Starting phenix.real_space_refine
on Wed Sep 17 10:16:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qpv_53284/09_2025/9qpv_53284.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qpv_53284/09_2025/9qpv_53284.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qpv_53284/09_2025/9qpv_53284.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qpv_53284/09_2025/9qpv_53284.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qpv_53284/09_2025/9qpv_53284.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qpv_53284/09_2025/9qpv_53284.cif"
  }
  resolution = 3.3
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    4912      2.51       5
     N    1413      2.21       5
     O    1433      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7776
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1000, 7776
          Classifications: {'peptide': 1000}
          Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 943}
          Chain breaks: 4
  Time building chain proxies: 2.25, per 1000 atoms: 0.29
  Number of scatterers: 7776
  At special positions: 0
  Unit cell: (63, 107.52, 133.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O    1433      8.00
     N    1413      7.00
     C    4912      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: 1.22
  Conformation dependent library (CDL) restraints added in 489.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1858

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 7 sheets defined
      58.4% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 4.248A  pdb=" N   ALA A  55 " --> pdb=" O   ASP A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 149
      removed outlier: 3.689A  pdb=" N   VAL A 147 " --> pdb=" O   LYS A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 158
      removed outlier: 3.547A  pdb=" N   HIS A 156 " --> pdb=" O   LYS A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 185
    Processing helix  chain 'A' and resid 185 through 190
    Processing helix  chain 'A' and resid 217 through 222
      removed outlier: 3.903A  pdb=" N   ARG A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 242
    Processing helix  chain 'A' and resid 243 through 244
      No H-bonds generated for 'chain 'A' and resid 243 through 244'
    Processing helix  chain 'A' and resid 245 through 249
    Processing helix  chain 'A' and resid 259 through 284
    Processing helix  chain 'A' and resid 289 through 311
    Processing helix  chain 'A' and resid 413 through 418
    Processing helix  chain 'A' and resid 421 through 452
      Proline residue:  A 434  - end of helix
    Processing helix  chain 'A' and resid 457 through 463
    Processing helix  chain 'A' and resid 464 through 466
      No H-bonds generated for 'chain 'A' and resid 464 through 466'
    Processing helix  chain 'A' and resid 470 through 486
    Processing helix  chain 'A' and resid 491 through 505
    Processing helix  chain 'A' and resid 506 through 510
    Processing helix  chain 'A' and resid 512 through 516
      removed outlier: 3.871A  pdb=" N   LEU A 516 " --> pdb=" O   PHE A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 531
      removed outlier: 3.692A  pdb=" N   ALA A 526 " --> pdb=" O   ALA A 522 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLN A 527 " --> pdb=" O   GLU A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 540
    Processing helix  chain 'A' and resid 541 through 554
    Processing helix  chain 'A' and resid 564 through 578
      removed outlier: 3.881A  pdb=" N   LEU A 578 " --> pdb=" O   ALA A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 599
    Processing helix  chain 'A' and resid 604 through 612
    Processing helix  chain 'A' and resid 614 through 627
      removed outlier: 3.593A  pdb=" N   GLY A 618 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ASP A 622 " --> pdb=" O   GLY A 618 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL A 625 " --> pdb=" O   LEU A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 671
    Processing helix  chain 'A' and resid 674 through 703
      removed outlier: 3.692A  pdb=" N   ARG A 678 " --> pdb=" O   SER A 674 " (cutoff:3.500A)
      Proline residue:  A 696  - end of helix
    Processing helix  chain 'A' and resid 730 through 746
    Processing helix  chain 'A' and resid 758 through 784
    Processing helix  chain 'A' and resid 786 through 831
      removed outlier: 3.753A  pdb=" N   MET A 791 " --> pdb=" O   LYS A 787 " (cutoff:3.500A)
      Proline residue:  A 792  - end of helix
      removed outlier: 4.025A  pdb=" N   VAL A 821 " --> pdb=" O   GLN A 817 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   GLN A 822 " --> pdb=" O   ALA A 818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 847
    Processing helix  chain 'A' and resid 850 through 860
    Processing helix  chain 'A' and resid 864 through 876
