -0.022 5.00e-02 4.00e+02   3.35e-02 1.80e+00
        pdb=" N   PRO A 625 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 625 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 625 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1119 "   -0.014 5.00e-02 4.00e+02   2.14e-02 7.33e-01
        pdb=" N   PRO A1120 "    0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO A1120 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A1120 "   -0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 239 "    0.014 5.00e-02 4.00e+02   2.10e-02 7.08e-01
        pdb=" N   PRO A 240 "   -0.036 5.00e-02 4.00e+02
        pdb=" CA  PRO A 240 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 240 "    0.012 5.00e-02 4.00e+02
  ... (remaining 1302 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 163
        2.71 -     3.26: 7549
        3.26 -     3.81: 11937
        3.81 -     4.35: 14242
        4.35 -     4.90: 24782
  Nonbonded interactions: 58673
  Sorted by model distance:
  nonbonded pdb=" O   TYR A1082 "
            pdb=" NE2 GLN A1115 "
     model   vdw
     2.165 3.120
  nonbonded pdb=" O   VAL A1001 "
            pdb=" OG1 THR A1002 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OE1 GLN A 524 "
            pdb=" ND2 ASN A 528 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OH  TYR A 530 "
            pdb=" O   PRO A 651 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" N   GLU A 545 "
            pdb=" OE1 GLU A 545 "
     model   vdw
     2.285 3.120
  ... (remaining 58668 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:             1.350
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.740
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
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   0.105   7482  Z= 0.165
  Angle     :  0.500   8.209  10153  Z= 0.247
  Chirality :  0.033   0.368   1129
  Planarity :  0.003   0.034   1305
  Dihedral  : 15.714  89.976   2822
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 2.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  4.30 %
    Favored  : 95.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.26), residues: 897
  helix:  1.44 (0.20), residues: 585
  sheet: -1.19 (0.84), residues: 32
  loop : -0.77 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1026 
 HIS   0.006   0.001   HIS A 243 
 PHE   0.006   0.001   PHE A1146 
 TYR   0.008   0.001   TYR A1140 
 ARG   0.009   0.001   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07093 (  456)
  hydrogen bonds       : angle       3.98569 ( 1332)
  covalent geometry    : bond        0.00332 ( 7482)
  covalent geometry    : angle       0.49971 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 150
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 TYR cc_start: 0.7928 (t80) cc_final: 0.7587 (t80)
REVERT: A  966 PHE cc_start: 0.8012 (m-10) cc_final: 0.7794 (m-10)
REVERT: A 1027 GLU cc_start: 0.6864 (mp0) cc_final: 0.6600 (mp0)
  outliers start: 5
  outliers final: 1
  residues processed: 154
  average time/residue: 0.2006
  time to fit residues: 40.8452
Evaluate side-chains
  122 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  920 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    0.3980
   chunk 68 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0170
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A 309 GLN
A 488 GLN
A 624 HIS
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.161306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.123942 restraints weight = 9001.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125207 restraints weight = 6527.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.126398 restraints weight = 5331.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7482  Z= 0.117
  Angle     :  0.534   6.871  10153  Z= 0.257
  Chirality :  0.036   0.216   1129
  Planarity :  0.004   0.039   1305
  Dihedral  :  3.761  43.528   1020
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.48 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.28), residues: 897
  helix:  2.36 (0.21), residues: 590
  sheet: -0.78 (0.91), residues: 32
  loop :  0.10 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 707 
 HIS   0.003   0.001   HIS A1175 
 PHE   0.008   0.001   PHE A 721 
 TYR   0.013   0.001   TYR A 264 
 ARG   0.004   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03169 (  456)
  hydrogen bonds       : angle       3.64646 ( 1332)
  covalent geometry    : bond        0.00271 ( 7482)
  covalent geometry    : angle       0.53361 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  509 PHE cc_start: 0.7959 (t80) cc_final: 0.7718 (t80)
REVERT: A  530 TYR cc_start: 0.8209 (t80) cc_final: 0.7766 (t80)
REVERT: A  884 TRP cc_start: 0.7683 (t60) cc_final: 0.7161 (t60)
  outliers start: 14
