Starting phenix.real_space_refine
on Sat Feb 15 00:00:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lxe_30006/02_2025/6lxe_30006.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lxe_30006/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lxe_30006/02_2025/6lxe_30006.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lxe_30006/02_2025/6lxe_30006.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lxe_30006/02_2025/6lxe_30006.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lxe_30006/02_2025/6lxe_30006.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3}
          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: 3.71, per 1000 atoms: 0.57
  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: 1.46
  Conformation dependent library (CDL) restraints added in 739.9 milliseconds
  
  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: 0.56
  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: 1.52

  Time building geometry restraints manager: 1.73 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:             0.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.850
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.250
-------------------------------------------------------------------------------
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      :  0.002   0.041   6669  Z= 0.154
  Angle     :  0.588   6.952   9029  Z= 0.329
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.008   0.001   TRP A 848 
 HIS   0.004   0.001   HIS A 983 
 PHE   0.008   0.001   PHE A 970 
 TYR   0.006   0.001   TYR A1229 
 ARG   0.002   0.000   ARG A 684 

*********************** 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  : 0.726 
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: 0.2006
  time to fit residues: 39.8553
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  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 20 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 38 optimal weight:    0.1980
   chunk 46 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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
A 724 GLN
A 858 GLN
A 868 HIS
A 909 ASN
A 915 ASN
A 924 GLN
A1038 HIS
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1144 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.093618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.077924 restraints weight = 42214.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.078985 restraints weight = 34310.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.079875 restraints weight = 29242.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6669  Z= 0.185
  Angle     :  0.617   8.002   9029  Z= 0.306
  Chirality :  0.041   0.133    992
  Planarity :  0.005   0.055   1177
  Dihedral  :  4.278  22.310    884
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.33 %
    Favored  : 94.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.41 (0.29), residues: 803
  helix:  0.01 (0.27), residues: 370
  sheet: -1.43 (0.86), residues: 39
  loop : -3.38 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 848 
 HIS   0.011   0.001   HIS A 630 
 PHE   0.029   0.001   PHE A1224 
 TYR   0.010   0.001   TYR A 574 
 ARG   0.005   0.001   ARG A1178 

*********************** 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
  132 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.759 
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  636 MET cc_start: 0.8121 (ppp) cc_final: 0.7912 (ppp)
REVERT: A  914 ARG cc_start: 0.8912 (ttm110) cc_final: 0.8316 (tpt170)
REVERT: A 1155 GLN cc_start: 0.5986 (mm110) cc_final: 0.5367 (tp40)
REVERT: A 1241 MET cc_start: 0.8290 (mmp) cc_final: 0.7787 (tpt)
REVERT: B  737 GLU cc_start: 0.9376 (mp0) cc_final: 0.9013 (mp0)
REVERT: B  739 MET cc_start: 0.8668 (mmp) cc_final: 0.8324 (mmt)
REVERT: C  739 MET cc_start: 0.7233 (tpt) cc_final: 0.6324 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1780
  time to fit residues: 31.6098
Evaluate side-chains
  103 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 33 optimal weight:   40.0000
   chunk 14 optimal weight:    8.9990
   chunk 76 optimal weight:   10.0000
   chunk 74 optimal weight:    9.9990
   overall best weight:    5.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 663 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 761 GLN
** 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**
A1169 HIS
A1173 HIS
A1222 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.083755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.071584 restraints weight = 44102.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.072738 restraints weight = 33807.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.073553 restraints weight = 27573.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6669  Z= 0.350
  Angle     :  0.778   9.423   9029  Z= 0.399
  Chirality :  0.046   0.131    992
  Planarity :  0.006   0.056   1177
  Dihedral  :  5.177  27.815    884
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 25.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.71 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  9.51 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.28), residues: 803
  helix: -0.54 (0.25), residues: 383
  sheet: -1.62 (0.84), residues: 39
  loop : -3.36 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 848 
 HIS   0.009   0.002   HIS A 700 
 PHE   0.020   0.003   PHE A 572 
 TYR   0.028   0.003   TYR A1229 
 ARG   0.006   0.001   ARG A1178 

