Starting phenix.real_space_refine
on Tue Jul 29 22:40:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oef_16825/07_2025/8oef_16825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oef_16825/07_2025/8oef_16825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oef_16825/07_2025/8oef_16825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oef_16825/07_2025/8oef_16825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oef_16825/07_2025/8oef_16825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oef_16825/07_2025/8oef_16825.cif"
  }
  resolution = 4.0
  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=   0.026
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 2315 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
     S      22      5.16       5
     C    3130      2.51       5
     N     828      2.21       5
     O     848      1.98       5
     H    4859      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9687
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 9687
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 31, 'TRANS': 580}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 124
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 13, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 103
  Time building chain proxies: 5.76, per 1000 atoms: 0.59
  Number of scatterers: 9687
  At special positions: 0
  Unit cell: (73.959, 80.607, 114.678, 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)
     S      22     16.00
     O     848      8.00
     N     828      7.00
     C    3130      6.00
     H    4859      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 447 " - pdb=" SG  CYS A 621 " distance=2.03

  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: 2.88
  Conformation dependent library (CDL) restraints added in 704.7 milliseconds
  

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 4 sheets defined
      51.0% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 293 through 307
      removed outlier: 3.735A  pdb=" N   ASP A 300 " --> pdb=" O   GLY A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 328
      removed outlier: 3.523A  pdb=" N   ILE A 319 " --> pdb=" O   GLN A 315 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ASN A 325 " --> pdb=" O   ARG A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 345
    Processing helix  chain 'A' and resid 364 through 378
    Processing helix  chain 'A' and resid 413 through 430
      removed outlier: 3.582A  pdb=" N   LYS A 421 " --> pdb=" O   CYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 448
      removed outlier: 3.536A  pdb=" N   LEU A 436 " --> pdb=" O   LYS A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 473
      removed outlier: 3.997A  pdb=" N   PHE A 462 " --> pdb=" O   PRO A 458 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA A 463 " --> pdb=" O   PRO A 459 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LEU A 464 " --> pdb=" O   TYR A 460 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   MET A 465 " --> pdb=" O   VAL A 461 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 466 " --> pdb=" O   PHE A 462 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   LEU A 470 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 494
    Processing helix  chain 'A' and resid 550 through 564
      removed outlier: 4.032A  pdb=" N   LEU A 554 " --> pdb=" O   PRO A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 587
      removed outlier: 3.904A  pdb=" N   LYS A 586 " --> pdb=" O   SER A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 626
      removed outlier: 3.687A  pdb=" N   PHE A 615 " --> pdb=" O   SER A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1013
      removed outlier: 3.692A  pdb=" N   PHE A1012 " --> pdb=" O   CYS A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1037
      removed outlier: 3.898A  pdb=" N   ASP A1036 " --> pdb=" O   PHE A1032 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1090
      removed outlier: 3.532A  pdb=" N   VAL A1086 " --> pdb=" O   GLU A1082 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LYS A1089 " --> pdb=" O   ARG A1085 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   HIS A1090 " --> pdb=" O   VAL A1086 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1124 through 1140
      removed outlier: 3.614A  pdb=" N   ILE A1140 " --> pdb=" O   ALA A1136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1158
      removed outlier: 3.826A  pdb=" N   LYS A1145 " --> pdb=" O   ASP A1141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1184
    Processing helix  chain 'A' and resid 1219 through 1224
      removed outlier: 3.599A  pdb=" N   TYR A1223 " --> pdb=" O   GLU A1219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1233 through 1247
      removed outlier: 3.520A  pdb=" N   LEU A1242 " --> pdb=" O   TRP A1238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1265 through 1270
      removed outlier: 4.391A  pdb=" N   LYS A1269 " --> pdb=" O   THR A1265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1293 through 1313
      removed outlier: 3.547A  pdb=" N   ILE A1313 " --> pdb=" O   ARG A1309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1326 through 1330
    Processing helix  chain 'A' and resid 1331 through 1336
    Processing sheet with id=AA1, first strand: chain 'A' and resid 335 through 338
      removed outlier: 6.672A  pdb=" N   VAL A 353 " --> pdb=" O   LYS A 408 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   SER A 410 " --> pdb=" O   VAL A 353 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ILE A 355 " --> pdb=" O   SER A 410 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   VAL A 395 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ASP A 388 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ARG A 399 " --> pdb=" O   ASP A 384 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   ASP A 384 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 498 through 502
      removed outlier: 7.102A  pdb=" N   ILE A 508 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   ILE A 502 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   VAL A 506 " --> pdb=" O   ILE A 502 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY A 535 " --> pdb=" O   TRP A 509 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 572 through 573
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1040 through 1045

    219 hydrogen bonds defined for protein.
