Starting phenix.real_space_refine
on Thu Jul 31 05:29:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zc4_14619/07_2025/7zc4_14619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zc4_14619/07_2025/7zc4_14619.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zc4_14619/07_2025/7zc4_14619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zc4_14619/07_2025/7zc4_14619.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zc4_14619/07_2025/7zc4_14619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zc4_14619/07_2025/7zc4_14619.cif"
  }
  resolution = 3.24
  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=   0.001 sd=   0.015
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 7224 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: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    4630      2.51       5
     N    1303      2.21       5
     O    1291      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7272
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7272
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 926, 7254
          Classifications: {'peptide': 926}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 62, 'TRANS': 863}
          Chain breaks: 5
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 45
      Conformer: "B"
        Number of residues, atoms: 926, 7254
          Classifications: {'peptide': 926}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 62, 'TRANS': 863}
          Chain breaks: 5
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 108
          Unresolved non-hydrogen angles: 137
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 45
          bond proxies already assigned to first conformer: 7404
  Time building chain proxies: 7.56, per 1000 atoms: 1.04
  Number of scatterers: 7272
  At special positions: 0
  Unit cell: (79.79, 93.93, 107.06, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1291      8.00
     N    1303      7.00
     C    4630      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: 1.97
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1772

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 6 sheets defined
      69.0% alpha, 3.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 221 through 236
    Processing helix  chain 'A' and resid 238 through 252
    Processing helix  chain 'A' and resid 252 through 259
    Processing helix  chain 'A' and resid 260 through 275
    Processing helix  chain 'A' and resid 276 through 291
    Processing helix  chain 'A' and resid 295 through 310
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 3.565A  pdb=" N   ILE A 316 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 336
    Processing helix  chain 'A' and resid 340 through 354
    Processing helix  chain 'A' and resid 371 through 379
      removed outlier: 4.533A  pdb=" N   ASP A 376 " --> pdb=" O   LYS A 372 " (cutoff:3.500A)
      removed outlier: 5.120A  pdb=" N   VAL A 377 " --> pdb=" O   LEU A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 410
    Processing helix  chain 'A' and resid 424 through 463
    Processing helix  chain 'A' and resid 467 through 473
    Processing helix  chain 'A' and resid 475 through 490
    Processing helix  chain 'A' and resid 496 through 520
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 3.862A  pdb=" N   CYS A 535 " --> pdb=" O   ARG A 531 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   LEU A 536 " --> pdb=" O   LYS A 532 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU A 537 " --> pdb=" O   TYR A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 557
    Processing helix  chain 'A' and resid 561 through 565
    Processing helix  chain 'A' and resid 568 through 587
    Processing helix  chain 'A' and resid 624 through 635
    Processing helix  chain 'A' and resid 676 through 687
    Processing helix  chain 'A' and resid 688 through 705
      removed outlier: 3.806A  pdb=" N   LEU A 692 " --> pdb=" O   PRO A 688 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   GLY A 694 " --> pdb=" O   THR A 690 " (cutoff:3.500A)
      removed outlier: 4.846A  pdb=" N   ALA A 695 " --> pdb=" O   ALA A 691 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   CYS A 705 " --> pdb=" O   GLN A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 723
      removed outlier: 3.524A  pdb=" N   ALA A 723 " --> pdb=" O   GLN A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 789
    Processing helix  chain 'A' and resid 814 through 817
    Processing helix  chain 'A' and resid 818 through 824
