Starting phenix.real_space_refine
on Sat Aug 23 08:18:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lxe_30006/08_2025/6lxe_30006.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lxe_30006/08_2025/6lxe_30006.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lxe_30006/08_2025/6lxe_30006.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lxe_30006/08_2025/6lxe_30006.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lxe_30006/08_2025/6lxe_30006.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lxe_30006/08_2025/6lxe_30006.map"
  }
  resolution = 4.2
  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
  Anisotropic ADP refinement not supported. Converting 5260 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      41      5.16       5
     C    4145      2.51       5
     N    1144      2.21       5
     O    1187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s

  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: 6519
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 768, 6133
          Classifications: {'peptide': 768}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 41, 'TRANS': 726}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 159
          Unresolved non-hydrogen angles: 197
          Unresolved non-hydrogen dihedrals: 138
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 6, 'TYR:plan': 2, 'TRP:plan': 1, 'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 84
    Chain: "B"
      Number of atoms: 205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 205
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
    Chain: "C"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 179
          Classifications: {'peptide': 21}
          Link IDs: {'TRANS': 20}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    868  SG  CYS A 561      46.109  27.096  56.345  1.00175.10           S
  ATOM   1826  SG  CYS A 676      43.492  29.089  55.869  1.00148.02           S
  ATOM    676  SG  CYS A 536      30.126  51.769  48.423  1.00151.24           S
  ATOM    691  SG  CYS A 538      29.902  54.514  44.875  1.00154.18           S

  Time building chain proxies: 1.17, per 1000 atoms: 0.18
  Number of scatterers: 6519
  At special positions: 0
  Unit cell: (93.826, 117.828, 112.373, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      41     16.00
     O    1187      8.00
     N    1144      7.00
     C    4145      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: 0.47
  Conformation dependent library (CDL) restraints added in 266.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1401 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 676 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 609 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 680 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 561 "
      pdb="  ZN A1402 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 536 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A1026 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A 549 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 538 "
      Number of angles added : 4


  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1556

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 3 sheets defined
      49.0% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 438 through 452
      removed outlier: 4.940A  pdb=" N   LYS A 447 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   PHE A 448 " --> pdb=" O   LEU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 546 through 550
    Processing helix  chain 'A' and resid 641 through 654
    Processing helix  chain 'A' and resid 698 through 709
    Processing helix  chain 'A' and resid 719 through 726
      removed outlier: 4.292A  pdb=" N   GLU A 726 " --> pdb=" O   MET A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 736
    Processing helix  chain 'A' and resid 790 through 804
    Processing helix  chain 'A' and resid 811 through 829
      removed outlier: 4.114A  pdb=" N   LYS A 815 " --> pdb=" O   LYS A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 861
      removed outlier: 4.199A  pdb=" N   CYS A 857 " --> pdb=" O   ARG A 853 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   MET A 861 " --> pdb=" O   CYS A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 876
      removed outlier: 4.439A  pdb=" N   VAL A 865 " --> pdb=" O   MET A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 884
    Processing helix  chain 'A' and resid 890 through 897
      removed outlier: 3.834A  pdb=" N   GLN A 894 " --> pdb=" O   ARG A 890 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 919
    Processing helix  chain 'A' and resid 965 through 988
      removed outlier: 3.861A  pdb=" N   ALA A 974 " --> pdb=" O   PHE A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1005
      removed outlier: 3.515A  pdb=" N   GLN A1005 " --> pdb=" O   THR A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1014
      removed outlier: 3.757A  pdb=" N   LEU A1009 " --> pdb=" O   GLN A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1032 through 1055
      removed outlier: 3.626A  pdb=" N   GLY A1055 " --> pdb=" O   VAL A1051 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1056 through 1069
      removed outlier: 3.724A  pdb=" N   ALA A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1080
    Processing helix  chain 'A' and resid 1084 through 1089
    Processing helix  chain 'A' and resid 1094 through 1098
    Processing helix  chain 'A' and resid 1104 through 1115
    Processing helix  chain 'A' and resid 1121 through 1128
    Processing helix  chain 'A' and resid 1145 through 1165
      removed outlier: 3.817A  pdb=" N   LEU A1149 " --> pdb=" O   ARG A1145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1180
    Processing helix  chain 'A' and resid 1183 through 1195
      removed outlier: 4.255A  pdb=" N   GLN A1187 " --> pdb=" O   ASN A1183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1232
    Processing helix  chain 'A' and resid 1233 through 1245
      removed outlier: 3.954A  pdb=" N   VAL A1237 " --> pdb=" O   ASP A1233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1255
      removed outlier: 3.547A  pdb=" N   PHE A1252 " --> pdb=" O   ARG A1248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 750
    Processing helix  chain 'C' and resid 730 through 747
    Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415
      removed outlier: 6.338A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 621
      removed outlier: 3.741A  pdb=" N   PHE A 604 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 740 through 742