    642 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: 3.48

  Time building geometry restraints manager: 3.50 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4845
        1.03 -     1.23: 14
        1.23 -     1.42: 2021
        1.42 -     1.62: 2879
        1.62 -     1.81: 30
  Bond restraints: 9789
  Sorted by residual:
  bond pdb=" CB  ASP A1036 "
       pdb=" CG  ASP A1036 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.03e+00
  bond pdb=" CB  GLN A 315 "
       pdb=" CG  GLN A 315 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.10e-01
  bond pdb=" CB  GLN A 402 "
       pdb=" CG  GLN A 402 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.01e-01
  bond pdb=" N   VAL A 409 "
       pdb=" CA  VAL A 409 "
    ideal  model  delta    sigma   weight residual
    1.465  1.475 -0.010 1.38e-02 5.25e+03 4.93e-01
  bond pdb=" N   ARG A 345 "
       pdb=" CA  ARG A 345 "
    ideal  model  delta    sigma   weight residual
    1.457  1.466 -0.009 1.29e-02 6.01e+03 4.54e-01
  ... (remaining 9784 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.90: 17719
        5.90 -    11.80: 0
       11.80 -    17.70: 0
       17.70 -    23.60: 2
       23.60 -    29.50: 4
  Bond angle restraints: 17725
  Sorted by residual:
  angle pdb=" CG1 ILE A 618 "
        pdb=" CD1 ILE A 618 "
        pdb="HD11 ILE A 618 "
      ideal   model   delta    sigma   weight residual
     109.00   79.50   29.50 3.00e+00 1.11e-01 9.67e+01
  angle pdb=" CG1 ILE A 618 "
        pdb=" CD1 ILE A 618 "
        pdb="HD13 ILE A 618 "
      ideal   model   delta    sigma   weight residual
     109.00   79.66   29.34 3.00e+00 1.11e-01 9.57e+01
  angle pdb="HD11 ILE A 618 "
        pdb=" CD1 ILE A 618 "
        pdb="HD12 ILE A 618 "
      ideal   model   delta    sigma   weight residual
     110.00   81.10   28.90 3.00e+00 1.11e-01 9.28e+01
  angle pdb="HD12 ILE A 618 "
        pdb=" CD1 ILE A 618 "
        pdb="HD13 ILE A 618 "
      ideal   model   delta    sigma   weight residual
     110.00   81.19   28.81 3.00e+00 1.11e-01 9.22e+01
  angle pdb="HD11 ILE A 618 "
        pdb=" CD1 ILE A 618 "
        pdb="HD13 ILE A 618 "
      ideal   model   delta    sigma   weight residual
     110.00  132.66  -22.66 3.00e+00 1.11e-01 5.71e+01
  ... (remaining 17720 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.55: 4074
       16.55 -    33.09: 389
       33.09 -    49.63: 102
       49.63 -    66.18: 28
       66.18 -    82.72: 9
  Dihedral angle restraints: 4602
    sinusoidal: 2491
      harmonic: 2111
  Sorted by residual:
  dihedral pdb=" CA  ASP A 597 "
           pdb=" CB  ASP A 597 "
           pdb=" CG  ASP A 597 "
           pdb=" OD1 ASP A 597 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.86   56.86     1      2.00e+01 2.50e-03 1.09e+01
  dihedral pdb=" CG  ARG A1132 "
           pdb=" CD  ARG A1132 "
           pdb=" NE  ARG A1132 "
           pdb=" CZ  ARG A1132 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.77  -43.77     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CB  ARG A 534 "
           pdb=" CG  ARG A 534 "
           pdb=" CD  ARG A 534 "
           pdb=" NE  ARG A 534 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  126.44   53.56     3      1.50e+01 4.44e-03 9.21e+00
  ... (remaining 4599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 493
       0.025 -    0.050: 170
       0.050 -    0.076: 44
       0.076 -    0.101: 32
       0.101 -    0.126: 28
  Chirality restraints: 767
  Sorted by residual:
  chirality pdb=" CA  ILE A1189 "
            pdb=" N   ILE A1189 "
            pdb=" C   ILE A1189 "
            pdb=" CB  ILE A1189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.96e-01
  chirality pdb=" CA  ILE A 383 "
            pdb=" N   ILE A 383 "
            pdb=" C   ILE A 383 "
            pdb=" CB  ILE A 383 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  chirality pdb=" CA  ILE A 502 "
            pdb=" N   ILE A 502 "
            pdb=" C   ILE A 502 "
            pdb=" CB  ILE A 502 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  ... (remaining 764 not shown)

  Planarity restraints: 1410
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1013 "    0.032 5.00e-02 4.00e+02   4.86e-02 3.78e+00
        pdb=" N   PRO A1014 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A1014 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1014 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A1017 "   -0.006 2.00e-02 2.50e+03   1.19e-02 1.41e+00
        pdb=" C   ILE A1017 "    0.021 2.00e-02 2.50e+03
        pdb=" O   ILE A1017 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLU A1018 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1185 "   -0.019 5.00e-02 4.00e+02   2.79e-02 1.25e+00
        pdb=" N   PRO A1186 "    0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO A1186 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A1186 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1407 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 565