    Processing helix  chain 'A' and resid 836 through 850
    Processing helix  chain 'A' and resid 856 through 867
    Processing helix  chain 'A' and resid 867 through 877
    Processing helix  chain 'A' and resid 883 through 888
      removed outlier: 4.122A  pdb=" N   GLY A 887 " --> pdb=" O   LYS A 883 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA A 888 " --> pdb=" O   TRP A 884 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 883 through 888'
    Processing helix  chain 'A' and resid 890 through 907
    Processing helix  chain 'A' and resid 925 through 935
    Processing helix  chain 'A' and resid 937 through 944
    Processing helix  chain 'A' and resid 954 through 973
    Processing helix  chain 'A' and resid 976 through 981
    Processing helix  chain 'A' and resid 986 through 1000
    Processing helix  chain 'A' and resid 1008 through 1017
      removed outlier: 3.783A  pdb=" N   LEU A1017 " --> pdb=" O   ARG A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1021 through 1023
      No H-bonds generated for 'chain 'A' and resid 1021 through 1023'
    Processing helix  chain 'A' and resid 1024 through 1044
    Processing helix  chain 'A' and resid 1044 through 1063
    Processing helix  chain 'A' and resid 1111 through 1143
      Proline residue:  A1120  - end of helix
    Processing helix  chain 'A' and resid 1159 through 1177
    Processing helix  chain 'A' and resid 1178 through 1191
    Processing helix  chain 'A' and resid 1197 through 1210
      removed outlier: 4.093A  pdb=" N   GLN A1203 " --> pdb=" O   LEU A1199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1218 through 1223
      removed outlier: 3.639A  pdb=" N   GLN A1221 " --> pdb=" O   ASP A1218 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 412 through 415
    Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 607
    Processing sheet with id=AA3, first strand: chain 'A' and resid 794 through 795
    Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 800
    Processing sheet with id=AA5, first strand: chain 'A' and resid 919 through 921
      removed outlier: 3.952A  pdb=" N   TYR A1153 " --> pdb=" O   GLN A 921 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1069 through 1071

    465 hydrogen bonds defined for protein.
    1359 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.17

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1472
        1.33 -     1.45: 1667
        1.45 -     1.57: 4236
        1.57 -     1.69: 0
        1.69 -     1.81: 73
  Bond restraints: 7448
  Sorted by residual:
  bond pdb=" CG  PHE A 802 "
       pdb=" CD1 PHE A 802 "
    ideal  model  delta    sigma   weight residual
    1.384  1.349  0.035 2.10e-02 2.27e+03 2.73e+00
  bond pdb=" CE2 PHE A 802 "
       pdb=" CZ  PHE A 802 "
    ideal  model  delta    sigma   weight residual
    1.382  1.333  0.049 3.00e-02 1.11e+03 2.68e+00
  bond pdb=" CA  VAL A 603 "
       pdb=" C   VAL A 603 "
    ideal  model  delta    sigma   weight residual
    1.525  1.551 -0.026 2.10e-02 2.27e+03 1.53e+00
  bond pdb=" CA  MET A 800 "
       pdb=" C   MET A 800 "
    ideal  model  delta    sigma   weight residual
    1.528  1.545 -0.017 1.39e-02 5.18e+03 1.46e+00
  bond pdb=" CG  ASN A 799 "
       pdb=" OD1 ASN A 799 "
    ideal  model  delta    sigma   weight residual
    1.231  1.208  0.023 1.90e-02 2.77e+03 1.44e+00
  ... (remaining 7443 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 9732
        1.52 -     3.04: 324
        3.04 -     4.57: 54
        4.57 -     6.09: 15
        6.09 -     7.61: 4
  Bond angle restraints: 10129
  Sorted by residual:
  angle pdb=" N   PHE A 802 "
        pdb=" CA  PHE A 802 "
        pdb=" CB  PHE A 802 "
      ideal   model   delta    sigma   weight residual
     110.12  116.45   -6.33 1.47e+00 4.63e-01 1.85e+01
  angle pdb=" CA  PHE A 802 "
        pdb=" CB  PHE A 802 "
        pdb=" CG  PHE A 802 "
      ideal   model   delta    sigma   weight residual
     113.80  117.36   -3.56 1.00e+00 1.00e+00 1.27e+01
  angle pdb=" C   THR A 357 "
        pdb=" N   PHE A 358 "
        pdb=" CA  PHE A 358 "
      ideal   model   delta    sigma   weight residual
     121.54  126.65   -5.11 1.91e+00 2.74e-01 7.17e+00
  angle pdb=" CA  TYR A 999 "
        pdb=" CB  TYR A 999 "
        pdb=" CG  TYR A 999 "
      ideal   model   delta    sigma   weight residual
     113.90  118.66   -4.76 1.80e+00 3.09e-01 6.98e+00
  angle pdb=" C   MET A 323 "
        pdb=" N   SER A 324 "
        pdb=" CA  SER A 324 "
      ideal   model   delta    sigma   weight residual
