Starting phenix.real_space_refine
on Fri Aug 22 19:25:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7a8p_11679/08_2025/7a8p_11679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7a8p_11679/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7a8p_11679/08_2025/7a8p_11679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7a8p_11679/08_2025/7a8p_11679.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7a8p_11679/08_2025/7a8p_11679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7a8p_11679/08_2025/7a8p_11679.map"
  }
  resolution = 3.5
  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=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.32, per 1000 atoms: 0.18
  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: 0.53
  Conformation dependent library (CDL) restraints added in 349.8 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.17
  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: 1.06

  Time building geometry restraints manager: 0.67 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:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.020
  Find NCS groups from input model:        0.150
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.890
-------------------------------------------------------------------------------
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 : 3.20
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.009   0.001   ARG A 550 
 TYR   0.008   0.001   TYR A1140 
 PHE   0.006   0.001   PHE A1146 
 TRP   0.006   0.001   TRP A1026 
 HIS   0.006   0.001   HIS A 243 

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

*********************** 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  : 0.183 
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: 0.6598 (mp0)
  outliers start: 5
  outliers final: 1
  residues processed: 154
  average time/residue: 0.0879
  time to fit residues: 17.8492
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  : 0.274 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.0050
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7196

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.159827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.122416 restraints weight = 9097.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.124279 restraints weight = 6519.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.125147 restraints weight = 6006.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.125407 restraints weight = 4492.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.125889 restraints weight = 3871.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.1189

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= 0.125
  Angle     :  0.544   6.939  10153  Z= 0.262
  Chirality :  0.037   0.242   1129
  Planarity :  0.004   0.040   1305
  Dihedral  :  3.754  40.738   1020
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.48 %
    Favored  : 88.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.28), residues: 897
  helix:  2.34 (0.21), residues: 589
  sheet: -0.87 (0.90), residues: 32
  loop :  0.05 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 550 
 TYR   0.012   0.001   TYR A 264 
 PHE   0.009   0.001   PHE A 721 
 TRP   0.008   0.001   TRP A 707 
 HIS   0.004   0.001   HIS A1175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7482)
  covalent geometry    : angle       0.54443 (10153)
  hydrogen bonds       : bond        0.03268 (  456)
  hydrogen bonds       : angle       3.67194 ( 1332)

*********************** 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
  140 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  363 GLN cc_start: 0.5783 (tp40) cc_final: 0.5583 (tp40)
REVERT: A  509 PHE cc_start: 0.7969 (t80) cc_final: 0.7734 (t80)
REVERT: A  530 TYR cc_start: 0.8202 (t80) cc_final: 0.7705 (t80)
REVERT: A  966 PHE cc_start: 0.8054 (m-10) cc_final: 0.7813 (m-10)
  outliers start: 16
  outliers final: 7
  residues processed: 133
  average time/residue: 0.0793
  time to fit residues: 14.4267
Evaluate side-chains
  119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
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  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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 89 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 250 HIS
A 921 GLN
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1150 HIS
** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1164 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.149019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.113858 restraints weight = 9279.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.111554 restraints weight = 7133.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.113267 restraints weight = 7143.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.113410 restraints weight = 5164.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.113918 restraints weight = 5467.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.052   7482  Z= 0.344
  Angle     :  0.764   8.670  10153  Z= 0.380
  Chirality :  0.047   0.240   1129
  Planarity :  0.006   0.051   1305
  Dihedral  :  5.236  55.770   1020
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 15.55 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.27), residues: 897
  helix:  1.57 (0.20), residues: 584
  sheet: -1.34 (0.88), residues: 32
  loop : -0.55 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 782 
 TYR   0.016   0.003   TYR A 931 
 PHE   0.019   0.003   PHE A 721 
 TRP   0.030   0.004   TRP A 707 
 HIS   0.011   0.002   HIS A1138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00837 ( 7482)
  covalent geometry    : angle       0.76447 (10153)
  hydrogen bonds       : bond        0.05667 (  456)
  hydrogen bonds       : angle       4.49510 ( 1332)