*********************** 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
  119 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.742 
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  530 MET cc_start: 0.7598 (tmm) cc_final: 0.7344 (tmm)
REVERT: A  606 MET cc_start: 0.8045 (mtp) cc_final: 0.7812 (mtp)
REVERT: A  699 MET cc_start: 0.8222 (mmm) cc_final: 0.7881 (mmm)
REVERT: A  861 MET cc_start: 0.7216 (tmm) cc_final: 0.6940 (tmm)
REVERT: A  862 MET cc_start: 0.8973 (mmt) cc_final: 0.8667 (mmt)
REVERT: A  891 CYS cc_start: 0.8801 (t) cc_final: 0.8446 (m)
REVERT: A  914 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8227 (tpt170)
REVERT: A 1021 PHE cc_start: 0.8157 (m-80) cc_final: 0.7925 (m-10)
REVERT: A 1154 MET cc_start: 0.4778 (mtp) cc_final: 0.4264 (mtt)
REVERT: A 1155 GLN cc_start: 0.5618 (mm110) cc_final: 0.4922 (mm110)
REVERT: A 1236 TYR cc_start: 0.8428 (t80) cc_final: 0.8171 (t80)
REVERT: B  739 MET cc_start: 0.8401 (mmp) cc_final: 0.8054 (mmt)
REVERT: B  748 GLU cc_start: 0.8252 (pt0) cc_final: 0.7817 (pp20)
REVERT: C  730 HIS cc_start: 0.9421 (p-80) cc_final: 0.9097 (p-80)
REVERT: C  739 MET cc_start: 0.7748 (tpt) cc_final: 0.7436 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 119
  average time/residue: 0.1829
  time to fit residues: 29.4995
Evaluate side-chains
  85 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 54 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 71 optimal weight:    0.2980
   chunk 65 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 35 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    3.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 915 ASN
** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1165 HIS
A1173 HIS
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.085629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.073266 restraints weight = 42693.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.074477 restraints weight = 32464.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.075329 restraints weight = 26385.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6669  Z= 0.260
  Angle     :  0.703  10.026   9029  Z= 0.353
  Chirality :  0.044   0.127    992
  Planarity :  0.005   0.063   1177
  Dihedral  :  5.123  25.265    884
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 21.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.29), residues: 803
  helix: -0.23 (0.26), residues: 374
  sheet: -1.75 (0.81), residues: 39
  loop : -3.23 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1078 
 HIS   0.008   0.002   HIS A 964 
 PHE   0.031   0.002   PHE A1224 
 TYR   0.021   0.002   TYR A1229 
 ARG   0.006   0.001   ARG A1178 

*********************** 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
  122 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.700 
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: 0.8221 (mtp) cc_final: 0.7882 (mtp)
REVERT: A  699 MET cc_start: 0.8397 (mmm) cc_final: 0.8117 (mmm)
REVERT: A  862 MET cc_start: 0.8890 (mmt) cc_final: 0.8650 (mmt)
REVERT: A  899 HIS cc_start: 0.8118 (t-170) cc_final: 0.7883 (t-170)
REVERT: A  914 ARG cc_start: 0.8831 (ttm110) cc_final: 0.8175 (tpt170)
REVERT: A  966 GLU cc_start: 0.8712 (pm20) cc_final: 0.8430 (pm20)
REVERT: A 1021 PHE cc_start: 0.8028 (m-80) cc_final: 0.7747 (m-10)
REVERT: A 1155 GLN cc_start: 0.5800 (mm110) cc_final: 0.5070 (mm-40)
REVERT: A 1241 MET cc_start: 0.8906 (mmp) cc_final: 0.8279 (tpt)
REVERT: A 1242 ASN cc_start: 0.8406 (p0) cc_final: 0.8199 (p0)
REVERT: B  739 MET cc_start: 0.8443 (mmp) cc_final: 0.8160 (mmt)
REVERT: B  748 GLU cc_start: 0.8112 (pt0) cc_final: 0.7668 (pp20)
REVERT: C  741 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8694 (ttp80)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1760
  time to fit residues: 28.8076
Evaluate side-chains
  85 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 34 optimal weight:   10.0000
   chunk 38 optimal weight:   20.0000
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 61 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 58 optimal weight:    8.9990
   overall best weight:    3.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 630 HIS
A 888 GLN
A 915 ASN
** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1155 GLN
A1173 HIS
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.085272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.072846 restraints weight = 42081.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.074050 restraints weight = 32078.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.074895 restraints weight = 26048.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6669  Z= 0.249
  Angle     :  0.709  11.654   9029  Z= 0.356
  Chirality :  0.044   0.124    992
  Planarity :  0.005   0.065   1177
  Dihedral  :  5.187  25.438    884
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 21.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.76 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.29), residues: 803
  helix: -0.26 (0.26), residues: 377
  sheet: -1.64 (0.81), residues: 39
  loop : -3.21 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1078 
 HIS   0.007   0.001   HIS A 630 
 PHE   0.022   0.002   PHE A1224 
 TYR   0.020   0.002   TYR A1229 
 ARG   0.007   0.001   ARG A1178 