     121.54  126.26   -4.72 1.91e+00 2.74e-01 6.11e+00
  ... (remaining 10124 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 3963
       16.72 -    33.45: 443
       33.45 -    50.17: 90
       50.17 -    66.90: 23
       66.90 -    83.62: 13
  Dihedral angle restraints: 4532
    sinusoidal: 1811
      harmonic: 2721
  Sorted by residual:
  dihedral pdb=" CA  ASP A 873 "
           pdb=" CB  ASP A 873 "
           pdb=" CG  ASP A 873 "
           pdb=" OD1 ASP A 873 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.31   58.31     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CA  ASP A 310 "
           pdb=" CB  ASP A 310 "
           pdb=" CG  ASP A 310 "
           pdb=" OD1 ASP A 310 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.27   58.27     1      2.00e+01 2.50e-03 1.14e+01
  dihedral pdb=" CG  ARG A 431 "
           pdb=" CD  ARG A 431 "
           pdb=" NE  ARG A 431 "
           pdb=" CZ  ARG A 431 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -135.03  -44.97     2      1.50e+01 4.44e-03 1.07e+01
  ... (remaining 4529 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 914
       0.048 -    0.097: 173
       0.097 -    0.145: 43
       0.145 -    0.194: 4
       0.194 -    0.242: 2
  Chirality restraints: 1136
  Sorted by residual:
  chirality pdb=" CA  HIS A1150 "
            pdb=" N   HIS A1150 "
            pdb=" C   HIS A1150 "
            pdb=" CB  HIS A1150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  VAL A1149 "
            pdb=" N   VAL A1149 "
            pdb=" C   VAL A1149 "
            pdb=" CB  VAL A1149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.69e-01
  chirality pdb=" CA  PHE A 802 "
            pdb=" N   PHE A 802 "
            pdb=" C   PHE A 802 "
            pdb=" CB  PHE A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.69e-01
  ... (remaining 1133 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 553 "    0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   TRP A 553 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   TRP A 553 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A 554 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 900 "    0.014 2.00e-02 2.50e+03   2.82e-02 7.96e+00
        pdb=" C   GLU A 900 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   GLU A 900 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 901 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 802 "   -0.030 2.00e-02 2.50e+03   2.10e-02 7.70e+00
        pdb=" CG  PHE A 802 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 802 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 802 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 802 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 802 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 802 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 104
        2.70 -     3.25: 7490
        3.25 -     3.80: 12475
        3.80 -     4.35: 15963
        4.35 -     4.90: 25657
  Nonbonded interactions: 61689
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 485 "
            pdb=" OG1 THR A 640 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" NH2 ARG A 782 "
            pdb=" OG  SER A 818 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" NH2 ARG A 411 "
            pdb=" OE1 GLU A 642 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" O   GLN A 585 "
            pdb=" NE2 GLN A 588 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" OD1 ASN A 265 "
            pdb=" OG  SER A 298 "
     model   vdw
     2.343 3.040
  ... (remaining 61684 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     24.630
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5578
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7448  Z= 0.159
  Angle     :  0.662   7.612  10129  Z= 0.362
  Chirality :  0.043   0.242   1136
  Planarity :  0.005   0.036   1316
  Dihedral  : 15.191  83.623   2760
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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:  2.81 (0.28), residues: 917
  helix:  2.66 (0.21), residues: 606
  sheet: -0.84 (0.98), residues: 32
  loop :  0.45 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 553 
 HIS   0.011   0.001   HIS A1150 
 PHE   0.045   0.002   PHE A 802 
 TYR   0.025   0.002   TYR A 461 
 ARG   0.006   0.001   ARG A 477 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10666 (  465)
  hydrogen bonds       : angle       5.00520 ( 1359)
  covalent geometry    : bond        0.00327 ( 7448)