*********************** 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
  139 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  456 LEU cc_start: 0.7991 (mt) cc_final: 0.7731 (mt)
REVERT: A  530 TYR cc_start: 0.8213 (t80) cc_final: 0.7756 (t80)
REVERT: A  838 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7958 (tt)
REVERT: A  890 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7206 (mm-30)
  outliers start: 28
  outliers final: 17
  residues processed: 131
  average time/residue: 0.0696
  time to fit residues: 12.8933
Evaluate side-chains
  125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  460 VAL
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  692 LEU
Chi-restraints excluded: chain A residue  696 LEU
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  951 VAL
Chi-restraints excluded: chain A residue  955 VAL
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1132 MET
Chi-restraints excluded: chain A residue 1150 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 322 GLN
A 527 GLN
A 719 GLN
A1035 GLN
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1150 HIS
** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.154197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.118987 restraints weight = 9295.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.117447 restraints weight = 7118.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.119134 restraints weight = 7357.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.119776 restraints weight = 4904.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.120001 restraints weight = 5029.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2410

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= 0.138
  Angle     :  0.565   9.142  10153  Z= 0.277
  Chirality :  0.038   0.229   1129
  Planarity :  0.005   0.065   1305
  Dihedral  :  4.326  38.905   1020
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.19 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.01 (0.28), residues: 897
  helix:  2.17 (0.21), residues: 587
  sheet: -1.44 (0.85), residues: 32
  loop : -0.11 (0.37), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 256 
 TYR   0.010   0.001   TYR A 530 
 PHE   0.010   0.001   PHE A 802 
 TRP   0.020   0.002   TRP A 707 
 HIS   0.014   0.001   HIS A1150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7482)
  covalent geometry    : angle       0.56511 (10153)
  hydrogen bonds       : bond        0.04097 (  456)
  hydrogen bonds       : angle       4.02408 ( 1332)

*********************** 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
  137 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 115
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A  456 LEU cc_start: 0.7858 (mt) cc_final: 0.7530 (mt)
REVERT: A  459 GLU cc_start: 0.7546 (tm-30) cc_final: 0.6810 (tm-30)
REVERT: A  509 PHE cc_start: 0.7907 (t80) cc_final: 0.7690 (t80)
REVERT: A  530 TYR cc_start: 0.8158 (t80) cc_final: 0.7662 (t80)
REVERT: A  890 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7208 (mm-30)
REVERT: A  999 TYR cc_start: 0.8226 (m-80) cc_final: 0.7924 (m-80)
  outliers start: 22
  outliers final: 15
  residues processed: 130
  average time/residue: 0.0677
  time to fit residues: 12.4492
Evaluate side-chains
  122 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
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  838 LEU
Chi-restraints excluded: chain A residue  920 HIS
Chi-restraints excluded: chain A residue  939 VAL
Chi-restraints excluded: chain A residue 1003 ARG
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1132 MET
Chi-restraints excluded: chain A residue 1150 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0050
   chunk 55 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1150 HIS
** 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 = 0.3842 r_free = 0.3842 target = 0.155852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.119725 restraints weight = 9163.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.119995 restraints weight = 7016.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.121503 restraints weight = 6615.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.121559 restraints weight = 4454.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.122235 restraints weight = 4075.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2466

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= 0.118
  Angle     :  0.536   9.063  10153  Z= 0.261
  Chirality :  0.037   0.179   1129
  Planarity :  0.005   0.057   1305
  Dihedral  :  3.977  22.971   1020
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.45 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.34 (0.28), residues: 897
  helix:  2.38 (0.21), residues: 589
  sheet: -1.29 (0.86), residues: 32
  loop :  0.13 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 256 
 TYR   0.008   0.001   TYR A 530 
 PHE   0.017   0.001   PHE A 229 
 TRP   0.016   0.001   TRP A 707 
 HIS   0.008   0.001   HIS A1150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7482)
  covalent geometry    : angle       0.53603 (10153)
  hydrogen bonds       : bond        0.03752 (  456)
  hydrogen bonds       : angle       3.91399 ( 1332)