        2.21 -     2.80: 20212
        2.80 -     3.40: 26175
        3.40 -     4.00: 32770
        4.00 -     4.60: 50327
  Nonbonded interactions: 130049
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 311 "
            pdb=" H   GLU A 311 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" H   THR A1015 "
            pdb=" OE1 GLU A1018 "
     model   vdw
     1.637 2.450
  nonbonded pdb=" O   PHE A 561 "
            pdb=" H   PHE A 566 "
     model   vdw
     1.689 2.450
  nonbonded pdb=" O   HIS A1111 "
            pdb=" H   GLY A1115 "
     model   vdw
     1.690 2.450
  nonbonded pdb=" HH  TYR A1171 "
            pdb=" OD1 ASP A1280 "
     model   vdw
     1.706 2.450
  ... (remaining 130044 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.080
  Construct map_model_manager:             0.190
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     26.480
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4623
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   0.027   4931  Z= 0.095
  Angle     :  0.473   4.775   6675  Z= 0.238
  Chirality :  0.037   0.126    767
  Planarity :  0.003   0.049    840
  Dihedral  : 15.212  82.725   1808
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.98 %
    Favored  : 88.02 %
  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:  0.95 (0.35), residues: 592
  helix:  1.53 (0.32), residues: 253
  sheet: -1.02 (0.63), residues: 60
  loop :  0.31 (0.40), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 485 
 HIS   0.010   0.001   HIS A1090 
 PHE   0.013   0.001   PHE A 382 
 TYR   0.014   0.001   TYR A 481 
 ARG   0.008   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24719 (  219)
  hydrogen bonds       : angle       7.08863 (  642)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.21348 (    2)
  covalent geometry    : bond        0.00212 ( 4930)
  covalent geometry    : angle       0.47337 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  67 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1149 TYR cc_start: 0.7494 (m-80) cc_final: 0.7122 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.4000
  time to fit residues: 33.7581
Evaluate side-chains
  66 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0770
   chunk 25 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 24 optimal weight:    0.1980
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 35 optimal weight:    0.1980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
A 358 GLN
A 610 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.210461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.179885 restraints weight = 37125.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.189145 restraints weight = 22014.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.195039 restraints weight = 14036.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.4697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4749
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4931  Z= 0.129
  Angle     :  0.521   5.233   6675  Z= 0.276
  Chirality :  0.039   0.155    767
  Planarity :  0.004   0.045    840
  Dihedral  :  3.334  14.477    651
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 10.65 %
    Favored  : 88.78 %
  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:  0.96 (0.35), residues: 592
  helix:  1.50 (0.31), residues: 263
  sheet: -1.00 (0.60), residues: 60
  loop :  0.30 (0.40), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 555 
 HIS   0.004   0.001   HIS A1090 
 PHE   0.014   0.001   PHE A 615 
 TYR   0.014   0.001   TYR A1009 
 ARG   0.002   0.000   ARG A1088 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05999 (  219)
  hydrogen bonds       : angle       5.41414 (  642)
  SS BOND              : bond        0.00358 (    1)
  SS BOND              : angle       0.31596 (    2)
  covalent geometry    : bond        0.00257 ( 4930)
  covalent geometry    : angle       0.52074 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.724 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1149 TYR cc_start: 0.7646 (m-80) cc_final: 0.7086 (m-80)
REVERT: A 1244 PHE cc_start: 0.4245 (t80) cc_final: 0.3620 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 75
  average time/residue: 0.3708
  time to fit residues: 36.0264
Evaluate side-chains
  69 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1042 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 16 optimal weight:    0.0870
   chunk 49 optimal weight:    0.5980
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 40 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.4758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.207812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.178670 restraints weight = 36869.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.187611 restraints weight = 21443.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.193339 restraints weight = 13433.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4785