    278 hydrogen bonds defined for protein.
    810 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.71

  Time building geometry restraints manager: 0.64 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: 2181
        1.34 -     1.46: 1457
        1.46 -     1.58: 2966
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 6669
  Sorted by residual:
  bond pdb=" C   VAL A 714 "
       pdb=" N   PRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.015 1.11e-02 8.12e+03 1.94e+00
  bond pdb=" C   THR A 898 "
       pdb=" N   HIS A 899 "
    ideal  model  delta    sigma   weight residual
    1.331  1.306  0.025 2.07e-02 2.33e+03 1.40e+00
  bond pdb=" CB  PRO A 581 "
       pdb=" CG  PRO A 581 "
    ideal  model  delta    sigma   weight residual
    1.492  1.533 -0.041 5.00e-02 4.00e+02 6.81e-01
  bond pdb=" CA  ILE A 767 "
       pdb=" CB  ILE A 767 "
    ideal  model  delta    sigma   weight residual
    1.540  1.532  0.008 1.01e-02 9.80e+03 6.30e-01
  bond pdb=" N   ALA A 712 "
       pdb=" CA  ALA A 712 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.010 1.29e-02 6.01e+03 6.30e-01
  ... (remaining 6664 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 8708
        1.39 -     2.78: 260
        2.78 -     4.17: 40
        4.17 -     5.56: 19
        5.56 -     6.95: 2
  Bond angle restraints: 9029
  Sorted by residual:
  angle pdb=" C   ARG A 562 "
        pdb=" N   PRO A 563 "
        pdb=" CA  PRO A 563 "
      ideal   model   delta    sigma   weight residual
     118.85  122.90   -4.05 1.09e+00 8.42e-01 1.38e+01
  angle pdb=" N   CYS A 536 "
        pdb=" CA  CYS A 536 "
        pdb=" C   CYS A 536 "
      ideal   model   delta    sigma   weight residual
     108.20  113.11   -4.91 1.71e+00 3.42e-01 8.25e+00
  angle pdb=" C   LYS A 559 "
        pdb=" N   PRO A 560 "
        pdb=" CA  PRO A 560 "
      ideal   model   delta    sigma   weight residual
     119.84  122.83   -2.99 1.25e+00 6.40e-01 5.71e+00
  angle pdb=" C   HIS A 630 "
        pdb=" N   PHE A 631 "
        pdb=" CA  PHE A 631 "
      ideal   model   delta    sigma   weight residual
     121.54  126.00   -4.46 1.91e+00 2.74e-01 5.45e+00
  angle pdb=" CA  LEU C 735 "
        pdb=" CB  LEU C 735 "
        pdb=" CG  LEU C 735 "
      ideal   model   delta    sigma   weight residual
     116.30  123.25   -6.95 3.50e+00 8.16e-02 3.94e+00
  ... (remaining 9024 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3600
       17.92 -    35.84: 347
       35.84 -    53.76: 63
       53.76 -    71.68: 13
       71.68 -    89.60: 9
  Dihedral angle restraints: 4032
    sinusoidal: 1643
      harmonic: 2389
  Sorted by residual:
  dihedral pdb=" CA  PRO A 779 "
           pdb=" C   PRO A 779 "
           pdb=" N   ALA A 780 "
           pdb=" CA  ALA A 780 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.89  -22.11     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  TRP A 848 "
           pdb=" C   TRP A 848 "
           pdb=" N   LYS A 849 "
           pdb=" CA  LYS A 849 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.78  -19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  PHE A 631 "
           pdb=" C   PHE A 631 "
           pdb=" N   ILE A 632 "
           pdb=" CA  ILE A 632 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.99  -16.01     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 4029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 500
       0.024 -    0.047: 289
       0.047 -    0.071: 128
       0.071 -    0.094: 50
       0.094 -    0.118: 25
  Chirality restraints: 992
  Sorted by residual:
  chirality pdb=" CA  ILE A 576 "
            pdb=" N   ILE A 576 "
            pdb=" C   ILE A 576 "
            pdb=" CB  ILE A 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.46e-01
  chirality pdb=" CA  ILE A 592 "
            pdb=" N   ILE A 592 "
            pdb=" C   ILE A 592 "
            pdb=" CB  ILE A 592 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.43e-01
  chirality pdb=" CA  VAL A 742 "
            pdb=" N   VAL A 742 "
            pdb=" C   VAL A 742 "
            pdb=" CB  VAL A 742 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.26e-01
  ... (remaining 989 not shown)