    Processing helix  chain 'A' and resid 877 through 890
    Processing helix  chain 'A' and resid 909 through 914
    Processing helix  chain 'A' and resid 916 through 920
    Processing helix  chain 'A' and resid 923 through 927
    Processing helix  chain 'A' and resid 929 through 940
      removed outlier: 3.660A  pdb=" N   PHE A 936 " --> pdb=" O   LEU A 932 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 940 through 950
    Processing helix  chain 'A' and resid 954 through 959
    Processing helix  chain 'A' and resid 962 through 972
    Processing helix  chain 'A' and resid 977 through 981
    Processing helix  chain 'A' and resid 985 through 998
    Processing helix  chain 'A' and resid 1033 through 1038
    Processing helix  chain 'A' and resid 1073 through 1081
      removed outlier: 3.717A  pdb=" N   VAL A1077 " --> pdb=" O   VAL A1073 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1161 through 1165
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 71
      removed outlier: 4.213A  pdb=" N   LEU A 122 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 71
      removed outlier: 6.616A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   LEU A 255 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   LEU A  41 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 101
      removed outlier: 6.454A  pdb=" N   ARG A  92 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   LEU A 101 " --> pdb=" O   GLU A  90 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   GLU A  90 " --> pdb=" O   LEU A 101 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 630 through 633
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1092 through 1093
      removed outlier: 4.459A  pdb=" N   ILE A1025 " --> pdb=" O   VAL A1093 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   THR A1022 " --> pdb=" O   ALA A1007 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1067 through 1072
      removed outlier: 3.553A  pdb=" N   ILE A1117 " --> pdb=" O   ASP A1129 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ARG A1119 " --> pdb=" O   HIS A1127 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   HIS A1127 " --> pdb=" O   ARG A1119 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1067 through 1072

    465 hydrogen bonds defined for protein.
    1311 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: 1.45

  Time building geometry restraints manager: 1.54 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2670
        1.34 -     1.46: 1222
        1.46 -     1.57: 4012
        1.57 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 7936
  Sorted by residual:
  bond pdb=" CB  VAL A 849 "
       pdb=" CG2 VAL A 849 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.35e+00
  bond pdb=" N   ARG A  66 "
       pdb=" CA  ARG A  66 "
    ideal  model  delta    sigma   weight residual
    1.455  1.439  0.016 1.61e-02 3.86e+03 9.98e-01
  bond pdb=" CG  GLN A 769 "
       pdb=" CD  GLN A 769 "
    ideal  model  delta    sigma   weight residual
    1.516  1.493  0.023 2.50e-02 1.60e+03 8.60e-01
  bond pdb=" CB  VAL A1133 "
       pdb=" CG2 VAL A1133 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.41e-01
  bond pdb=" C   ARG A 938 "
       pdb=" N   PHE A 939 "
    ideal  model  delta    sigma   weight residual
    1.324  1.346 -0.022 2.56e-02 1.53e+03 7.29e-01
  ... (remaining 7931 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 10567
        2.21 -     4.42: 182
        4.42 -     6.64: 32
        6.64 -     8.85: 2
        8.85 -    11.06: 1
  Bond angle restraints: 10784
  Sorted by residual:
  angle pdb=" C   VAL A1090 "
        pdb=" N   LEU A1091 "
        pdb=" CA  LEU A1091 "
      ideal   model   delta    sigma   weight residual
     121.75  127.52   -5.77 1.73e+00 3.34e-01 1.11e+01
  angle pdb=" N   ASN A 579 "
        pdb=" CA  ASN A 579 "
        pdb=" C   ASN A 579 "
      ideal   model   delta    sigma   weight residual
     109.81  117.14   -7.33 2.21e+00 2.05e-01 1.10e+01
  angle pdb=" CA  LEU A 642 "
        pdb=" CB  LEU A 642 "
        pdb=" CG  LEU A 642 "
      ideal   model   delta    sigma   weight residual
     116.30  105.24   11.06 3.50e+00 8.16e-02 9.99e+00
  angle pdb=" C   LEU A1089 "
        pdb=" N   VAL A1090 "
        pdb=" CA  VAL A1090 "
      ideal   model   delta    sigma   weight residual
     122.58  118.22    4.36 1.48e+00 4.57e-01 8.68e+00
  angle pdb=" N   LEU A1089 "
        pdb=" CA  LEU A1089 "
        pdb=" C   LEU A1089 "
      ideal   model   delta    sigma   weight residual
     112.03  115.88   -3.85 1.31e+00 5.83e-01 8.63e+00
  ... (remaining 10779 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.35: 4362
       16.35 -    32.69: 363
       32.69 -    49.04: 49
       49.04 -    65.39: 20
       65.39 -    81.73: 9
  Dihedral angle restraints: 4803
    sinusoidal: 1923
      harmonic: 2880
  Sorted by residual:
  dihedral pdb=" CA  THR A 455 "
           pdb=" C   THR A 455 "
           pdb=" N   GLU A 456 "
           pdb=" CA  GLU A 456 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.52   29.48     0      5.00e+00 4.00e-02 3.48e+01
  dihedral pdb=" CA  THR A 515 "
           pdb=" C   THR A 515 "
           pdb=" N   LEU A 516 "
           pdb=" CA  LEU A 516 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.78  -29.22     0      5.00e+00 4.00e-02 3.42e+01
  dihedral pdb=" CA  ASN A  75 "
           pdb=" C   ASN A  75 "
           pdb=" N   GLY A  76 "
           pdb=" CA  GLY A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.92  -29.08     0      5.00e+00 4.00e-02 3.38e+01
  ... (remaining 4800 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 834
       0.042 -    0.085: 267
       0.085 -    0.127: 78
       0.127 -    0.169: 18
       0.169 -    0.212: 3
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" CG  LEU A 176 "
            pdb=" CB  LEU A 176 "
            pdb=" CD1 LEU A 176 "
            pdb=" CD2 LEU A 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CG  LEU A 436 "
            pdb=" CB  LEU A 436 "
            pdb=" CD1 LEU A 436 "
            pdb=" CD2 LEU A 436 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.08e-01
  chirality pdb=" CA  ASN A 579 "
            pdb=" N   ASN A 579 "
            pdb=" C   ASN A 579 "
            pdb=" CB  ASN A 579 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.05e-01
  ... (remaining 1197 not shown)

  Planarity restraints: 1425
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 466 "   -0.009 2.00e-02 2.50e+03   2.71e-02 1.47e+01
        pdb=" CG  TYR A 466 "    0.008 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 466 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 466 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 466 "    0.038 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 466 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 466 "    0.037 2.00e-02 2.50e+03
        pdb=" OH  TYR A 466 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  66 "   -0.213 9.50e-02 1.11e+02   9.64e-02 7.39e+00
        pdb=" NE  ARG A  66 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  66 "   -0.021 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  66 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  66 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 493 "    0.014 2.00e-02 2.50e+03   2.70e-02 7.31e+00
        pdb=" C   GLU A 493 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   GLU A 493 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A 494 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1422 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.74: 524
        2.74 -     3.28: 8483
        3.28 -     3.82: 13267
        3.82 -     4.36: 16460
        4.36 -     4.90: 27188
  Nonbonded interactions: 65922
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 982 "
            pdb=" OH  TYR A 989 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OE1 GLN A 863 "
            pdb=" NH2 ARG A 938 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   SER A 796 "
            pdb=" OG1 THR A 799 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OH  TYR A 907 "
            pdb=" O   ARG A1044 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OE1 GLN A 190 "
            pdb=" OH  TYR A 224 "
     model   vdw
     2.291 3.040
  ... (remaining 65917 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  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:             0.020
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.070
  Find NCS groups from input model:        0.030
  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:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6594
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   0.038   7936  Z= 0.160
  Angle     :  0.758  11.062  10784  Z= 0.429
  Chirality :  0.047   0.212   1200
  Planarity :  0.010   0.096   1425
  Dihedral  : 13.050  81.731   2945
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -2.28 (0.24), residues: 990
  helix: -1.48 (0.19), residues: 516
  sheet: -0.56 (0.51), residues: 106
  loop : -1.60 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.003   ARG A  66 
 TYR   0.042   0.006   TYR A 466 
 PHE   0.019   0.003   PHE A  61 
 TRP   0.020   0.002   TRP A 925 
 HIS   0.003   0.001   HIS A1138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7936)
  covalent geometry    : angle       0.75838 (10784)
  hydrogen bonds       : bond        0.14031 (  445)
  hydrogen bonds       : angle       7.47294 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 ARG cc_start: 0.8014 (mmm160) cc_final: 0.7781 (mmm-85)
REVERT: A  630 THR cc_start: 0.7554 (m) cc_final: 0.7243 (p)
REVERT: A  874 ARG cc_start: 0.6501 (mtt180) cc_final: 0.5959 (ptp-170)