*********************** 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
  135 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  456 LEU cc_start: 0.7775 (mt) cc_final: 0.7436 (mt)
REVERT: A  459 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6974 (tm-30)
REVERT: A  509 PHE cc_start: 0.7919 (t80) cc_final: 0.7626 (t80)
REVERT: A  530 TYR cc_start: 0.8182 (t80) cc_final: 0.7607 (t80)
REVERT: A  771 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.5653 (pt0)
REVERT: A  890 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7168 (mm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 129
  average time/residue: 0.0708
  time to fit residues: 12.5887
Evaluate side-chains
  120 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  476 GLU
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 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 51 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0770
   chunk 11 optimal weight:    0.5980
   chunk 43 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.7340

-------------------------------------------------------------------------------
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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
A 945 ASN
** 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 = 0.3852 r_free = 0.3852 target = 0.157035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.120696 restraints weight = 9113.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.119329 restraints weight = 7289.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.121278 restraints weight = 7616.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.121490 restraints weight = 5006.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.121897 restraints weight = 4935.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7482  Z= 0.117
  Angle     :  0.526   9.117  10153  Z= 0.254
  Chirality :  0.036   0.173   1129
  Planarity :  0.005   0.055   1305
  Dihedral  :  3.829  20.841   1020
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.95 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.28), residues: 897
  helix:  2.52 (0.21), residues: 589
  sheet: -1.10 (0.89), residues: 32
  loop :  0.23 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 782 
 TYR   0.008   0.001   TYR A 530 
 PHE   0.017   0.001   PHE A 229 
 TRP   0.015   0.001   TRP A 707 
 HIS   0.012   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7482)
  covalent geometry    : angle       0.52581 (10153)
  hydrogen bonds       : bond        0.03568 (  456)
  hydrogen bonds       : angle       3.84650 ( 1332)

*********************** 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
  131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  456 LEU cc_start: 0.7774 (mt) cc_final: 0.7444 (mt)
REVERT: A  459 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7117 (tm-30)
REVERT: A  509 PHE cc_start: 0.7882 (t80) cc_final: 0.7549 (t80)
REVERT: A  530 TYR cc_start: 0.8215 (t80) cc_final: 0.7643 (t80)
REVERT: A  771 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.5822 (pt0)
REVERT: A  890 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7160 (mm-30)
  outliers start: 23
  outliers final: 17
  residues processed: 125
  average time/residue: 0.0753
  time to fit residues: 12.7904
Evaluate side-chains
  119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  305 CYS
Chi-restraints excluded: chain A residue  476 GLU
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  776 ARG
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
Chi-restraints excluded: chain A residue 1150 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 40 optimal weight:    0.0870
   chunk 71 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.7562

-------------------------------------------------------------------------------
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 309 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 = 0.3857 r_free = 0.3857 target = 0.157323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.119712 restraints weight = 9063.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.120106 restraints weight = 6898.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.121372 restraints weight = 5627.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.121634 restraints weight = 4567.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.121986 restraints weight = 4164.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7482  Z= 0.116
  Angle     :  0.527   9.202  10153  Z= 0.255
  Chirality :  0.037   0.169   1129
  Planarity :  0.005   0.054   1305
  Dihedral  :  3.738  20.712   1020
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.59 (0.28), residues: 897
  helix:  2.57 (0.21), residues: 589
  sheet: -1.11 (0.90), residues: 32
  loop :  0.21 (0.38), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 256 
 TYR   0.011   0.001   TYR A 282 
 PHE   0.017   0.001   PHE A 229 
 TRP   0.014   0.001   TRP A 707 
 HIS   0.009   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7482)
  covalent geometry    : angle       0.52697 (10153)
  hydrogen bonds       : bond        0.03488 (  456)
  hydrogen bonds       : angle       3.85221 ( 1332)