  Planarity restraints: 1177
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 580 "    0.029 5.00e-02 4.00e+02   4.34e-02 3.01e+00
        pdb=" N   PRO A 581 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 581 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 581 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 579 "    0.023 5.00e-02 4.00e+02   3.43e-02 1.88e+00
        pdb=" N   PRO A 580 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 580 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 580 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 579 "    0.006 2.00e-02 2.50e+03   1.12e-02 1.26e+00
        pdb=" C   SER A 579 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   SER A 579 "    0.007 2.00e-02 2.50e+03
        pdb=" N   PRO A 580 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1174 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 72
        2.60 -     3.18: 5710
        3.18 -     3.75: 10902
        3.75 -     4.33: 13621
        4.33 -     4.90: 21403
  Nonbonded interactions: 51708
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 433 "
            pdb=" CG2 THR A 565 "
     model   vdw
     2.030 3.460
  nonbonded pdb=" O   ARG A1213 "
            pdb=" OG1 THR A1216 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   ARG A 914 "
            pdb=" OG  SER A 918 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   GLN A1096 "
            pdb=" OG1 THR A1100 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" N   GLY A 739 "
            pdb=" O   ILE A 754 "
     model   vdw
     2.253 3.120
  ... (remaining 51703 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 729 through 749)
  selection = chain 'C'
}

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:             0.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.510
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
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      :  0.017   0.660   6677  Z= 0.474
  Angle     :  0.777  31.319   9033  Z= 0.346
  Chirality :  0.038   0.118    992
  Planarity :  0.003   0.043   1177
  Dihedral  : 15.295  89.603   2476
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 16.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  7.06 %
    Favored  : 92.80 %
  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: -3.22 (0.27), residues: 803
  helix: -0.83 (0.25), residues: 367
  sheet: -1.64 (0.87), residues: 39
  loop : -3.62 (0.27), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 684 
 TYR   0.006   0.001   TYR A1229 
 PHE   0.008   0.001   PHE A 970 
 TRP   0.008   0.001   TRP A 848 
 HIS   0.004   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 6669)
  covalent geometry    : angle       0.58840 ( 9029)
  hydrogen bonds       : bond        0.11001 (  278)
  hydrogen bonds       : angle       4.80294 (  810)
  metal coordination   : bond        0.47784 (    8)
  metal coordination   : angle      24.13672 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 150
  time to evaluate  : 0.241 
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  861 MET cc_start: 0.7725 (mtm) cc_final: 0.7288 (mtt)
REVERT: A  872 TYR cc_start: 0.8182 (t80) cc_final: 0.7952 (t80)
REVERT: A  914 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8080 (tpt170)
REVERT: A 1011 MET cc_start: 0.9073 (ptm) cc_final: 0.8745 (ppp)
REVERT: A 1021 PHE cc_start: 0.8098 (m-80) cc_final: 0.7806 (m-80)
REVERT: A 1241 MET cc_start: 0.8061 (mmp) cc_final: 0.7487 (tpp)
  outliers start: 1
  outliers final: 1
  residues processed: 151
  average time/residue: 0.0756
  time to fit residues: 15.1844
Evaluate side-chains
  101 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 456 GLN
A 531 ASN
A 630 HIS
** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 GLN
A 858 GLN
A 868 HIS
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 ASN
A 915 ASN
A 924 GLN
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1144 GLN
A1169 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.086812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.074414 restraints weight = 43581.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.075371 restraints weight = 33488.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.076294 restraints weight = 28122.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.076845 restraints weight = 23973.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.077403 restraints weight = 21401.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6677  Z= 0.200
  Angle     :  0.729  10.788   9033  Z= 0.362
  Chirality :  0.043   0.126    992
  Planarity :  0.005   0.054   1177
  Dihedral  :  4.754  25.170    884
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 20.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  7.06 %
    Favored  : 92.65 %
  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: -2.74 (0.28), residues: 803
  helix: -0.36 (0.26), residues: 378
  sheet: -1.72 (0.86), residues: 39
  loop : -3.48 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1178 
 TYR   0.021   0.002   TYR A1229 
 PHE   0.029   0.002   PHE A1224 
 TRP   0.013   0.002   TRP A 848 
 HIS   0.010   0.002   HIS A 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6669)
  covalent geometry    : angle       0.71929 ( 9029)
  hydrogen bonds       : bond        0.04044 (  278)
  hydrogen bonds       : angle       4.74488 (  810)
  metal coordination   : bond        0.02875 (    8)
  metal coordination   : angle       5.70976 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 123
  time to evaluate  : 0.268 
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: A  861 MET cc_start: 0.7328 (mtm) cc_final: 0.7098 (tmm)
REVERT: A  909 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8161 (m110)
REVERT: A  914 ARG cc_start: 0.8931 (ttm110) cc_final: 0.8268 (tpt170)
REVERT: A 1107 LEU cc_start: 0.8192 (mp) cc_final: 0.7917 (tt)
REVERT: A 1124 LEU cc_start: 0.9287 (mp) cc_final: 0.8865 (mp)
REVERT: A 1155 GLN cc_start: 0.5410 (mm110) cc_final: 0.4608 (tp40)
REVERT: A 1241 MET cc_start: 0.8564 (mmp) cc_final: 0.8242 (mmm)
REVERT: B  739 MET cc_start: 0.8371 (mmp) cc_final: 0.7936 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0708
  time to fit residues: 11.9975
Evaluate side-chains
  92 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 76 optimal weight:    0.0040
   chunk 7 optimal weight:    0.0170
   chunk 40 optimal weight:   10.0000
   chunk 35 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.9832