REVERT: A 1132 MET cc_start: 0.6228 (mmt) cc_final: 0.5950 (tpp)
REVERT: A 1165 LEU cc_start: 0.8537 (mp) cc_final: 0.8318 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1254
  time to fit residues: 38.9146
Evaluate side-chains
  161 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.3980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 156 HIS
A 201 GLN
A 206 HIS
** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 755 ASN
** A 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.145562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.115423 restraints weight = 14596.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 3.92
r_work: 0.3570 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   7936  Z= 0.234
  Angle     :  0.817  10.157  10784  Z= 0.421
  Chirality :  0.047   0.199   1200
  Planarity :  0.007   0.058   1425
  Dihedral  :  6.202  28.573   1100
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.57 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.76 (0.26), residues: 990
  helix:  0.05 (0.22), residues: 522
  sheet: -0.81 (0.45), residues: 124
  loop : -1.05 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 165 
 TYR   0.027   0.003   TYR A 465 
 PHE   0.035   0.004   PHE A 513 
 TRP   0.019   0.002   TRP A 439 
 HIS   0.004   0.001   HIS A1131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 7936)
  covalent geometry    : angle       0.81656 (10784)
  hydrogen bonds       : bond        0.05538 (  445)
  hydrogen bonds       : angle       5.66277 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 184
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLN cc_start: 0.7669 (pp30) cc_final: 0.7258 (pp30)
REVERT: A  308 ARG cc_start: 0.8472 (mmm160) cc_final: 0.7995 (mmm-85)
REVERT: A  417 ASP cc_start: 0.8265 (m-30) cc_final: 0.7742 (p0)
REVERT: A  527 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8465 (mt0)
REVERT: A  590 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7652 (mpp)
REVERT: A  630 THR cc_start: 0.7806 (m) cc_final: 0.7320 (p)
REVERT: A  658 ARG cc_start: 0.8475 (mtm110) cc_final: 0.8160 (mtm-85)
REVERT: A  748 TYR cc_start: 0.7849 (m-80) cc_final: 0.7627 (m-80)
REVERT: A  749 SER cc_start: 0.8795 (m) cc_final: 0.8562 (p)
REVERT: A  950 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: A  994 LEU cc_start: 0.8667 (mt) cc_final: 0.8285 (mt)
REVERT: A 1001 ARG cc_start: 0.7765 (ttt90) cc_final: 0.7167 (ttm-80)
REVERT: A 1027 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7960 (mp)
REVERT: A 1081 LEU cc_start: 0.8461 (pt) cc_final: 0.8218 (pt)
REVERT: A 1132 MET cc_start: 0.8041 (mmt) cc_final: 0.7675 (tpp)
  outliers start: 19
  outliers final: 12
  residues processed: 190
  average time/residue: 0.1107
  time to fit residues: 26.9221
Evaluate side-chains
  157 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  767 VAL
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  888 MET
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1139 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 91 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 84 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 460 HIS
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 998 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.146423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.118604 restraints weight = 14373.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 3.69
r_work: 0.3618 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.4634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7936  Z= 0.174
  Angle     :  0.740   9.202  10784  Z= 0.376
  Chirality :  0.045   0.302   1200
  Planarity :  0.006   0.064   1425
  Dihedral  :  5.652  27.137   1100
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.09 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.41 (0.26), residues: 990
  helix:  0.33 (0.22), residues: 522
  sheet: -0.78 (0.44), residues: 126
  loop : -0.82 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 293 
 TYR   0.021   0.002   TYR A  45 
 PHE   0.020   0.002   PHE A 946 
 TRP   0.012   0.002   TRP A 956 
 HIS   0.003   0.001   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7936)
  covalent geometry    : angle       0.74033 (10784)
  hydrogen bonds       : bond        0.04957 (  445)
  hydrogen bonds       : angle       5.33636 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 152
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLN cc_start: 0.7573 (pp30) cc_final: 0.7222 (pp30)
REVERT: A  145 MET cc_start: 0.7143 (mmm) cc_final: 0.6869 (mmt)
REVERT: A  154 ARG cc_start: 0.7523 (tmm-80) cc_final: 0.7172 (ttp80)
REVERT: A  308 ARG cc_start: 0.8502 (mmm160) cc_final: 0.8032 (mmm-85)
REVERT: A  417 ASP cc_start: 0.8237 (m-30) cc_final: 0.7760 (p0)
REVERT: A  527 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8577 (mt0)
REVERT: A  590 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7585 (mpp)