*********************** 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
  125 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A  456 LEU cc_start: 0.7806 (mt) cc_final: 0.7480 (mt)
REVERT: A  509 PHE cc_start: 0.7955 (t80) cc_final: 0.7680 (t80)
REVERT: A  530 TYR cc_start: 0.8251 (t80) cc_final: 0.7665 (t80)
REVERT: A  771 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.5884 (pt0)
REVERT: A 1042 GLU cc_start: 0.7667 (tt0) cc_final: 0.7287 (tt0)
  outliers start: 20
  outliers final: 15
  residues processed: 121
  average time/residue: 0.0837
  time to fit residues: 13.6767
Evaluate side-chains
  117 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
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  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 1030 HIS
Chi-restraints excluded: chain A residue 1039 SER
Chi-restraints excluded: chain A residue 1150 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 69 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 72 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 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 = 0.3839 r_free = 0.3839 target = 0.155633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.118335 restraints weight = 9223.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.118974 restraints weight = 6962.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.120021 restraints weight = 5651.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.120260 restraints weight = 4577.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.120629 restraints weight = 4055.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2706

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= 0.134
  Angle     :  0.550   9.468  10153  Z= 0.267
  Chirality :  0.037   0.172   1129
  Planarity :  0.005   0.054   1305
  Dihedral  :  3.770  19.977   1020
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.71 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.28), residues: 897
  helix:  2.56 (0.21), residues: 587
  sheet: -1.01 (0.92), residues: 32
  loop :  0.18 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 481 
 TYR   0.008   0.001   TYR A 282 
 PHE   0.015   0.001   PHE A 229 
 TRP   0.014   0.001   TRP A 707 
 HIS   0.007   0.001   HIS A 250 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7482)
  covalent geometry    : angle       0.54999 (10153)
  hydrogen bonds       : bond        0.03651 (  456)
  hydrogen bonds       : angle       3.90653 ( 1332)

*********************** 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
  131 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  425 LYS cc_start: 0.7744 (pttm) cc_final: 0.7349 (mmmt)
REVERT: A  456 LEU cc_start: 0.7838 (mt) cc_final: 0.7530 (mt)
REVERT: A  509 PHE cc_start: 0.7933 (t80) cc_final: 0.7587 (t80)
REVERT: A  530 TYR cc_start: 0.8252 (t80) cc_final: 0.7684 (t80)
REVERT: A  771 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.5982 (pt0)
REVERT: A 1042 GLU cc_start: 0.7716 (tt0) cc_final: 0.7321 (tt0)
  outliers start: 23
  outliers final: 17
  residues processed: 125
  average time/residue: 0.0802
  time to fit residues: 13.6943
Evaluate side-chains
  120 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
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  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
Chi-restraints excluded: chain A residue 1150 HIS
Chi-restraints excluded: chain A residue 1160 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 73 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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**
** 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 = 0.3838 r_free = 0.3838 target = 0.155369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.118084 restraints weight = 9123.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.118711 restraints weight = 6955.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.119719 restraints weight = 5610.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.119973 restraints weight = 4572.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.120361 restraints weight = 4026.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2773

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= 0.134
  Angle     :  0.553   9.683  10153  Z= 0.266
  Chirality :  0.037   0.169   1129
  Planarity :  0.005   0.055   1305
  Dihedral  :  3.778  20.249   1020
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.22 %
    Favored  : 78.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.49 (0.28), residues: 897
  helix:  2.49 (0.21), residues: 587
  sheet: -1.02 (0.92), residues: 32
  loop :  0.17 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 256 
 TYR   0.013   0.001   TYR A 282 
 PHE   0.009   0.001   PHE A 802 
 TRP   0.015   0.001   TRP A 707 
 HIS   0.004   0.001   HIS A1138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 7482)
  covalent geometry    : angle       0.55349 (10153)
  hydrogen bonds       : bond        0.03679 (  456)
  hydrogen bonds       : angle       3.92932 ( 1332)