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

Flipped N/Q/H residues before XYZ refinement:
A 630 HIS
A 663 ASN
A 888 GLN
A 915 ASN
** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1165 HIS
A1169 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.090790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.078034 restraints weight = 42520.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.079326 restraints weight = 32414.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.080213 restraints weight = 26154.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.080954 restraints weight = 22286.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.081451 restraints weight = 19571.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6677  Z= 0.116
  Angle     :  0.626   7.948   9033  Z= 0.304
  Chirality :  0.041   0.183    992
  Planarity :  0.004   0.048   1177
  Dihedral  :  4.433  23.395    884
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.34 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.91 %
    Favored  : 93.95 %
  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: -2.19 (0.29), residues: 803
  helix:  0.14 (0.27), residues: 374
  sheet: -1.15 (0.86), residues: 39
  loop : -3.27 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1178 
 TYR   0.011   0.001   TYR A1236 
 PHE   0.016   0.001   PHE A1128 
 TRP   0.008   0.001   TRP A1078 
 HIS   0.007   0.001   HIS A 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6669)
  covalent geometry    : angle       0.61860 ( 9029)
  hydrogen bonds       : bond        0.03320 (  278)
  hydrogen bonds       : angle       4.44444 (  810)
  metal coordination   : bond        0.02868 (    8)
  metal coordination   : angle       4.59876 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.236 
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: A  606 MET cc_start: 0.7620 (mtp) cc_final: 0.7319 (mtp)
REVERT: A  660 TYR cc_start: 0.6791 (t80) cc_final: 0.6327 (t80)
REVERT: A  699 MET cc_start: 0.8322 (mmm) cc_final: 0.8012 (mmm)
REVERT: A  888 GLN cc_start: 0.8593 (tp40) cc_final: 0.8385 (tp-100)
REVERT: A  914 ARG cc_start: 0.8922 (ttm110) cc_final: 0.8339 (tpt170)
REVERT: A 1124 LEU cc_start: 0.9263 (mp) cc_final: 0.8822 (mp)
REVERT: A 1128 PHE cc_start: 0.8120 (m-80) cc_final: 0.7778 (m-80)
REVERT: A 1241 MET cc_start: 0.8061 (mmp) cc_final: 0.7619 (tpt)
REVERT: A 1242 ASN cc_start: 0.7940 (p0) cc_final: 0.7730 (p0)
REVERT: B  737 GLU cc_start: 0.9268 (mp0) cc_final: 0.8838 (mp0)
REVERT: B  739 MET cc_start: 0.8386 (mmp) cc_final: 0.8043 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 133
  average time/residue: 0.0619
  time to fit residues: 11.2856
Evaluate side-chains
  89 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 79 optimal weight:    0.5980
   chunk 68 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9980
   chunk 58 optimal weight:    9.9990
   chunk 10 optimal weight:    5.9990
   chunk 16 optimal weight:    8.9990
   chunk 60 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    2.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 630 HIS
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 736 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.088200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.075515 restraints weight = 42688.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.076778 restraints weight = 32262.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.077766 restraints weight = 25868.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.078551 restraints weight = 21806.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.078880 restraints weight = 18930.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7215
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6677  Z= 0.138
  Angle     :  0.639   8.288   9033  Z= 0.317
  Chirality :  0.042   0.130    992
  Planarity :  0.004   0.048   1177
  Dihedral  :  4.551  23.483    884
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.76 %
    Favored  : 94.09 %
  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: -2.14 (0.29), residues: 803
  helix:  0.14 (0.27), residues: 380
  sheet: -1.13 (0.85), residues: 39
  loop : -3.24 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1178 
 TYR   0.017   0.002   TYR A1229 
 PHE   0.014   0.001   PHE A 679 
 TRP   0.008   0.001   TRP A1078 
 HIS   0.005   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6669)
  covalent geometry    : angle       0.63398 ( 9029)
  hydrogen bonds       : bond        0.03492 (  278)
  hydrogen bonds       : angle       4.54298 (  810)
  metal coordination   : bond        0.03380 (    8)
  metal coordination   : angle       4.03242 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  606 MET cc_start: 0.7902 (mtp) cc_final: 0.7292 (mtp)
REVERT: A  888 GLN cc_start: 0.8808 (tp40) cc_final: 0.8590 (tp-100)
REVERT: A  914 ARG cc_start: 0.8857 (ttm110) cc_final: 0.8285 (tpt170)
REVERT: A 1021 PHE cc_start: 0.7997 (m-80) cc_final: 0.7791 (m-10)
REVERT: A 1124 LEU cc_start: 0.9320 (mp) cc_final: 0.8873 (mp)
REVERT: A 1128 PHE cc_start: 0.8399 (m-80) cc_final: 0.7827 (m-80)
REVERT: A 1196 MET cc_start: 0.3185 (mmm) cc_final: 0.2875 (mmm)
REVERT: A 1241 MET cc_start: 0.8649 (mmp) cc_final: 0.8055 (tpt)