  outliers final: 5
  residues processed: 133
  average time/residue: 0.1914
  time to fit residues: 34.5718
Evaluate side-chains
  120 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 59 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 893 GLN
A 921 GLN
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1164 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.157784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.121500 restraints weight = 9092.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.120516 restraints weight = 6969.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.122107 restraints weight = 7191.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7482  Z= 0.157
  Angle     :  0.554   8.082  10153  Z= 0.268
  Chirality :  0.038   0.220   1129
  Planarity :  0.004   0.045   1305
  Dihedral  :  3.825  28.325   1020
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.27 %
    Favored  : 84.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.28), residues: 897
  helix:  2.41 (0.21), residues: 588
  sheet: -1.03 (0.89), residues: 32
  loop :  0.12 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 707 
 HIS   0.005   0.001   HIS A1138 
 PHE   0.013   0.002   PHE A 721 
 TYR   0.009   0.001   TYR A 931 
 ARG   0.004   0.000   ARG A 782 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  456)
  hydrogen bonds       : angle       3.80532 ( 1332)
  covalent geometry    : bond        0.00383 ( 7482)
  covalent geometry    : angle       0.55378 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 115
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8105 (mm)
REVERT: A  509 PHE cc_start: 0.7941 (t80) cc_final: 0.7693 (t80)
REVERT: A  530 TYR cc_start: 0.8214 (t80) cc_final: 0.7674 (t80)
  outliers start: 19
  outliers final: 12
  residues processed: 127
  average time/residue: 0.1984
  time to fit residues: 34.5084
Evaluate side-chains
  120 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1132 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 17 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 250 HIS
A 527 GLN
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1164 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.157521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.119820 restraints weight = 9129.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.120270 restraints weight = 6823.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.121588 restraints weight = 5466.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7482  Z= 0.130
  Angle     :  0.529   8.543  10153  Z= 0.256
  Chirality :  0.038   0.203   1129
  Planarity :  0.004   0.052   1305
  Dihedral  :  3.848  29.342   1020
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 15.42 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.28), residues: 897
  helix:  2.54 (0.21), residues: 589
  sheet: -0.96 (0.89), residues: 32
  loop :  0.23 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 884 
 HIS   0.004   0.001   HIS A1138 
 PHE   0.009   0.001   PHE A 794 
 TYR   0.010   0.001   TYR A 282 
 ARG   0.006   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03574 (  456)
  hydrogen bonds       : angle       3.80658 ( 1332)
  covalent geometry    : bond        0.00311 ( 7482)
  covalent geometry    : angle       0.52853 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7775 (mm)
REVERT: A  456 LEU cc_start: 0.7583 (mt) cc_final: 0.7237 (mt)
REVERT: A  509 PHE cc_start: 0.7972 (t80) cc_final: 0.7705 (t80)
REVERT: A  530 TYR cc_start: 0.8254 (t80) cc_final: 0.7689 (t80)
  outliers start: 20
  outliers final: 12
  residues processed: 127
  average time/residue: 0.1901
  time to fit residues: 33.6520
Evaluate side-chains
  113 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue  938 SER
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1132 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 75 optimal weight:    7.9990
   chunk 80 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0870
   chunk 23 optimal weight:    8.9990
   chunk 66 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
A 249 HIS
A 719 GLN
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.157518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.120950 restraints weight = 8959.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.121977 restraints weight = 6541.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.122742 restraints weight = 5567.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7482  Z= 0.122
  Angle     :  0.514   8.614  10153  Z= 0.250
  Chirality :  0.037   0.183   1129
  Planarity :  0.005   0.058   1305
  Dihedral  :  3.775  28.012   1020
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.42 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.28), residues: 897