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4931  Z= 0.109
  Angle     :  0.479   4.588   6675  Z= 0.249
  Chirality :  0.039   0.150    767
  Planarity :  0.003   0.046    840
  Dihedral  :  3.332  13.187    651
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.65 %
    Favored  : 88.40 %
  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:  1.13 (0.35), residues: 592
  helix:  1.74 (0.31), residues: 264
  sheet: -0.62 (0.61), residues: 55
  loop :  0.17 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 555 
 HIS   0.003   0.001   HIS A1024 
 PHE   0.011   0.001   PHE A 382 
 TYR   0.005   0.001   TYR A1009 
 ARG   0.002   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04955 (  219)
  hydrogen bonds       : angle       4.87835 (  642)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       0.08960 (    2)
  covalent geometry    : bond        0.00228 ( 4930)
  covalent geometry    : angle       0.47917 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  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: symmetry clash
   revert: symmetry clash
REVERT: A 1149 TYR cc_start: 0.7595 (m-80) cc_final: 0.7071 (m-80)
REVERT: A 1244 PHE cc_start: 0.4355 (t80) cc_final: 0.4043 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 74
  average time/residue: 0.3926
  time to fit residues: 37.0506
Evaluate side-chains
  71 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ARG
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1266 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0870
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 43 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 32 optimal weight:    0.1980
   overall best weight:    0.4958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.207749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.177719 restraints weight = 36903.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.186847 restraints weight = 21413.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.192826 restraints weight = 13353.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4825
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4931  Z= 0.106
  Angle     :  0.473   4.430   6675  Z= 0.243
  Chirality :  0.039   0.144    767
  Planarity :  0.004   0.044    840
  Dihedral  :  3.371  14.451    651
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.46 %
    Favored  : 88.21 %
  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:  1.23 (0.35), residues: 592
  helix:  1.85 (0.31), residues: 264
  sheet: -0.73 (0.62), residues: 55
  loop :  0.23 (0.41), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1238 
 HIS   0.003   0.001   HIS A1286 
 PHE   0.012   0.001   PHE A 382 
 TYR   0.015   0.001   TYR A1009 
 ARG   0.006   0.000   ARG A1165 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04238 (  219)
  hydrogen bonds       : angle       4.68143 (  642)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       0.28644 (    2)
  covalent geometry    : bond        0.00229 ( 4930)
  covalent geometry    : angle       0.47272 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  78 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.586 
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: symmetry clash
   revert: symmetry clash
REVERT: A 1244 PHE cc_start: 0.4426 (t80) cc_final: 0.4174 (t80)
REVERT: A 1269 LYS cc_start: 0.8773 (tptt) cc_final: 0.8029 (tptt)
  outliers start: 7
  outliers final: 7
  residues processed: 75
  average time/residue: 0.4715
  time to fit residues: 45.7594
Evaluate side-chains
  77 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 1.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ARG
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1062 CYS
Chi-restraints excluded: chain A residue 1157 MET
Chi-restraints excluded: chain A residue 1266 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
A 472 GLN
** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.201278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.170373 restraints weight = 36046.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.178904 restraints weight = 21564.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.184810 restraints weight = 13920.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.4587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5103
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4931  Z= 0.189
  Angle     :  0.566   9.628   6675  Z= 0.296
  Chirality :  0.040   0.143    767
  Planarity :  0.004   0.044    840
  Dihedral  :  3.773  15.953    651
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.46 %
    Favored  : 87.83 %
  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:  0.88 (0.35), residues: 592
  helix:  1.79 (0.32), residues: 259
  sheet: -0.94 (0.66), residues: 55