REVERT: B  737 GLU cc_start: 0.9245 (mp0) cc_final: 0.8886 (mp0)
REVERT: B  739 MET cc_start: 0.8599 (mmp) cc_final: 0.8179 (mmt)
REVERT: B  748 GLU cc_start: 0.8076 (pt0) cc_final: 0.7699 (pp20)
  outliers start: 1
  outliers final: 1
  residues processed: 126
  average time/residue: 0.0880
  time to fit residues: 14.8354
Evaluate side-chains
  88 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 77 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 35 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
A1045 GLN
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1142 HIS
A1169 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.084375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.072115 restraints weight = 43760.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.073267 restraints weight = 33578.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.074135 restraints weight = 27461.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.074765 restraints weight = 23451.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.075287 restraints weight = 20797.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7348
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6677  Z= 0.215
  Angle     :  0.773  14.763   9033  Z= 0.385
  Chirality :  0.045   0.140    992
  Planarity :  0.005   0.054   1177
  Dihedral  :  5.161  25.770    884
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 23.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  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: -2.52 (0.29), residues: 803
  helix: -0.20 (0.26), residues: 376
  sheet: -1.59 (0.81), residues: 39
  loop : -3.34 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 741 
 TYR   0.027   0.002   TYR A1229 
 PHE   0.018   0.002   PHE A 847 
 TRP   0.010   0.002   TRP A1078 
 HIS   0.007   0.002   HIS A 964 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 6669)
  covalent geometry    : angle       0.75385 ( 9029)
  hydrogen bonds       : bond        0.04149 (  278)
  hydrogen bonds       : angle       4.97845 (  810)
  metal coordination   : bond        0.02793 (    8)
  metal coordination   : angle       8.06531 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  530 MET cc_start: 0.7321 (tmm) cc_final: 0.6869 (tmm)
REVERT: A  660 TYR cc_start: 0.7180 (t80) cc_final: 0.6373 (t80)
REVERT: A  699 MET cc_start: 0.8275 (mmm) cc_final: 0.8008 (mmm)
REVERT: A  888 GLN cc_start: 0.9057 (tp40) cc_final: 0.8798 (tp-100)
REVERT: A  897 MET cc_start: 0.8470 (tmm) cc_final: 0.8267 (ppp)
REVERT: A  914 ARG cc_start: 0.8866 (ttm110) cc_final: 0.8248 (tpt170)
REVERT: A 1124 LEU cc_start: 0.9302 (mp) cc_final: 0.8939 (mp)
REVERT: A 1128 PHE cc_start: 0.8444 (m-80) cc_final: 0.7888 (m-80)
REVERT: A 1155 GLN cc_start: 0.5602 (mm110) cc_final: 0.5393 (tp40)
REVERT: A 1241 MET cc_start: 0.8903 (mmp) cc_final: 0.8302 (tpt)
REVERT: B  737 GLU cc_start: 0.9169 (mp0) cc_final: 0.8848 (mp0)
REVERT: B  739 MET cc_start: 0.8446 (mmp) cc_final: 0.8031 (mmt)
REVERT: B  748 GLU cc_start: 0.8048 (pt0) cc_final: 0.7675 (pp20)
REVERT: C  739 MET cc_start: 0.7639 (tpt) cc_final: 0.6512 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0796
  time to fit residues: 12.6266
Evaluate side-chains
  83 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 46 optimal weight:    6.9990
   chunk 58 optimal weight:    0.5980
   chunk 65 optimal weight:   20.0000
   chunk 19 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 49 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 GLN
** A1169 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 = 0.4010 r_free = 0.4010 target = 0.087780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.074947 restraints weight = 41800.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.076191 restraints weight = 32026.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.077137 restraints weight = 26012.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.077864 restraints weight = 22107.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.078369 restraints weight = 19429.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6677  Z= 0.129
  Angle     :  0.677  10.837   9033  Z= 0.332
  Chirality :  0.043   0.126    992
  Planarity :  0.004   0.068   1177
  Dihedral  :  4.872  24.380    884
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  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: -2.26 (0.29), residues: 803
  helix:  0.01 (0.27), residues: 383
  sheet: -1.36 (0.80), residues: 39
  loop : -3.26 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1178 
 TYR   0.015   0.002   TYR A1229 
 PHE   0.011   0.001   PHE A 679 
 TRP   0.009   0.001   TRP A1078 
 HIS   0.007   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6669)
  covalent geometry    : angle       0.66501 ( 9029)
  hydrogen bonds       : bond        0.03631 (  278)
  hydrogen bonds       : angle       4.69414 (  810)
  metal coordination   : bond        0.02223 (    8)
  metal coordination   : angle       5.96792 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.268 
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: A  530 MET cc_start: 0.7109 (tmm) cc_final: 0.6780 (tmm)
REVERT: A  606 MET cc_start: 0.8538 (mtm) cc_final: 0.8330 (mtp)
REVERT: A  660 TYR cc_start: 0.7002 (t80) cc_final: 0.6277 (t80)