  covalent geometry    : angle       0.66183 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  269 LEU cc_start: 0.7496 (mm) cc_final: 0.7283 (mm)
REVERT: A  533 TYR cc_start: 0.5654 (t80) cc_final: 0.5216 (t80)
REVERT: A  778 GLU cc_start: 0.6536 (tm-30) cc_final: 0.6189 (tp30)
REVERT: A  987 ARG cc_start: 0.6277 (tmt170) cc_final: 0.5949 (tmt170)
REVERT: A 1154 TRP cc_start: 0.6101 (m-10) cc_final: 0.5034 (m-10)
REVERT: A 1177 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6457 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2461
  time to fit residues: 37.1076
Evaluate side-chains
  101 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.1980
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 83 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
A 588 GLN
A 659 HIS
A 893 GLN
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN
A1165 GLN
A1170 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.202564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.173532 restraints weight = 31071.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.4240 rms_B_bonded: 5.10
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4240
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4240 r_free = 0.4240    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4240 r_free = 0.4240    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4240
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6027
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7448  Z= 0.209
  Angle     :  0.665  12.829  10129  Z= 0.335
  Chirality :  0.043   0.175   1136
  Planarity :  0.005   0.049   1316
  Dihedral  :  3.905  16.655   1010
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  7.40 %
    Favored  : 91.69 %
  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:  2.24 (0.27), residues: 917
  helix:  2.08 (0.20), residues: 606
  sheet: -0.56 (0.82), residues: 42
  loop :  0.58 (0.39), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1154 
 HIS   0.007   0.002   HIS A 512 
 PHE   0.026   0.003   PHE A 802 
 TYR   0.020   0.002   TYR A1227 
 ARG   0.005   0.001   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05125 (  465)
  hydrogen bonds       : angle       4.51061 ( 1359)
  covalent geometry    : bond        0.00499 ( 7448)
  covalent geometry    : angle       0.66504 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
REVERT: A  269 LEU cc_start: 0.7706 (mm) cc_final: 0.7478 (mm)
REVERT: A  403 GLN cc_start: 0.6171 (tp40) cc_final: 0.5147 (tp40)
REVERT: A  503 GLU cc_start: 0.6177 (tp30) cc_final: 0.5828 (tp30)
REVERT: A  648 MET cc_start: 0.7082 (mtm) cc_final: 0.6697 (mtp)
REVERT: A  852 LYS cc_start: 0.7282 (mmmt) cc_final: 0.7041 (mmmm)
REVERT: A  993 THR cc_start: 0.6070 (t) cc_final: 0.5833 (t)
  outliers start: 7
  outliers final: 3
  residues processed: 104
  average time/residue: 0.2183
  time to fit residues: 30.2657
Evaluate side-chains
  101 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  772 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0870
   chunk 17 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 73 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.202853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.174525 restraints weight = 29279.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.4215 rms_B_bonded: 4.59
r_work: 0.3997 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3993
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3993 r_free = 0.3993    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3993 r_free = 0.3993    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6227
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7448  Z= 0.189
  Angle     :  0.627  11.777  10129  Z= 0.313
  Chirality :  0.041   0.197   1136
  Planarity :  0.005   0.045   1316
  Dihedral  :  3.905  14.340   1010
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.83 %
    Favored  : 89.74 %
  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:  2.02 (0.27), residues: 917
  helix:  1.90 (0.20), residues: 603
  sheet: -0.46 (0.81), residues: 42
  loop :  0.50 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1154 
 HIS   0.007   0.001   HIS A 512 
 PHE   0.021   0.002   PHE A1186 
 TYR   0.016   0.002   TYR A 530 
 ARG   0.006   0.001   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04774 (  465)
  hydrogen bonds       : angle       4.35418 ( 1359)
  covalent geometry    : bond        0.00449 ( 7448)
  covalent geometry    : angle       0.62660 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 GLN cc_start: 0.6642 (tp40) cc_final: 0.5312 (tp40)