REVERT: A  638 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7357 (mm-30)
REVERT: A  749 SER cc_start: 0.8755 (m) cc_final: 0.8519 (p)
REVERT: A  869 TRP cc_start: 0.7973 (t60) cc_final: 0.7599 (t60)
REVERT: A  994 LEU cc_start: 0.8760 (mt) cc_final: 0.8511 (mp)
REVERT: A 1027 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7891 (mp)
REVERT: A 1081 LEU cc_start: 0.8374 (pt) cc_final: 0.8162 (pt)
REVERT: A 1132 MET cc_start: 0.8076 (mmt) cc_final: 0.7651 (mmt)
  outliers start: 21
  outliers final: 9
  residues processed: 163
  average time/residue: 0.1157
  time to fit residues: 24.1619
Evaluate side-chains
  146 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 VAL
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1139 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   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 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 GLN
A 998 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.148913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.122046 restraints weight = 14563.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 3.62
r_work: 0.3767 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.5655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7936  Z= 0.192
  Angle     :  0.742   9.318  10784  Z= 0.374
  Chirality :  0.046   0.219   1200
  Planarity :  0.006   0.065   1425
  Dihedral  :  5.384  23.952   1100
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.59 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.37 (0.26), residues: 990
  helix:  0.50 (0.22), residues: 512
  sheet: -0.77 (0.44), residues: 121
  loop : -1.01 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 165 
 TYR   0.019   0.002   TYR A  45 
 PHE   0.023   0.003   PHE A 946 
 TRP   0.014   0.002   TRP A 956 
 HIS   0.004   0.001   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 7936)
  covalent geometry    : angle       0.74154 (10784)
  hydrogen bonds       : bond        0.04851 (  445)
  hydrogen bonds       : angle       5.27327 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 155
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ILE cc_start: 0.7536 (mm) cc_final: 0.7311 (mm)
REVERT: A  104 GLN cc_start: 0.7436 (pp30) cc_final: 0.7121 (pp30)
REVERT: A  145 MET cc_start: 0.7268 (mmm) cc_final: 0.7014 (mmt)
REVERT: A  308 ARG cc_start: 0.8342 (mmm160) cc_final: 0.7988 (mmm-85)
REVERT: A  417 ASP cc_start: 0.8179 (m-30) cc_final: 0.7804 (p0)
REVERT: A  590 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7901 (mpp)
REVERT: A  695 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6994 (mt-10)
REVERT: A  748 TYR cc_start: 0.7834 (m-80) cc_final: 0.7586 (m-80)
REVERT: A  957 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.5361 (m-80)
REVERT: A 1001 ARG cc_start: 0.7534 (ttm170) cc_final: 0.7300 (ttm-80)
REVERT: A 1027 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8003 (mp)
REVERT: A 1132 MET cc_start: 0.8064 (mmt) cc_final: 0.7672 (tpp)
  outliers start: 24
  outliers final: 14
  residues processed: 171
  average time/residue: 0.1143
  time to fit residues: 25.1352
Evaluate side-chains
  144 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  834 VAL
Chi-restraints excluded: chain A residue  912 VAL
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  957 TYR
Chi-restraints excluded: chain A residue  988 ILE
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1040 THR
Chi-restraints excluded: chain A residue 1139 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 94 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 63 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 93 optimal weight:    0.3980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 772 ASN
** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.150771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.123677 restraints weight = 14434.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 3.65
r_work: 0.3789 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.6249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7936  Z= 0.160
  Angle     :  0.719   9.128  10784  Z= 0.359
  Chirality :  0.045   0.312   1200
  Planarity :  0.006   0.064   1425
  Dihedral  :  5.188  23.171   1100
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.97 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.29 (0.26), residues: 990
  helix:  0.58 (0.22), residues: 516
  sheet: -0.83 (0.44), residues: 121
  loop : -0.98 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 293 
 TYR   0.018   0.002   TYR A  45 
 PHE   0.020   0.003   PHE A 770 
 TRP   0.030   0.002   TRP A 869 
 HIS   0.003   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7936)
  covalent geometry    : angle       0.71882 (10784)
  hydrogen bonds       : bond        0.04491 (  445)