REVERT: A  862 MET cc_start: 0.9141 (mmm) cc_final: 0.8787 (mmm)
REVERT: A  888 GLN cc_start: 0.8982 (tp40) cc_final: 0.8725 (tp-100)
REVERT: A  914 ARG cc_start: 0.8873 (ttm110) cc_final: 0.8250 (tpt170)
REVERT: A 1124 LEU cc_start: 0.9293 (mp) cc_final: 0.8903 (mp)
REVERT: A 1128 PHE cc_start: 0.8458 (m-80) cc_final: 0.7855 (m-80)
REVERT: A 1241 MET cc_start: 0.8801 (mmp) cc_final: 0.8244 (tpt)
REVERT: B  748 GLU cc_start: 0.8074 (pt0) cc_final: 0.7749 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0777
  time to fit residues: 12.3014
Evaluate side-chains
  87 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 8 optimal weight:   20.0000
   chunk 10 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 60 optimal weight:   10.0000
   chunk 50 optimal weight:    0.5980
   chunk 37 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    5.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 832 ASN
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 909 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.079983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.068079 restraints weight = 44639.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.069166 restraints weight = 34225.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.069990 restraints weight = 28147.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.070606 restraints weight = 24174.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.070963 restraints weight = 21500.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.4798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   6677  Z= 0.267
  Angle     :  0.863  16.402   9033  Z= 0.436
  Chirality :  0.049   0.153    992
  Planarity :  0.006   0.071   1177
  Dihedral  :  5.748  28.057    884
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 29.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.71 %
    Favored  : 88.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  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: -2.84 (0.28), residues: 803
  helix: -0.67 (0.25), residues: 377
  sheet: -1.87 (0.83), residues: 37
  loop : -3.23 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1178 
 TYR   0.031   0.003   TYR A1081 
 PHE   0.020   0.003   PHE A 847 
 TRP   0.010   0.002   TRP A 848 
 HIS   0.009   0.002   HIS A 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00569 ( 6669)
  covalent geometry    : angle       0.84345 ( 9029)
  hydrogen bonds       : bond        0.04649 (  278)
  hydrogen bonds       : angle       5.45829 (  810)
  metal coordination   : bond        0.03412 (    8)
  metal coordination   : angle       8.61864 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.288 
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  606 MET cc_start: 0.8668 (mtm) cc_final: 0.8405 (mtp)
REVERT: A  628 THR cc_start: 0.8457 (p) cc_final: 0.8246 (p)
REVERT: A  660 TYR cc_start: 0.7161 (t80) cc_final: 0.6427 (t80)
REVERT: A  699 MET cc_start: 0.8525 (mmp) cc_final: 0.8308 (mmp)
REVERT: A  888 GLN cc_start: 0.9060 (tp40) cc_final: 0.8828 (tp-100)
REVERT: A  897 MET cc_start: 0.8327 (ppp) cc_final: 0.8022 (ppp)
REVERT: A  914 ARG cc_start: 0.8884 (ttm110) cc_final: 0.8251 (tpt170)
REVERT: A 1155 GLN cc_start: 0.6809 (tp-100) cc_final: 0.6535 (mm-40)
REVERT: A 1241 MET cc_start: 0.9102 (mmp) cc_final: 0.8613 (mmp)
REVERT: A 1242 ASN cc_start: 0.8824 (t0) cc_final: 0.7976 (p0)
REVERT: C  734 LYS cc_start: 0.9410 (pttm) cc_final: 0.9179 (mmtt)
REVERT: C  739 MET cc_start: 0.7729 (tpt) cc_final: 0.7320 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0908
  time to fit residues: 12.6107
Evaluate side-chains
  81 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 79 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 630 HIS
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.081090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.069053 restraints weight = 45920.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.070089 restraints weight = 35068.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.070952 restraints weight = 28859.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.071567 restraints weight = 24700.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.071989 restraints weight = 21945.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.5015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6677  Z= 0.221
  Angle     :  0.803  14.870   9033  Z= 0.402
  Chirality :  0.047   0.143    992
  Planarity :  0.006   0.069   1177
  Dihedral  :  5.674  25.278    884
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 25.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.71 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  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: -2.75 (0.29), residues: 803
  helix: -0.60 (0.26), residues: 376
  sheet: -1.95 (0.85), residues: 37
  loop : -3.17 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1178 
 TYR   0.022   0.002   TYR A1229 
 PHE   0.032   0.003   PHE A 631 
 TRP   0.008   0.002   TRP A 848 
 HIS   0.008   0.002   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 6669)
  covalent geometry    : angle       0.78704 ( 9029)
  hydrogen bonds       : bond        0.04374 (  278)
  hydrogen bonds       : angle       5.24141 (  810)
  metal coordination   : bond        0.02659 (    8)