  loop : -0.19 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1238 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.011   0.001   PHE A 382 
 TYR   0.008   0.001   TYR A1171 
 ARG   0.003   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04639 (  219)
  hydrogen bonds       : angle       4.80338 (  642)
  SS BOND              : bond        0.00274 (    1)
  SS BOND              : angle       0.44290 (    2)
  covalent geometry    : bond        0.00393 ( 4930)
  covalent geometry    : angle       0.56627 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  82 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.745 
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: symmetry clash
REVERT: A  318 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8523 (mm-30)
REVERT: A  462 PHE cc_start: 0.7474 (m-80) cc_final: 0.7231 (m-80)
REVERT: A  566 PHE cc_start: 0.6738 (t80) cc_final: 0.6327 (t80)
REVERT: A 1269 LYS cc_start: 0.8829 (tptt) cc_final: 0.8100 (tptt)
  outliers start: 9
  outliers final: 8
  residues processed: 78
  average time/residue: 0.5310
  time to fit residues: 53.9074
Evaluate side-chains
  80 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 1.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ARG
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1062 CYS
Chi-restraints excluded: chain A residue 1157 MET
Chi-restraints excluded: chain A residue 1266 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1111 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4785 r_free = 0.4785 target = 0.200308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.168758 restraints weight = 34178.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.177651 restraints weight = 19727.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.183917 restraints weight = 12400.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.4614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5123
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4931  Z= 0.150
  Angle     :  0.532   4.484   6675  Z= 0.278
  Chirality :  0.040   0.140    767
  Planarity :  0.004   0.043    840
  Dihedral  :  3.859  15.076    651
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.03 %
    Favored  : 87.26 %
  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:  0.66 (0.35), residues: 592
  helix:  1.67 (0.31), residues: 259
  sheet: -1.14 (0.66), residues: 55
  loop : -0.35 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1238 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.018   0.002   PHE A1244 
 TYR   0.009   0.001   TYR A1245 
 ARG   0.003   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04342 (  219)
  hydrogen bonds       : angle       4.71591 (  642)
  SS BOND              : bond        0.00243 (    1)
  SS BOND              : angle       0.32768 (    2)
  covalent geometry    : bond        0.00321 ( 4930)
  covalent geometry    : angle       0.53223 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  86 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.796 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8475 (mm-30)
REVERT: A  462 PHE cc_start: 0.7433 (m-80) cc_final: 0.7135 (m-80)
REVERT: A 1244 PHE cc_start: 0.4882 (t80) cc_final: 0.4616 (t80)
REVERT: A 1269 LYS cc_start: 0.8800 (tptt) cc_final: 0.8054 (tptt)
  outliers start: 9
  outliers final: 6
  residues processed: 84
  average time/residue: 0.3808
  time to fit residues: 41.0371
Evaluate side-chains
  81 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ARG
Chi-restraints excluded: chain A residue  447 CYS
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1062 CYS
Chi-restraints excluded: chain A residue 1266 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 415 ASN
** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1193 GLN
A1298 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.199670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.169449 restraints weight = 34291.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.177908 restraints weight = 20087.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.183857 restraints weight = 12724.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.4608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5135
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4931  Z= 0.133
  Angle     :  0.517   4.685   6675  Z= 0.270
  Chirality :  0.039   0.139    767
  Planarity :  0.004   0.042    840
  Dihedral  :  3.842  14.892    651
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.22 %
    Favored  : 86.69 %
  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:  0.66 (0.35), residues: 592
  helix:  1.71 (0.31), residues: 259
  sheet: -1.23 (0.66), residues: 55
  loop : -0.37 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.010   0.001   PHE A 382 
 TYR   0.017   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04050 (  219)
  hydrogen bonds       : angle       4.63033 (  642)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.20661 (    2)