REVERT: A  503 GLU cc_start: 0.6650 (tp30) cc_final: 0.6207 (tp30)
REVERT: A  690 THR cc_start: 0.5343 (OUTLIER) cc_final: 0.5042 (p)
REVERT: A 1223 LYS cc_start: 0.6816 (tptp) cc_final: 0.6252 (mmtm)
  outliers start: 11
  outliers final: 6
  residues processed: 98
  average time/residue: 0.2828
  time to fit residues: 36.4182
Evaluate side-chains
  96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0980
   chunk 20 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 84 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 68 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.201936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.173617 restraints weight = 28337.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.4208 rms_B_bonded: 4.46
r_work: 0.3991 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3987 r_free = 0.3987    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3987 r_free = 0.3987    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3987
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6243
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7448  Z= 0.183
  Angle     :  0.610  11.391  10129  Z= 0.304
  Chirality :  0.040   0.167   1136
  Planarity :  0.005   0.053   1316
  Dihedral  :  3.939  14.844   1010
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.74 %
    Favored  : 89.22 %
  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:  1.93 (0.27), residues: 917
  helix:  1.84 (0.20), residues: 604
  sheet: -0.46 (0.79), residues: 42
  loop :  0.43 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 271 
 HIS   0.006   0.001   HIS A1125 
 PHE   0.018   0.002   PHE A 802 
 TYR   0.013   0.001   TYR A 299 
 ARG   0.008   0.000   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04654 (  465)
  hydrogen bonds       : angle       4.31384 ( 1359)
  covalent geometry    : bond        0.00433 ( 7448)
  covalent geometry    : angle       0.61044 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  503 GLU cc_start: 0.6599 (tp30) cc_final: 0.6172 (tp30)
REVERT: A  690 THR cc_start: 0.5367 (OUTLIER) cc_final: 0.5072 (p)
REVERT: A 1223 LYS cc_start: 0.6870 (tptp) cc_final: 0.6574 (tptp)
  outliers start: 8
  outliers final: 7
  residues processed: 98
  average time/residue: 0.2659
  time to fit residues: 35.0942
Evaluate side-chains
  96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  690 THR
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 33 optimal weight:    0.4980
   chunk 32 optimal weight:    0.4980
   chunk 49 optimal weight:    0.6980
   chunk 80 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0470
   chunk 40 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0050
   chunk 59 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.3292

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

Flipped N/Q/H residues before XYZ refinement:
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 659 HIS
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.205720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.177684 restraints weight = 26248.808|
|-----------------------------------------------------------------------------|
r_work (start): 0.4249 rms_B_bonded: 4.43
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4243
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4243 r_free = 0.4243    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4242 r_free = 0.4242    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5994
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7448  Z= 0.137
  Angle     :  0.560  11.003  10129  Z= 0.276
  Chirality :  0.038   0.193   1136
  Planarity :  0.005   0.044   1316
  Dihedral  :  3.741  14.949   1010
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.04 %
    Favored  : 87.92 %
  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:  2.22 (0.27), residues: 917
  helix:  2.04 (0.20), residues: 605
  sheet: -0.25 (0.97), residues: 32
  loop :  0.58 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1154 
 HIS   0.005   0.001   HIS A1125 
 PHE   0.015   0.002   PHE A 802 
 TYR   0.013   0.001   TYR A1227 
 ARG   0.005   0.000   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04167 (  465)
  hydrogen bonds       : angle       4.11847 ( 1359)
  covalent geometry    : bond        0.00317 ( 7448)
  covalent geometry    : angle       0.55958 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 GLN cc_start: 0.6281 (tp40) cc_final: 0.5889 (tp40)
REVERT: A  503 GLU cc_start: 0.6079 (tp30) cc_final: 0.5750 (tp30)
REVERT: A  522 GLN cc_start: 0.6937 (tp40) cc_final: 0.6536 (tp40)