  hydrogen bonds       : angle       5.20956 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 139
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLN cc_start: 0.7469 (pp30) cc_final: 0.7136 (pp30)
REVERT: A  308 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7871 (mmm-85)
REVERT: A  527 GLN cc_start: 0.8717 (mt0) cc_final: 0.8415 (mt0)
REVERT: A  590 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8025 (mpp)
REVERT: A  609 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7629 (m-80)
REVERT: A  957 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.5476 (m-80)
REVERT: A 1132 MET cc_start: 0.8108 (mmt) cc_final: 0.7671 (tpp)
  outliers start: 21
  outliers final: 12
  residues processed: 148
  average time/residue: 0.1106
  time to fit residues: 21.2200
Evaluate side-chains
  133 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  957 TYR
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1139 SER
Chi-restraints excluded: chain A residue 1160 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 35 optimal weight:    0.4980
   chunk 38 optimal weight:    1.9990
   chunk 98 optimal weight:    8.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.153671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.124756 restraints weight = 14894.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 3.84
r_work: 0.3769 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.6693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7936  Z= 0.163
  Angle     :  0.726   9.358  10784  Z= 0.364
  Chirality :  0.045   0.207   1200
  Planarity :  0.006   0.064   1425
  Dihedral  :  5.114  23.450   1100
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.35 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.20 (0.26), residues: 990
  helix:  0.67 (0.23), residues: 517
  sheet: -0.87 (0.44), residues: 119
  loop : -0.95 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 179 
 TYR   0.043   0.002   TYR A  45 
 PHE   0.050   0.003   PHE A 798 
 TRP   0.027   0.002   TRP A 968 
 HIS   0.004   0.001   HIS A 843 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7936)
  covalent geometry    : angle       0.72565 (10784)
  hydrogen bonds       : bond        0.04444 (  445)
  hydrogen bonds       : angle       5.22207 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLN cc_start: 0.7592 (pp30) cc_final: 0.7221 (pp30)
REVERT: A  159 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7246 (tt0)
REVERT: A  308 ARG cc_start: 0.8345 (mmm160) cc_final: 0.7977 (mmm-85)
REVERT: A  527 GLN cc_start: 0.8710 (mt0) cc_final: 0.8335 (mt0)
REVERT: A  590 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8122 (mpp)
REVERT: A  748 TYR cc_start: 0.7759 (m-80) cc_final: 0.7264 (m-80)
REVERT: A  957 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.5732 (m-80)
REVERT: A 1001 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.7133 (ttm-80)
REVERT: A 1119 ARG cc_start: 0.8444 (mmt90) cc_final: 0.8219 (mmt90)
REVERT: A 1132 MET cc_start: 0.8016 (mmt) cc_final: 0.7631 (tpp)
  outliers start: 24
  outliers final: 15
  residues processed: 137
  average time/residue: 0.1105
  time to fit residues: 19.7355
Evaluate side-chains
  138 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  590 MET
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  767 VAL
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  957 TYR
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1073 VAL
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1139 SER
Chi-restraints excluded: chain A residue 1160 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 96 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 180 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.151564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.124703 restraints weight = 14520.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 3.62
r_work: 0.3765 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.7190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7936  Z= 0.182
  Angle     :  0.742   9.182  10784  Z= 0.373
  Chirality :  0.045   0.200   1200
  Planarity :  0.005   0.062   1425
  Dihedral  :  5.114  25.182   1100
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 16.23 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.27 (0.27), residues: 990
  helix:  0.65 (0.22), residues: 512
  sheet: -0.94 (0.44), residues: 119
  loop : -0.99 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1163 
 TYR   0.030   0.002   TYR A  45 
 PHE   0.045   0.003   PHE A 798 
 TRP   0.027   0.002   TRP A1070 
 HIS   0.003   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 7936)
  covalent geometry    : angle       0.74241 (10784)
  hydrogen bonds       : bond        0.04542 (  445)
  hydrogen bonds       : angle       5.31255 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 127
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLN cc_start: 0.7512 (pp30) cc_final: 0.7128 (pp30)