  covalent geometry    : bond        0.00289 ( 4930)
  covalent geometry    : angle       0.51687 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  85 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.768 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8462 (mm-30)
REVERT: A  462 PHE cc_start: 0.7465 (m-80) cc_final: 0.7150 (m-80)
REVERT: A 1244 PHE cc_start: 0.4968 (t80) cc_final: 0.4659 (t80)
REVERT: A 1269 LYS cc_start: 0.8821 (tptt) cc_final: 0.8082 (tptt)
  outliers start: 11
  outliers final: 10
  residues processed: 80
  average time/residue: 0.4000
  time to fit residues: 40.6607
Evaluate side-chains
  82 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ARG
Chi-restraints excluded: chain A residue  447 CYS
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue 1017 ILE
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1062 CYS
Chi-restraints excluded: chain A residue 1157 MET
Chi-restraints excluded: chain A residue 1266 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.199151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.168505 restraints weight = 34421.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.177013 restraints weight = 19993.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.183033 restraints weight = 12626.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.4604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5172
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4931  Z= 0.135
  Angle     :  0.524   4.951   6675  Z= 0.274
  Chirality :  0.039   0.137    767
  Planarity :  0.004   0.041    840
  Dihedral  :  3.911  14.818    651
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.17 %
    Favored  : 85.74 %
  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:  0.70 (0.35), residues: 592
  helix:  1.75 (0.31), residues: 259
  sheet: -1.20 (0.68), residues: 55
  loop : -0.37 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.009   0.001   PHE A 440 
 TYR   0.013   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04000 (  219)
  hydrogen bonds       : angle       4.56199 (  642)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.14755 (    2)
  covalent geometry    : bond        0.00293 ( 4930)
  covalent geometry    : angle       0.52377 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.765 
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: symmetry clash
   revert: symmetry clash
REVERT: A  318 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8467 (mm-30)
REVERT: A  462 PHE cc_start: 0.7512 (m-80) cc_final: 0.7186 (m-80)
REVERT: A 1269 LYS cc_start: 0.8798 (tptt) cc_final: 0.8077 (tptt)
  outliers start: 11
  outliers final: 10
  residues processed: 80
  average time/residue: 0.4558
  time to fit residues: 48.1899
Evaluate side-chains
  80 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  345 ARG
Chi-restraints excluded: chain A residue  447 CYS
Chi-restraints excluded: chain A residue 1017 ILE
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1062 CYS
Chi-restraints excluded: chain A residue 1093 LEU
Chi-restraints excluded: chain A residue 1266 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 55 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4764 r_free = 0.4764 target = 0.198190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.167819 restraints weight = 34229.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.176180 restraints weight = 20295.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4581 r_free = 0.4581 target = 0.182000 restraints weight = 12954.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.4596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5196
moved from start:          0.3993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4931  Z= 0.131
  Angle     :  0.532   6.297   6675  Z= 0.280
  Chirality :  0.040   0.206    767
  Planarity :  0.004   0.041    840
  Dihedral  :  3.940  16.508    651
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.12 %
    Favored  : 85.17 %
  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:  0.65 (0.35), residues: 592
  helix:  1.78 (0.31), residues: 259
  sheet: -1.29 (0.68), residues: 55
  loop : -0.45 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1238 
 HIS   0.003   0.001   HIS A 309 
 PHE   0.020   0.001   PHE A1244 
 TYR   0.012   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  219)
  hydrogen bonds       : angle       4.50565 (  642)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       0.15685 (    2)
  covalent geometry    : bond        0.00285 ( 4930)
  covalent geometry    : angle       0.53216 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  83 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.756 
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: symmetry clash
   revert: symmetry clash
REVERT: A  318 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8463 (mm-30)
REVERT: A  462 PHE cc_start: 0.7414 (m-80) cc_final: 0.7090 (m-80)