REVERT: A  899 MET cc_start: 0.4143 (mtt) cc_final: 0.3808 (mtt)
REVERT: A 1140 TYR cc_start: 0.5890 (t80) cc_final: 0.5549 (t80)
  outliers start: 8
  outliers final: 5
  residues processed: 94
  average time/residue: 0.3170
  time to fit residues: 38.7729
Evaluate side-chains
  92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  278 LYS
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 26 optimal weight:    0.1980
   chunk 49 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 51 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4521 r_free = 0.4521 target = 0.201429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.174034 restraints weight = 28523.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 4.65
r_work: 0.4024 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.4024
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4025 r_free = 0.4025    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4025 r_free = 0.4025    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6223
moved from start:          0.3015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7448  Z= 0.148
  Angle     :  0.569  11.068  10129  Z= 0.281
  Chirality :  0.038   0.186   1136
  Planarity :  0.005   0.044   1316
  Dihedral  :  3.768  15.639   1010
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 11.17 %
    Favored  : 87.92 %
  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:  2.22 (0.27), residues: 917
  helix:  2.03 (0.20), residues: 605
  sheet: -0.27 (0.98), residues: 32
  loop :  0.59 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1154 
 HIS   0.006   0.001   HIS A 250 
 PHE   0.017   0.002   PHE A 802 
 TYR   0.014   0.001   TYR A1227 
 ARG   0.005   0.000   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04222 (  465)
  hydrogen bonds       : angle       4.12248 ( 1359)
  covalent geometry    : bond        0.00347 ( 7448)
  covalent geometry    : angle       0.56905 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  522 GLN cc_start: 0.7351 (tp40) cc_final: 0.6957 (tp40)
REVERT: A  899 MET cc_start: 0.4290 (mtt) cc_final: 0.3981 (mtt)
REVERT: A 1140 TYR cc_start: 0.6391 (t80) cc_final: 0.5979 (t80)
  outliers start: 7
  outliers final: 6
  residues processed: 93
  average time/residue: 0.2724
  time to fit residues: 33.4299
Evaluate side-chains
  92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  657 SER
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 78 optimal weight:    0.1980
   chunk 72 optimal weight:    0.0970
   chunk 66 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 84 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0010
   chunk 17 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
A1165 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.202673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.174773 restraints weight = 34228.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.4244 rms_B_bonded: 5.49
r_work (final): 0.4244
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4242
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4242 r_free = 0.4242    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4242 r_free = 0.4242    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4242
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5994
moved from start:          0.3135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7448  Z= 0.123
  Angle     :  0.557  11.925  10129  Z= 0.270
  Chirality :  0.038   0.268   1136
  Planarity :  0.005   0.045   1316
  Dihedral  :  3.644  16.064   1010
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.95 %
    Favored  : 87.27 %
  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 (0.27), residues: 917
  helix:  2.19 (0.21), residues: 606
  sheet: -0.15 (0.96), residues: 32
  loop :  0.61 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1154 
 HIS   0.005   0.001   HIS A 250 
 PHE   0.015   0.002   PHE A 802 
 TYR   0.013   0.001   TYR A 999 
 ARG   0.004   0.000   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03918 (  465)
  hydrogen bonds       : angle       3.99474 ( 1359)
  covalent geometry    : bond        0.00278 ( 7448)
  covalent geometry    : angle       0.55668 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 TYR cc_start: 0.6521 (t80) cc_final: 0.6281 (t80)
REVERT: A  522 GLN cc_start: 0.6942 (tp40) cc_final: 0.6591 (tp40)
REVERT: A  729 LEU cc_start: 0.6877 (mt) cc_final: 0.6446 (mt)
REVERT: A  899 MET cc_start: 0.4113 (mtt) cc_final: 0.3790 (mtt)