*********************** 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
  118 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.721 
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  530 MET cc_start: 0.7376 (tmm) cc_final: 0.6991 (tmm)
REVERT: A  606 MET cc_start: 0.8229 (mtp) cc_final: 0.7928 (mtp)
REVERT: A  699 MET cc_start: 0.8300 (mmm) cc_final: 0.8058 (mmm)
REVERT: A  862 MET cc_start: 0.8914 (mmt) cc_final: 0.8593 (mmt)
REVERT: A  899 HIS cc_start: 0.8192 (t-170) cc_final: 0.7746 (t-170)
REVERT: A  914 ARG cc_start: 0.8820 (ttm110) cc_final: 0.8205 (tpt170)
REVERT: A  966 GLU cc_start: 0.8824 (pm20) cc_final: 0.8554 (pm20)
REVERT: A 1155 GLN cc_start: 0.7075 (tp-100) cc_final: 0.6722 (mm110)
REVERT: A 1241 MET cc_start: 0.8950 (mmp) cc_final: 0.8368 (tpt)
REVERT: A 1242 ASN cc_start: 0.8416 (p0) cc_final: 0.8209 (p0)
REVERT: B  737 GLU cc_start: 0.9169 (mp0) cc_final: 0.8841 (mp0)
REVERT: B  739 MET cc_start: 0.8407 (mmp) cc_final: 0.8138 (mmt)
REVERT: B  748 GLU cc_start: 0.8151 (pt0) cc_final: 0.7733 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 118
  average time/residue: 0.2310
  time to fit residues: 35.8592
Evaluate side-chains
  85 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 32 optimal weight:    0.0020
   chunk 50 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 65 optimal weight:    7.9990
   chunk 10 optimal weight:    8.9990
   chunk 79 optimal weight:    0.8980
   chunk 5 optimal weight:   20.0000
   overall best weight:    1.1792

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

Flipped N/Q/H residues before XYZ refinement:
A 888 GLN
A 915 ASN
A1045 GLN
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1142 HIS
A1173 HIS
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.088429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.075841 restraints weight = 42098.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.077008 restraints weight = 32968.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.077893 restraints weight = 27177.729|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.4017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6669  Z= 0.189
  Angle     :  0.684  10.013   9029  Z= 0.333
  Chirality :  0.042   0.119    992
  Planarity :  0.004   0.063   1177
  Dihedral  :  5.016  25.852    884
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.22 %
    Favored  : 91.78 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.21 (0.29), residues: 803
  helix:  0.12 (0.28), residues: 376
  sheet: -1.44 (0.82), residues: 39
  loop : -3.24 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1078 
 HIS   0.007   0.001   HIS A 983 
 PHE   0.020   0.001   PHE A1224 
 TYR   0.012   0.001   TYR A1229 
 ARG   0.007   0.000   ARG A1066 

*********************** 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
  122 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.956 
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  530 MET cc_start: 0.7474 (tmm) cc_final: 0.7026 (tmm)
REVERT: A  606 MET cc_start: 0.8367 (mtp) cc_final: 0.8024 (mtp)
REVERT: A  699 MET cc_start: 0.8362 (mmm) cc_final: 0.8160 (mmm)
REVERT: A  899 HIS cc_start: 0.7866 (t-170) cc_final: 0.7582 (t-170)
REVERT: A  914 ARG cc_start: 0.8817 (ttm110) cc_final: 0.8340 (tpt170)
REVERT: A  966 GLU cc_start: 0.8437 (pm20) cc_final: 0.8068 (pm20)
REVERT: A 1241 MET cc_start: 0.8838 (mmp) cc_final: 0.8057 (tpt)
REVERT: A 1242 ASN cc_start: 0.8201 (p0) cc_final: 0.7903 (p0)
REVERT: B  739 MET cc_start: 0.8437 (mmp) cc_final: 0.8139 (mmt)
REVERT: B  748 GLU cc_start: 0.8201 (pt0) cc_final: 0.7815 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1808
  time to fit residues: 29.7021
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  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 75 optimal weight:    0.3980
   chunk 37 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 11 optimal weight:    8.9990
   chunk 69 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9980
   chunk 64 optimal weight:    8.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 630 HIS
A 832 ASN
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 888 GLN
A 915 ASN
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 736 GLN ** 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 = 0.3993 r_free = 0.3993 target = 0.087159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.074536 restraints weight = 42696.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.075748 restraints weight = 32763.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.076664 restraints weight = 26786.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.4234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6669  Z= 0.213
  Angle     :  0.683  10.215   9029  Z= 0.341
  Chirality :  0.043   0.133    992
  Planarity :  0.005   0.064   1177
  Dihedral  :  5.063  26.748    884
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 19.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.29), residues: 803
  helix:  0.03 (0.27), residues: 376
  sheet: -1.21 (0.86), residues: 39
  loop : -3.20 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1078 
 HIS   0.006   0.001   HIS A 983 
 PHE   0.021   0.002   PHE A 631 
 TYR   0.019   0.002   TYR A 872 
 ARG   0.005   0.000   ARG A1178 