*********************** 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
  123 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  425 LYS cc_start: 0.7578 (pttm) cc_final: 0.7297 (mmmt)
REVERT: A  456 LEU cc_start: 0.7861 (mt) cc_final: 0.7540 (mt)
REVERT: A  509 PHE cc_start: 0.7916 (t80) cc_final: 0.7540 (t80)
REVERT: A  530 TYR cc_start: 0.8255 (t80) cc_final: 0.7734 (t80)
REVERT: A  771 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6051 (pt0)
  outliers start: 22
  outliers final: 17
  residues processed: 117
  average time/residue: 0.0794
  time to fit residues: 12.7376
Evaluate side-chains
  116 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
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  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
Chi-restraints excluded: chain A residue 1150 HIS
Chi-restraints excluded: chain A residue 1160 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 79 optimal weight:    0.2980
   chunk 42 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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**
** 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 = 0.3849 r_free = 0.3849 target = 0.156581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.120042 restraints weight = 9162.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.119969 restraints weight = 6986.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.121556 restraints weight = 6558.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.121876 restraints weight = 4465.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.122253 restraints weight = 4072.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2826

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= 0.119
  Angle     :  0.563   9.746  10153  Z= 0.271
  Chirality :  0.037   0.164   1129
  Planarity :  0.005   0.054   1305
  Dihedral  :  3.727  19.293   1020
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.72 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.28), residues: 897
  helix:  2.51 (0.21), residues: 587
  sheet: -1.03 (0.94), residues: 32
  loop :  0.23 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 256 
 TYR   0.019   0.001   TYR A 282 
 PHE   0.017   0.001   PHE A 229 
 TRP   0.015   0.001   TRP A 707 
 HIS   0.004   0.001   HIS A1138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 7482)
  covalent geometry    : angle       0.56316 (10153)
  hydrogen bonds       : bond        0.03553 (  456)
  hydrogen bonds       : angle       3.94536 ( 1332)

********************** 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
  123 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.295 
Fit side-chains
REVERT: A  425 LYS cc_start: 0.7660 (pttm) cc_final: 0.7389 (mmmt)
REVERT: A  456 LEU cc_start: 0.7853 (mt) cc_final: 0.7541 (mt)
REVERT: A  509 PHE cc_start: 0.7906 (t80) cc_final: 0.7629 (t80)
REVERT: A  530 TYR cc_start: 0.8246 (t80) cc_final: 0.7699 (t80)
REVERT: A  771 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.5992 (pt0)
  outliers start: 19
  outliers final: 15
  residues processed: 118
  average time/residue: 0.0755
  time to fit residues: 12.2723
Evaluate side-chains
  119 residues out of total 791 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
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  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 1039 SER
Chi-restraints excluded: chain A residue 1132 MET
Chi-restraints excluded: chain A residue 1150 HIS
Chi-restraints excluded: chain A residue 1160 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 78 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 63 optimal weight:    0.1980
   chunk 39 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 47 optimal weight:    0.2980
   chunk 4 optimal weight:    9.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 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 = 0.3841 r_free = 0.3841 target = 0.155778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.119169 restraints weight = 9199.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.118319 restraints weight = 7151.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.119850 restraints weight = 6597.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.120465 restraints weight = 4756.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.120858 restraints weight = 4295.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2905

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= 0.132
  Angle     :  0.580   9.923  10153  Z= 0.279
  Chirality :  0.037   0.167   1129
  Planarity :  0.005   0.055   1305
  Dihedral  :  3.759  19.878   1020
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.23 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.42 (0.28), residues: 897
  helix:  2.48 (0.21), residues: 587
  sheet: -1.54 (0.85), residues: 37
  loop :  0.17 (0.38), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1003 
 TYR   0.008   0.001   TYR A 530 
 PHE   0.012   0.001   PHE A 497 
 TRP   0.014   0.001   TRP A 707 
 HIS   0.004   0.001   HIS A1138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7482)
  covalent geometry    : angle       0.58039 (10153)
  hydrogen bonds       : bond        0.03666 (  456)
  hydrogen bonds       : angle       3.98282 ( 1332)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1111.31 seconds
wall clock time: 19 minutes 49.73 seconds (1189.73 seconds total)