REVERT: A  159 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7424 (tt0)
REVERT: A  251 ASP cc_start: 0.8196 (m-30) cc_final: 0.6963 (t0)
REVERT: A  308 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7901 (mmm-85)
REVERT: A  527 GLN cc_start: 0.8709 (mt0) cc_final: 0.8412 (mt0)
REVERT: A  957 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.5876 (m-80)
REVERT: A  994 LEU cc_start: 0.8856 (mp) cc_final: 0.8646 (mp)
REVERT: A 1132 MET cc_start: 0.7790 (mmt) cc_final: 0.7422 (mmm)
  outliers start: 28
  outliers final: 15
  residues processed: 141
  average time/residue: 0.1150
  time to fit residues: 20.9635
Evaluate side-chains
  130 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  957 TYR
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1139 SER
Chi-restraints excluded: chain A residue 1160 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 19 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 865 HIS
** A1123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.147856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.120433 restraints weight = 14599.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 3.64
r_work: 0.3735 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.7681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7936  Z= 0.193
  Angle     :  0.732   8.515  10784  Z= 0.370
  Chirality :  0.047   0.301   1200
  Planarity :  0.005   0.061   1425
  Dihedral  :  5.146  25.349   1100
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.36 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.25 (0.27), residues: 990
  helix:  0.68 (0.23), residues: 509
  sheet: -0.79 (0.46), residues: 115
  loop : -1.06 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 179 
 TYR   0.030   0.002   TYR A  45 
 PHE   0.042   0.003   PHE A 798 
 TRP   0.017   0.002   TRP A 277 
 HIS   0.003   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 7936)
  covalent geometry    : angle       0.73209 (10784)
  hydrogen bonds       : bond        0.04664 (  445)
  hydrogen bonds       : angle       5.30823 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLN cc_start: 0.7453 (pp30) cc_final: 0.7067 (pp30)
REVERT: A  159 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7415 (tt0)
REVERT: A  179 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8063 (tpt90)
REVERT: A  308 ARG cc_start: 0.8344 (mmm160) cc_final: 0.7944 (mmm-85)
REVERT: A  527 GLN cc_start: 0.8736 (mt0) cc_final: 0.8422 (mt0)
REVERT: A  939 PHE cc_start: 0.7483 (m-10) cc_final: 0.7211 (m-10)
REVERT: A  957 TYR cc_start: 0.6672 (OUTLIER) cc_final: 0.6049 (m-80)
REVERT: A  989 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6351 (t80)
REVERT: A 1001 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7250 (ttm-80)
REVERT: A 1132 MET cc_start: 0.7724 (mmt) cc_final: 0.7426 (tpp)
  outliers start: 21
  outliers final: 11
  residues processed: 138
  average time/residue: 0.1133
  time to fit residues: 20.3201
Evaluate side-chains
  127 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  957 TYR
Chi-restraints excluded: chain A residue  989 TYR
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1139 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.149735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.122290 restraints weight = 14469.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 3.70
r_work: 0.3760 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.8025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7936  Z= 0.164
  Angle     :  0.738   8.744  10784  Z= 0.371
  Chirality :  0.047   0.287   1200
  Planarity :  0.005   0.064   1425
  Dihedral  :  5.105  24.962   1100
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 18.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.36 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.28 (0.27), residues: 990
  helix:  0.59 (0.22), residues: 518
  sheet: -0.43 (0.48), residues: 100
  loop : -1.12 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 179 
 TYR   0.029   0.002   TYR A  45 
 PHE   0.067   0.003   PHE A 798 
 TRP   0.014   0.002   TRP A 277 
 HIS   0.002   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 7936)
  covalent geometry    : angle       0.73810 (10784)
  hydrogen bonds       : bond        0.04495 (  445)
  hydrogen bonds       : angle       5.37385 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   89 HIS cc_start: 0.5721 (m90) cc_final: 0.5339 (m90)
REVERT: A  104 GLN cc_start: 0.7462 (pp30) cc_final: 0.7023 (pp30)
REVERT: A  179 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7934 (tpt90)
REVERT: A  251 ASP cc_start: 0.8218 (m-30) cc_final: 0.7473 (t70)
REVERT: A  308 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7918 (mmm-85)
REVERT: A  527 GLN cc_start: 0.8643 (mt0) cc_final: 0.8350 (mt0)
REVERT: A  791 MET cc_start: 0.8739 (mpp) cc_final: 0.8217 (tpt)