*********************** 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
  120 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.825 
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: 0.7605 (tmm) cc_final: 0.7215 (tmm)
REVERT: A  606 MET cc_start: 0.8447 (mtp) cc_final: 0.8209 (mtp)
REVERT: A  862 MET cc_start: 0.8824 (mmt) cc_final: 0.8605 (mmt)
REVERT: A  891 CYS cc_start: 0.8736 (t) cc_final: 0.8452 (m)
REVERT: A  897 MET cc_start: 0.8167 (ppp) cc_final: 0.7725 (ppp)
REVERT: A  899 HIS cc_start: 0.7903 (t-170) cc_final: 0.7599 (t-170)
REVERT: A  914 ARG cc_start: 0.8806 (ttm110) cc_final: 0.8248 (tpt170)
REVERT: A 1022 MET cc_start: 0.7403 (mtt) cc_final: 0.7167 (mtt)
REVERT: A 1155 GLN cc_start: 0.6996 (tp-100) cc_final: 0.6790 (mm-40)
REVERT: A 1241 MET cc_start: 0.8948 (mmp) cc_final: 0.8352 (tpt)
REVERT: A 1242 ASN cc_start: 0.8239 (p0) cc_final: 0.7966 (p0)
REVERT: B  737 GLU cc_start: 0.9131 (mp0) cc_final: 0.8863 (mp0)
REVERT: B  739 MET cc_start: 0.8478 (mmp) cc_final: 0.8187 (mmt)
REVERT: B  748 GLU cc_start: 0.8107 (pt0) cc_final: 0.7715 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1971
  time to fit residues: 31.7768
Evaluate side-chains
  92 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 61 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 66 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0770
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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**
A 915 ASN
A 964 HIS
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1142 HIS
A1169 HIS
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.089914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.077452 restraints weight = 43035.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.078675 restraints weight = 32518.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.079649 restraints weight = 26384.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.4173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6669  Z= 0.170
  Angle     :  0.665   8.681   9029  Z= 0.325
  Chirality :  0.042   0.145    992
  Planarity :  0.005   0.080   1177
  Dihedral  :  4.827  23.466    884
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.34 %
    Favored  : 91.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.30), residues: 803
  helix:  0.30 (0.28), residues: 375
  sheet: -0.99 (0.86), residues: 39
  loop : -3.10 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1078 
 HIS   0.006   0.001   HIS A 983 
 PHE   0.022   0.001   PHE A 631 
 TYR   0.014   0.001   TYR A 872 
 ARG   0.004   0.000   ARG A1178 

*********************** 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
  121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.728 
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: 0.8421 (mtp) cc_final: 0.8178 (mtp)
REVERT: A  862 MET cc_start: 0.8794 (mmt) cc_final: 0.8474 (mmt)
REVERT: A  888 GLN cc_start: 0.8867 (tp40) cc_final: 0.8536 (tp-100)
REVERT: A  899 HIS cc_start: 0.7855 (t-170) cc_final: 0.7591 (t-170)
REVERT: A  914 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8335 (tpt170)
REVERT: A 1241 MET cc_start: 0.8589 (mmp) cc_final: 0.7798 (tpt)
REVERT: A 1242 ASN cc_start: 0.8088 (p0) cc_final: 0.7810 (p0)
REVERT: B  739 MET cc_start: 0.8550 (mmp) cc_final: 0.8218 (mmt)
REVERT: B  748 GLU cc_start: 0.8107 (pt0) cc_final: 0.7752 (pp20)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1789
  time to fit residues: 28.8137
Evaluate side-chains
  94 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 48 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 71 optimal weight:    7.9990
   chunk 30 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9980
   chunk 8 optimal weight:    9.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
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 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 915 ASN
** A1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.087910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.075537 restraints weight = 44323.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.076701 restraints weight = 34345.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.077625 restraints weight = 28207.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.4388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6669  Z= 0.210
  Angle     :  0.695   9.886   9029  Z= 0.345
  Chirality :  0.043   0.133    992
  Planarity :  0.005   0.071   1177
  Dihedral  :  4.957  24.324    884
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 19.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.46 %
    Favored  : 90.54 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.01 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.96 (0.30), residues: 803
  helix:  0.27 (0.27), residues: 374
  sheet: -1.10 (0.85), residues: 39
  loop : -3.06 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1078 
 HIS   0.005   0.001   HIS A 630 
 PHE   0.026   0.002   PHE A 631 
 TYR   0.018   0.001   TYR A1229 
 ARG   0.006   0.000   ARG A1066 