  helix:  2.65 (0.21), residues: 589
  sheet: -0.88 (0.94), residues: 32
  loop :  0.28 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 707 
 HIS   0.004   0.001   HIS A1138 
 PHE   0.017   0.001   PHE A 229 
 TYR   0.006   0.001   TYR A 931 
 ARG   0.007   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  456)
  hydrogen bonds       : angle       3.77504 ( 1332)
  covalent geometry    : bond        0.00289 ( 7482)
  covalent geometry    : angle       0.51361 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.847 
Fit side-chains
REVERT: A  239 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7869 (mm)
REVERT: A  459 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6912 (tm-30)
REVERT: A  509 PHE cc_start: 0.7994 (t80) cc_final: 0.7688 (t80)
REVERT: A  530 TYR cc_start: 0.8251 (t80) cc_final: 0.7690 (t80)
REVERT: A  771 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.5597 (pt0)
REVERT: A  999 TYR cc_start: 0.8000 (m-80) cc_final: 0.7784 (m-80)
  outliers start: 23
  outliers final: 15
  residues processed: 130
  average time/residue: 0.1909
  time to fit residues: 34.4163
Evaluate side-chains
  121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  771 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue  938 SER
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1132 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 90 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.156730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.119426 restraints weight = 9060.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.120300 restraints weight = 6607.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.121355 restraints weight = 5436.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7482  Z= 0.120
  Angle     :  0.520   8.664  10153  Z= 0.254
  Chirality :  0.037   0.181   1129
  Planarity :  0.004   0.055   1305
  Dihedral  :  3.758  27.171   1020
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.19 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.28), residues: 897
  helix:  2.65 (0.21), residues: 589
  sheet: -0.87 (0.95), residues: 32
  loop :  0.33 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 707 
 HIS   0.014   0.001   HIS A 250 
 PHE   0.017   0.001   PHE A 229 
 TYR   0.007   0.001   TYR A 282 
 ARG   0.006   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  456)
  hydrogen bonds       : angle       3.79028 ( 1332)
  covalent geometry    : bond        0.00283 ( 7482)
  covalent geometry    : angle       0.52010 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.781 
Fit side-chains
REVERT: A  239 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7915 (mt)
REVERT: A  323 MET cc_start: 0.7459 (ttt) cc_final: 0.7102 (tmm)
REVERT: A  425 LYS cc_start: 0.7669 (pttm) cc_final: 0.7360 (mmmt)
REVERT: A  456 LEU cc_start: 0.7649 (mt) cc_final: 0.7324 (mt)
REVERT: A  459 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7088 (tm-30)
REVERT: A  509 PHE cc_start: 0.7990 (t80) cc_final: 0.7670 (t80)
REVERT: A  530 TYR cc_start: 0.8251 (t80) cc_final: 0.7687 (t80)
REVERT: A  771 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.5752 (pt0)
  outliers start: 21
  outliers final: 15
  residues processed: 123
  average time/residue: 0.1812
  time to fit residues: 31.0030
Evaluate side-chains
  121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  771 GLU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue  938 SER
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1079 ILE
Chi-restraints excluded: chain A residue 1132 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 37 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.153099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.116895 restraints weight = 9144.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.116487 restraints weight = 6783.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.118034 restraints weight = 6432.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7482  Z= 0.198
  Angle     :  0.587   9.154  10153  Z= 0.291
  Chirality :  0.040   0.201   1129
  Planarity :  0.005   0.054   1305
  Dihedral  :  3.959  26.805   1020
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.57 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.28), residues: 897
  helix:  2.40 (0.21), residues: 589
  sheet: -1.03 (0.93), residues: 32
  loop :  0.13 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 707 
 HIS   0.009   0.001   HIS A 250 
 PHE   0.013   0.002   PHE A 229 
 TYR   0.011   0.002   TYR A 999 
 ARG   0.007   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04209 (  456)
  hydrogen bonds       : angle       4.05525 ( 1332)
  covalent geometry    : bond        0.00480 ( 7482)