REVERT: A 1140 TYR cc_start: 0.5893 (t80) cc_final: 0.5574 (t80)
  outliers start: 6
  outliers final: 5
  residues processed: 93
  average time/residue: 0.2699
  time to fit residues: 33.1525
Evaluate side-chains
  91 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 86
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 67 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 37 optimal weight:    0.1980
   chunk 72 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1131 HIS
A1165 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.201676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.174683 restraints weight = 24682.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.4233 rms_B_bonded: 4.07
r_work: 0.4019 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4011
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4011 r_free = 0.4011    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4011 r_free = 0.4011    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4011
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6229
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7448  Z= 0.180
  Angle     :  0.619  10.938  10129  Z= 0.302
  Chirality :  0.040   0.218   1136
  Planarity :  0.005   0.046   1316
  Dihedral  :  3.873  17.367   1010
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 12.47 %
    Favored  : 86.36 %
  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 (0.27), residues: 917
  helix:  1.96 (0.21), residues: 604
  sheet: -0.24 (0.96), residues: 32
  loop :  0.48 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 271 
 HIS   0.006   0.001   HIS A1125 
 PHE   0.018   0.002   PHE A 802 
 TYR   0.015   0.002   TYR A1227 
 ARG   0.004   0.000   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04362 (  465)
  hydrogen bonds       : angle       4.16017 ( 1359)
  covalent geometry    : bond        0.00430 ( 7448)
  covalent geometry    : angle       0.61857 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
REVERT: A  260 THR cc_start: 0.7793 (t) cc_final: 0.7370 (p)
REVERT: A  282 TYR cc_start: 0.6810 (t80) cc_final: 0.6401 (t80)
REVERT: A  515 GLN cc_start: 0.6300 (mm-40) cc_final: 0.6067 (mm110)
REVERT: A  522 GLN cc_start: 0.7390 (tp40) cc_final: 0.7101 (tp40)
REVERT: A  899 MET cc_start: 0.4295 (mtt) cc_final: 0.3987 (mtt)
  outliers start: 8
  outliers final: 5
  residues processed: 95
  average time/residue: 0.2233
  time to fit residues: 27.9635
Evaluate side-chains
  90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 67 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9990
   chunk 34 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 91 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.199529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.172991 restraints weight = 22671.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.4232 rms_B_bonded: 3.74
r_work: 0.4042 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4055
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4055 r_free = 0.4055    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4055 r_free = 0.4055    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4055
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6188
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7448  Z= 0.172
  Angle     :  0.616  13.540  10129  Z= 0.300
  Chirality :  0.039   0.257   1136
  Planarity :  0.005   0.047   1316
  Dihedral  :  3.915  16.416   1010
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.99 %
    Favored  : 86.10 %
  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:  2.07 (0.27), residues: 917
  helix:  1.92 (0.21), residues: 604
  sheet: -0.08 (0.98), residues: 32
  loop :  0.48 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1154 
 HIS   0.009   0.001   HIS A 920 
 PHE   0.017   0.002   PHE A 802 
 TYR   0.012   0.001   TYR A 299 
 ARG   0.003   0.000   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04281 (  465)
  hydrogen bonds       : angle       4.17976 ( 1359)
  covalent geometry    : bond        0.00413 ( 7448)
  covalent geometry    : angle       0.61619 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 THR cc_start: 0.7697 (t) cc_final: 0.7224 (p)
REVERT: A  282 TYR cc_start: 0.6710 (t80) cc_final: 0.6281 (t80)
REVERT: A  503 GLU cc_start: 0.6673 (tp30) cc_final: 0.6252 (tp30)
REVERT: A  515 GLN cc_start: 0.6265 (mm-40) cc_final: 0.6050 (mm-40)
REVERT: A  805 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.5355 (mmt90)
REVERT: A  899 MET cc_start: 0.4240 (mtt) cc_final: 0.3974 (mtt)
  outliers start: 6
  outliers final: 5