  metal coordination   : angle       7.67144 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.272 
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  660 TYR cc_start: 0.7241 (t80) cc_final: 0.6545 (t80)
REVERT: A  862 MET cc_start: 0.8968 (mmt) cc_final: 0.8679 (mmm)
REVERT: A  897 MET cc_start: 0.8343 (ppp) cc_final: 0.8043 (ppp)
REVERT: A  914 ARG cc_start: 0.8901 (ttm110) cc_final: 0.8300 (tpt170)
REVERT: A  966 GLU cc_start: 0.8870 (pm20) cc_final: 0.8588 (pm20)
REVERT: A 1155 GLN cc_start: 0.6976 (tp-100) cc_final: 0.6596 (mm110)
REVERT: A 1241 MET cc_start: 0.8929 (mmp) cc_final: 0.8347 (mmp)
REVERT: C  739 MET cc_start: 0.7701 (tpt) cc_final: 0.7407 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0854
  time to fit residues: 11.7803
Evaluate side-chains
  77 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 61 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 40 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 630 HIS
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 888 GLN
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.084202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.072028 restraints weight = 43397.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.073217 restraints weight = 33118.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.074045 restraints weight = 26926.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.074709 restraints weight = 23047.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.075018 restraints weight = 20302.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.5020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6677  Z= 0.161
  Angle     :  0.744  11.433   9033  Z= 0.371
  Chirality :  0.046   0.308    992
  Planarity :  0.005   0.064   1177
  Dihedral  :  5.561  24.901    884
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 20.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  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: -2.68 (0.29), residues: 803
  helix: -0.41 (0.26), residues: 379
  sheet: -1.91 (0.86), residues: 37
  loop : -3.31 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 442 
 TYR   0.020   0.002   TYR A1229 
 PHE   0.032   0.002   PHE A 631 
 TRP   0.007   0.001   TRP A1078 
 HIS   0.008   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6669)
  covalent geometry    : angle       0.73210 ( 9029)
  hydrogen bonds       : bond        0.04036 (  278)
  hydrogen bonds       : angle       5.00545 (  810)
  metal coordination   : bond        0.02551 (    8)
  metal coordination   : angle       6.30985 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.266 
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: A  606 MET cc_start: 0.8252 (mtp) cc_final: 0.7920 (mtp)
REVERT: A  660 TYR cc_start: 0.7356 (t80) cc_final: 0.6592 (t80)
REVERT: A  862 MET cc_start: 0.9009 (mmt) cc_final: 0.8614 (mmm)
REVERT: A  914 ARG cc_start: 0.8883 (ttm110) cc_final: 0.8041 (tpt170)
REVERT: A  964 HIS cc_start: 0.6889 (p90) cc_final: 0.6302 (p-80)
REVERT: A 1155 GLN cc_start: 0.6883 (tp-100) cc_final: 0.6516 (mm-40)
REVERT: A 1236 TYR cc_start: 0.7970 (t80) cc_final: 0.7769 (t80)
REVERT: C  739 MET cc_start: 0.7521 (tpt) cc_final: 0.7178 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0830
  time to fit residues: 12.2263
Evaluate side-chains
  82 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 39 optimal weight:    9.9990
   chunk 76 optimal weight:    6.9990
   chunk 30 optimal weight:    8.9990
   chunk 38 optimal weight:    0.4980
   chunk 47 optimal weight:    8.9990
   chunk 64 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 630 HIS
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.085499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.073265 restraints weight = 43237.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.074408 restraints weight = 32997.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.075275 restraints weight = 26936.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.075936 restraints weight = 23055.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.076405 restraints weight = 20355.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.5042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6677  Z= 0.148
  Angle     :  0.755  10.323   9033  Z= 0.372
  Chirality :  0.045   0.165    992
  Planarity :  0.005   0.061   1177
  Dihedral  :  5.472  33.445    884
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 20.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.21 %
    Favored  : 89.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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 (0.29), residues: 803
  helix: -0.30 (0.26), residues: 378
  sheet: -1.89 (0.85), residues: 37
  loop : -3.24 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1178 
 TYR   0.019   0.002   TYR A1229 
 PHE   0.033   0.002   PHE A 631 
 TRP   0.008   0.001   TRP A1078 
 HIS   0.008   0.001   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6669)
  covalent geometry    : angle       0.74511 ( 9029)
  hydrogen bonds       : bond        0.03901 (  278)
  hydrogen bonds       : angle       4.93917 (  810)
  metal coordination   : bond        0.02122 (    8)
  metal coordination   : angle       5.87404 (    4)