REVERT: A  939 PHE cc_start: 0.7570 (m-10) cc_final: 0.7300 (m-10)
REVERT: A  957 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.6161 (m-80)
REVERT: A  989 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6408 (t80)
REVERT: A 1132 MET cc_start: 0.7749 (mmt) cc_final: 0.7532 (tpp)
  outliers start: 18
  outliers final: 16
  residues processed: 126
  average time/residue: 0.1168
  time to fit residues: 19.2153
Evaluate side-chains
  128 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 PHE
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  941 ILE
Chi-restraints excluded: chain A residue  957 TYR
Chi-restraints excluded: chain A residue  989 TYR
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1139 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 75 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0970
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 88 optimal weight:    9.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 457 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.147764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.118492 restraints weight = 14710.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 4.01
r_work: 0.3614 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.8292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7936  Z= 0.156
  Angle     :  0.735  10.086  10784  Z= 0.365
  Chirality :  0.046   0.224   1200
  Planarity :  0.005   0.063   1425
  Dihedral  :  5.021  23.451   1100
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 17.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.36 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.24 (0.27), residues: 990
  helix:  0.65 (0.23), residues: 518
  sheet: -0.78 (0.46), residues: 110
  loop : -1.03 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 179 
 TYR   0.029   0.002   TYR A  45 
 PHE   0.064   0.003   PHE A 798 
 TRP   0.013   0.002   TRP A 968 
 HIS   0.003   0.001   HIS A 536 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 7936)
  covalent geometry    : angle       0.73474 (10784)
  hydrogen bonds       : bond        0.04296 (  445)
  hydrogen bonds       : angle       5.34088 ( 1311)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 GLN cc_start: 0.7538 (pp30) cc_final: 0.7172 (pp30)
REVERT: A  179 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7924 (tpt90)
REVERT: A  251 ASP cc_start: 0.8285 (m-30) cc_final: 0.7376 (t70)
REVERT: A  308 ARG cc_start: 0.8365 (mmm160) cc_final: 0.7983 (mmm-85)
REVERT: A  527 GLN cc_start: 0.8848 (mt0) cc_final: 0.8511 (mt0)
REVERT: A  957 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.6417 (m-80)
REVERT: A  989 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6338 (t80)
REVERT: A 1132 MET cc_start: 0.7848 (mmt) cc_final: 0.7450 (mmm)
  outliers start: 17
  outliers final: 12
  residues processed: 129
  average time/residue: 0.1104
  time to fit residues: 18.6737
Evaluate side-chains
  122 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 SER
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  455 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain A residue  821 VAL
Chi-restraints excluded: chain A residue  957 TYR
Chi-restraints excluded: chain A residue  989 TYR
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1077 VAL
Chi-restraints excluded: chain A residue 1089 LEU
Chi-restraints excluded: chain A residue 1139 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 80 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.146630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.118245 restraints weight = 14508.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3773 rms_B_bonded: 3.90
r_work: 0.3615 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.8501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7936  Z= 0.165
  Angle     :  0.758  11.767  10784  Z= 0.378
  Chirality :  0.047   0.206   1200
  Planarity :  0.006   0.097   1425
  Dihedral  :  5.114  22.857   1100
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 18.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.62 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.36 %
    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: -0.38 (0.27), residues: 990
  helix:  0.56 (0.23), residues: 515
  sheet: -1.15 (0.44), residues: 125
  loop : -0.98 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 164 
 TYR   0.029   0.002   TYR A  45 
 PHE   0.062   0.003   PHE A 798 
 TRP   0.015   0.002   TRP A 277 
 HIS   0.014   0.001   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 7936)
  covalent geometry    : angle       0.75787 (10784)
  hydrogen bonds       : bond        0.04359 (  445)
  hydrogen bonds       : angle       5.40138 ( 1311)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2069.55 seconds
wall clock time: 36 minutes 10.20 seconds (2170.20 seconds total)