REVERT: A 1269 LYS cc_start: 0.8765 (tptt) cc_final: 0.8073 (tptt)
  outliers start: 9
  outliers final: 8
  residues processed: 79
  average time/residue: 0.4694
  time to fit residues: 48.2803
Evaluate side-chains
  78 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 1.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  447 CYS
Chi-restraints excluded: chain A residue 1017 ILE
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1266 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0870
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4752 r_free = 0.4752 target = 0.196735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.163562 restraints weight = 33272.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.172405 restraints weight = 19491.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.178757 restraints weight = 12446.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.4551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5267
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4931  Z= 0.144
  Angle     :  0.547   6.306   6675  Z= 0.289
  Chirality :  0.040   0.148    767
  Planarity :  0.004   0.042    840
  Dihedral  :  4.095  16.207    651
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.12 %
    Favored  : 84.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.57 (0.35), residues: 592
  helix:  1.73 (0.31), residues: 259
  sheet: -1.31 (0.68), residues: 55
  loop : -0.53 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A1238 
 HIS   0.004   0.001   HIS A1024 
 PHE   0.015   0.001   PHE A1244 
 TYR   0.022   0.001   TYR A1009 
 ARG   0.004   0.001   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04084 (  219)
  hydrogen bonds       : angle       4.54977 (  642)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.24825 (    2)
  covalent geometry    : bond        0.00309 ( 4930)
  covalent geometry    : angle       0.54699 ( 6673)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU  998 is missing expected H atoms. Skipping.
Residue TYR 1137 is missing expected H atoms. Skipping.
Residue MET 1151 is missing expected H atoms. Skipping.
Residue ILE 1189 is missing expected H atoms. Skipping.
Residue MET 1296 is missing expected H atoms. Skipping.
Residue THR 1297 is missing expected H atoms. Skipping.
Evaluate side-chains
  85 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.645 
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: symmetry clash
   revert: symmetry clash
REVERT: A  318 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8391 (mm-30)
REVERT: A  462 PHE cc_start: 0.7398 (m-80) cc_final: 0.7048 (m-80)
REVERT: A 1269 LYS cc_start: 0.8773 (tptt) cc_final: 0.8071 (tptt)
  outliers start: 10
  outliers final: 9
  residues processed: 80
  average time/residue: 0.4685
  time to fit residues: 49.7404
Evaluate side-chains
  81 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  447 CYS
Chi-restraints excluded: chain A residue  570 ASP
Chi-restraints excluded: chain A residue 1017 ILE
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1280 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    0.0970
   chunk 43 optimal weight:    0.8980
   chunk 41 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0770
   chunk 30 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.4136

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

Flipped N/Q/H residues before XYZ refinement:
** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.198736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.166368 restraints weight = 33987.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.175256 restraints weight = 19831.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.181553 restraints weight = 12569.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.4606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5184
moved from start:          0.4294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4931  Z= 0.106
  Angle     :  0.522   6.505   6675  Z= 0.272
  Chirality :  0.039   0.145    767
  Planarity :  0.004   0.043    840
  Dihedral  :  3.884  15.046    651
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 14.64 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.82 (0.35), residues: 592
  helix:  1.94 (0.31), residues: 259
  sheet: -1.28 (0.66), residues: 55
  loop : -0.37 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1238 
 HIS   0.003   0.001   HIS A1024 
 PHE   0.007   0.001   PHE A 440 
 TYR   0.020   0.001   TYR A1009 
 ARG   0.004   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03629 (  219)
  hydrogen bonds       : angle       4.37915 (  642)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       0.06599 (    2)
  covalent geometry    : bond        0.00238 ( 4930)
  covalent geometry    : angle       0.52209 ( 6673)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4434.08 seconds
wall clock time: 81 minutes 53.59 seconds (4913.59 seconds total)