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

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

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.271 
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: A  660 TYR cc_start: 0.7463 (t80) cc_final: 0.6695 (t80)
REVERT: A  862 MET cc_start: 0.8993 (mmt) cc_final: 0.8608 (mmm)
REVERT: A  914 ARG cc_start: 0.8863 (ttm110) cc_final: 0.8341 (tpt170)
REVERT: A 1155 GLN cc_start: 0.7025 (tp-100) cc_final: 0.6631 (mm-40)
REVERT: A 1212 LEU cc_start: 0.8488 (pt) cc_final: 0.8205 (pp)
REVERT: A 1217 LEU cc_start: 0.8862 (tt) cc_final: 0.8599 (mm)
REVERT: A 1241 MET cc_start: 0.8795 (mmp) cc_final: 0.8173 (tpt)
REVERT: B  739 MET cc_start: 0.8346 (mmp) cc_final: 0.8024 (mmt)
REVERT: C  730 HIS cc_start: 0.9287 (p-80) cc_final: 0.9056 (p-80)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.0873
  time to fit residues: 13.0375
Evaluate side-chains
  81 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 15 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 78 optimal weight:    7.9990
   chunk 67 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0010
   overall best weight:    4.9994

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

Flipped N/Q/H residues before XYZ refinement:
A 630 HIS
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 888 GLN
** A 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 ASN
A 915 ASN
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1142 HIS
A1256 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.079823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.068108 restraints weight = 46335.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.069242 restraints weight = 35077.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.070061 restraints weight = 28622.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.070672 restraints weight = 24496.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.071169 restraints weight = 21773.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.5524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6677  Z= 0.238
  Angle     :  0.863  14.777   9033  Z= 0.430
  Chirality :  0.048   0.152    992
  Planarity :  0.006   0.062   1177
  Dihedral  :  5.876  25.952    884
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 27.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.20 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.44 %
    Favored  : 98.41 %
  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: -2.88 (0.28), residues: 803
  helix: -0.72 (0.26), residues: 371
  sheet: -2.15 (0.80), residues: 37
  loop : -3.19 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1178 
 TYR   0.025   0.003   TYR A 986 
 PHE   0.034   0.003   PHE A 631 
 TRP   0.012   0.002   TRP A 848 
 HIS   0.009   0.002   HIS A 983 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 6669)
  covalent geometry    : angle       0.84664 ( 9029)
  hydrogen bonds       : bond        0.04476 (  278)
  hydrogen bonds       : angle       5.38750 (  810)
  metal coordination   : bond        0.02632 (    8)
  metal coordination   : angle       7.92252 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1139.96 seconds
wall clock time: 20 minutes 30.06 seconds (1230.06 seconds total)