*********************** 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
  119 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  682 MET cc_start: 0.6488 (ttm) cc_final: 0.6182 (ttm)
REVERT: A  888 GLN cc_start: 0.8950 (tp40) cc_final: 0.8646 (tp-100)
REVERT: A  891 CYS cc_start: 0.8674 (t) cc_final: 0.8452 (m)
REVERT: A  914 ARG cc_start: 0.8883 (ttm110) cc_final: 0.8286 (tpt170)
REVERT: A 1196 MET cc_start: 0.4916 (tpp) cc_final: 0.4376 (mpp)
REVERT: A 1241 MET cc_start: 0.8838 (mmp) cc_final: 0.8252 (tpt)
REVERT: B  737 GLU cc_start: 0.9094 (mp0) cc_final: 0.8770 (mp0)
REVERT: B  739 MET cc_start: 0.8381 (mmp) cc_final: 0.8109 (mmt)
REVERT: B  748 GLU cc_start: 0.8059 (pt0) cc_final: 0.7683 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1688
  time to fit residues: 27.2169
Evaluate side-chains
  88 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 27 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 4 optimal weight:    8.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 HIS
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1256 GLN
** B 736 GLN ** 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 = 0.3919 r_free = 0.3919 target = 0.081727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.069504 restraints weight = 45278.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.070604 restraints weight = 35058.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.071491 restraints weight = 28784.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.5027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6669  Z= 0.324
  Angle     :  0.821  11.943   9029  Z= 0.413
  Chirality :  0.047   0.180    992
  Planarity :  0.006   0.071   1177
  Dihedral  :  5.524  24.580    884
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 27.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.46 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.46 (0.29), residues: 803
  helix: -0.23 (0.26), residues: 370
  sheet: -1.82 (0.79), residues: 39
  loop : -3.14 (0.30), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 848 
 HIS   0.010   0.002   HIS A 630 
 PHE   0.032   0.002   PHE A 631 
 TYR   0.027   0.003   TYR A1229 
 ARG   0.006   0.001   ARG A1178 

********************** 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
  112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  606 MET cc_start: 0.8484 (mtp) cc_final: 0.8107 (mtp)
REVERT: A  660 TYR cc_start: 0.7514 (t80) cc_final: 0.6798 (t80)
REVERT: A  682 MET cc_start: 0.7100 (ttm) cc_final: 0.6826 (ttm)
REVERT: A  888 GLN cc_start: 0.9078 (tp40) cc_final: 0.8827 (tp-100)
REVERT: A  914 ARG cc_start: 0.8836 (ttm110) cc_final: 0.8303 (tpt170)
REVERT: A 1062 GLN cc_start: 0.8851 (tm-30) cc_final: 0.8630 (tm-30)
REVERT: A 1155 GLN cc_start: 0.7518 (mp-120) cc_final: 0.6974 (tp40)
REVERT: A 1196 MET cc_start: 0.5856 (tpp) cc_final: 0.5578 (tpp)
REVERT: A 1241 MET cc_start: 0.9053 (mmp) cc_final: 0.8509 (tpt)
REVERT: B  739 MET cc_start: 0.8409 (mmp) cc_final: 0.8188 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1799
  time to fit residues: 27.4452
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  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 5 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 37 optimal weight:   50.0000
   chunk 66 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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**
A1142 HIS
** B 736 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.088125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.075662 restraints weight = 42091.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.076870 restraints weight = 32588.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.077780 restraints weight = 26607.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.4850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6669  Z= 0.193
  Angle     :  0.712   8.641   9029  Z= 0.352
  Chirality :  0.043   0.158    992
  Planarity :  0.005   0.067   1177
  Dihedral  :  5.081  23.626    884
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.29 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.29), residues: 803
  helix:  0.20 (0.27), residues: 375
  sheet: -1.33 (0.85), residues: 39
  loop : -3.17 (0.29), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1078 
 HIS   0.008   0.001   HIS A 983 
 PHE   0.031   0.002   PHE A 631 
 TYR   0.013   0.001   TYR A1229 
 ARG   0.006   0.000   ARG A 753 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2122.64 seconds
wall clock time: 39 minutes 6.31 seconds (2346.31 seconds total)