  residues processed: 93
  average time/residue: 0.2283
  time to fit residues: 28.3209
Evaluate side-chains
  93 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  805 ARG
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    0.3980
   chunk 49 optimal weight:    0.0670
   chunk 4 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0020
   chunk 64 optimal weight:    0.0570
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    0.4980
   chunk 87 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   overall best weight:    0.2044

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1131 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.205065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.177704 restraints weight = 24017.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.4263 rms_B_bonded: 4.25
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4255 r_free = 0.4255    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4255 r_free = 0.4255    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4255
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5972
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7448  Z= 0.120
  Angle     :  0.570  13.239  10129  Z= 0.277
  Chirality :  0.037   0.240   1136
  Planarity :  0.005   0.047   1316
  Dihedral  :  3.710  16.542   1010
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 13.38 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.28), residues: 917
  helix:  2.17 (0.21), residues: 605
  sheet: -0.03 (0.98), residues: 32
  loop :  0.57 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1154 
 HIS   0.008   0.001   HIS A 920 
 PHE   0.013   0.001   PHE A 802 
 TYR   0.015   0.001   TYR A 999 
 ARG   0.003   0.000   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03857 (  465)
  hydrogen bonds       : angle       3.99334 ( 1359)
  covalent geometry    : bond        0.00269 ( 7448)
  covalent geometry    : angle       0.56997 (10129)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  282 TYR cc_start: 0.6409 (t80) cc_final: 0.6036 (t80)
REVERT: A  503 GLU cc_start: 0.6253 (tp30) cc_final: 0.5885 (tp30)
REVERT: A  522 GLN cc_start: 0.7005 (tp40) cc_final: 0.6519 (tp40)
REVERT: A  899 MET cc_start: 0.4123 (mtt) cc_final: 0.3879 (mtt)
REVERT: A 1153 TYR cc_start: 0.6901 (m-10) cc_final: 0.6505 (m-10)
  outliers start: 5
  outliers final: 5
  residues processed: 92
  average time/residue: 0.2101
  time to fit residues: 25.9705
Evaluate side-chains
  90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1124 ILE
Chi-restraints excluded: chain A residue 1148 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0060
   chunk 79 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 16 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0870
   chunk 33 optimal weight:    0.0020
   overall best weight:    0.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
** A 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1165 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.202421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.174070 restraints weight = 27463.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.4237 rms_B_bonded: 4.73
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4237
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4237 r_free = 0.4237    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4237 r_free = 0.4237    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.4237
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6008
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7448  Z= 0.131
  Angle     :  0.586  13.347  10129  Z= 0.285
  Chirality :  0.038   0.216   1136
  Planarity :  0.005   0.047   1316
  Dihedral  :  3.699  17.663   1010
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 13.51 %
    Favored  : 85.58 %
  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:  2.40 (0.28), residues: 917
  helix:  2.18 (0.21), residues: 605
  sheet: -0.07 (0.98), residues: 32
  loop :  0.60 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1154 
 HIS   0.009   0.001   HIS A 920 
 PHE   0.015   0.002   PHE A 802 
 TYR   0.015   0.001   TYR A 999 
 ARG   0.004   0.000   ARG A 516 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03925 (  465)
  hydrogen bonds       : angle       3.97711 ( 1359)
  covalent geometry    : bond        0.00303 ( 7448)
  covalent geometry    : angle       0.58625 (10129)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4613.59 seconds
wall clock time: 84 minutes 25.31 seconds (5065.31 seconds total)