  covalent geometry    : angle       0.58677 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.833 
Fit side-chains
REVERT: A  239 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7924 (mm)
REVERT: A  456 LEU cc_start: 0.7857 (mt) cc_final: 0.7510 (mt)
REVERT: A  459 GLU cc_start: 0.7405 (tm-30) cc_final: 0.7047 (tm-30)
REVERT: A  509 PHE cc_start: 0.7956 (t80) cc_final: 0.7748 (t80)
REVERT: A  530 TYR cc_start: 0.8265 (t80) cc_final: 0.7737 (t80)
REVERT: A  771 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.5929 (pt0)
REVERT: A 1042 GLU cc_start: 0.7722 (tt0) cc_final: 0.7355 (tt0)
  outliers start: 26
  outliers final: 18
  residues processed: 126
  average time/residue: 0.1852
  time to fit residues: 32.3399
Evaluate side-chains
  123 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  372 LYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  771 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue  938 SER
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1079 ILE
Chi-restraints excluded: chain A residue 1132 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 HIS ** 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 = 0.3844 r_free = 0.3844 target = 0.156182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.118932 restraints weight = 9035.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.119645 restraints weight = 6739.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.120469 restraints weight = 5474.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7482  Z= 0.125
  Angle     :  0.539   9.305  10153  Z= 0.263
  Chirality :  0.037   0.178   1129
  Planarity :  0.005   0.056   1305
  Dihedral  :  3.771  23.691   1020
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.20 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.28), residues: 897
  helix:  2.56 (0.21), residues: 589
  sheet: -0.98 (0.95), residues: 32
  loop :  0.17 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 707 
 HIS   0.004   0.001   HIS A1138 
 PHE   0.010   0.001   PHE A 802 
 TYR   0.013   0.001   TYR A 282 
 ARG   0.008   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  456)
  hydrogen bonds       : angle       3.92816 ( 1332)
  covalent geometry    : bond        0.00297 ( 7482)
  covalent geometry    : angle       0.53906 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  239 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7890 (mt)
REVERT: A  425 LYS cc_start: 0.7701 (pttm) cc_final: 0.7326 (mmmt)
REVERT: A  456 LEU cc_start: 0.7778 (mt) cc_final: 0.7444 (mt)
REVERT: A  509 PHE cc_start: 0.7922 (t80) cc_final: 0.7610 (t80)
REVERT: A  530 TYR cc_start: 0.8250 (t80) cc_final: 0.7685 (t80)
REVERT: A  771 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6002 (pt0)
REVERT: A 1042 GLU cc_start: 0.7657 (tt0) cc_final: 0.7303 (tt0)
REVERT: A 1064 MET cc_start: 0.7319 (ttm) cc_final: 0.7084 (mtp)
  outliers start: 24
  outliers final: 17
  residues processed: 126
  average time/residue: 0.2280
  time to fit residues: 40.1455
Evaluate side-chains
  125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  771 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue  938 SER
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1079 ILE
Chi-restraints excluded: chain A residue 1132 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 23 optimal weight:    8.9990
   chunk 80 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.157117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.119661 restraints weight = 9161.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.120289 restraints weight = 6678.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.121535 restraints weight = 5650.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7482  Z= 0.117
  Angle     :  0.550   9.478  10153  Z= 0.268
  Chirality :  0.037   0.175   1129
  Planarity :  0.005   0.055   1305
  Dihedral  :  3.726  22.852   1020
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.71 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.67 (0.28), residues: 897
  helix:  2.64 (0.21), residues: 587
  sheet: -0.95 (0.93), residues: 32
  loop :  0.24 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 707 
 HIS   0.003   0.001   HIS A1138 
 PHE   0.018   0.001   PHE A 229 
 TYR   0.006   0.001   TYR A 530 
 ARG   0.012   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03527 (  456)
  hydrogen bonds       : angle       3.88929 ( 1332)
  covalent geometry    : bond        0.00275 ( 7482)
  covalent geometry    : angle       0.55025 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A  239 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7766 (mm)
REVERT: A  425 LYS cc_start: 0.7715 (pttm) cc_final: 0.7334 (mmmt)
REVERT: A  456 LEU cc_start: 0.7722 (mt) cc_final: 0.7406 (mt)
REVERT: A  509 PHE cc_start: 0.7958 (t80) cc_final: 0.7651 (t80)
REVERT: A  530 TYR cc_start: 0.8248 (t80) cc_final: 0.7700 (t80)
REVERT: A  771 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6004 (pt0)
REVERT: A 1042 GLU cc_start: 0.7696 (tt0) cc_final: 0.7318 (tt0)
REVERT: A 1064 MET cc_start: 0.7268 (ttm) cc_final: 0.7037 (mtp)
  outliers start: 20
  outliers final: 16
  residues processed: 125
  average time/residue: 0.2187
  time to fit residues: 37.3406
Evaluate side-chains
  126 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  771 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue  938 SER
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1079 ILE
Chi-restraints excluded: chain A residue 1132 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 50 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.157136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.119495 restraints weight = 9208.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.120910 restraints weight = 6680.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.121741 restraints weight = 5166.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7482  Z= 0.124
  Angle     :  0.563   9.582  10153  Z= 0.271
  Chirality :  0.037   0.175   1129
  Planarity :  0.005   0.054   1305
  Dihedral  :  3.752  23.100   1020
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.96 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.28), residues: 897
  helix:  2.62 (0.21), residues: 587
  sheet: -0.98 (0.94), residues: 32
  loop :  0.23 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 441 
 HIS   0.004   0.001   HIS A1138 
 PHE   0.013   0.001   PHE A 497 
 TYR   0.006   0.001   TYR A 530 
 ARG   0.012   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (  456)
  hydrogen bonds       : angle       3.93213 ( 1332)
  covalent geometry    : bond        0.00292 ( 7482)
  covalent geometry    : angle       0.56321 (10153)

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

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

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1794 Ramachandran restraints generated.
    897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.427 
Fit side-chains
REVERT: A  239 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7835 (mm)
REVERT: A  268 MET cc_start: 0.8608 (mmm) cc_final: 0.8270 (mmm)
REVERT: A  425 LYS cc_start: 0.7759 (pttm) cc_final: 0.7351 (mmmt)
REVERT: A  456 LEU cc_start: 0.7756 (mt) cc_final: 0.7407 (mt)
REVERT: A  509 PHE cc_start: 0.7964 (t80) cc_final: 0.7644 (t80)
REVERT: A  530 TYR cc_start: 0.8265 (t80) cc_final: 0.7707 (t80)
REVERT: A  771 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.5993 (pt0)
REVERT: A 1064 MET cc_start: 0.7249 (ttm) cc_final: 0.7005 (mtp)
  outliers start: 19
  outliers final: 15
  residues processed: 123
  average time/residue: 0.2884
  time to fit residues: 50.3811
Evaluate side-chains
  121 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  486 VAL
Chi-restraints excluded: chain A residue  603 VAL
Chi-restraints excluded: chain A residue  668 THR
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  696 LEU
Chi-restraints excluded: chain A residue  771 GLU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue  938 SER
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1079 ILE
Chi-restraints excluded: chain A residue 1132 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 9 optimal weight:    0.3980
   chunk 40 optimal weight:    0.0370
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.157755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.120214 restraints weight = 9047.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.121314 restraints weight = 6823.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.122195 restraints weight = 5461.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7482  Z= 0.112
  Angle     :  0.558   9.701  10153  Z= 0.270
  Chirality :  0.038   0.201   1129
  Planarity :  0.005   0.053   1305
  Dihedral  :  3.707  22.864   1020
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.22 %
    Favored  : 78.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.71 (0.28), residues: 897
  helix:  2.68 (0.21), residues: 587
  sheet: -0.99 (0.95), residues: 32
  loop :  0.24 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 707 
 HIS   0.007   0.001   HIS A 250 
 PHE   0.017   0.001   PHE A 229 
 TYR   0.005   0.001   TYR A 931 
 ARG   0.011   0.000   ARG A 455 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03427 (  456)
  hydrogen bonds       : angle       3.89904 ( 1332)
  covalent geometry    : bond        0.00257 ( 7482)
  covalent geometry    : angle       0.55814 (10153)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2811.22 seconds
wall clock time: 51 minutes 43.19 seconds (3103.19 seconds total)