Starting phenix.real_space_refine
on Wed May 14 11:47:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oef_16825/05_2025/8oef_16825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oef_16825/05_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_16825/05_2025/8oef_16825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oef_16825/05_2025/8oef_16825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oef_16825/05_2025/8oef_16825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oef_16825/05_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-5687/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: 5.19, per 1000 atoms: 0.54
  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: 2.72
  Conformation dependent library (CDL) restraints added in 662.8 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: 0.74
  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: 3.00

  Time building geometry restraints manager: 3.43 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:             1.450
  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:             0.180
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     24.060
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.170
-------------------------------------------------------------------------------
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  : 0.690 
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: 0.4089
  time to fit residues: 34.4413
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  : 0.720 
-------------------------------------------------------------------------------
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 = 37125.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.189147 restraints weight = 22015.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.195017 restraints weight = 14036.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.4695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4750
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       5.41421 (  642)
  SS BOND              : bond        0.00358 (    1)
  SS BOND              : angle       0.31583 (    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  : 0.746 
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: 0.7655 (m-80) cc_final: 0.7093 (m-80)
REVERT: A 1244 PHE cc_start: 0.4250 (t80) cc_final: 0.3625 (t80)
  outliers start: 3
  outliers final: 1
  residues processed: 75
  average time/residue: 0.3620
  time to fit residues: 35.0345
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  : 0.812 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4833 r_free = 0.4833 target = 0.206175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.175542 restraints weight = 37090.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.184818 restraints weight = 21574.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.190887 restraints weight = 13452.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.4642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4889
moved from start:          0.1713

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= 0.131
  Angle     :  0.505   4.773   6675  Z= 0.265
  Chirality :  0.039   0.154    767
  Planarity :  0.004   0.047    840
  Dihedral  :  3.487  13.371    651
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 10.27 %
    Favored  : 88.59 %
  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:  1.03 (0.35), residues: 592
  helix:  1.71 (0.31), residues: 264
  sheet: -0.70 (0.64), residues: 55
  loop :  0.06 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.011   0.001   PHE A 382 
 TYR   0.007   0.001   TYR A1171 
 ARG   0.003   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05056 (  219)
  hydrogen bonds       : angle       4.92474 (  642)
  SS BOND              : bond        0.00301 (    1)
  SS BOND              : angle       0.19502 (    2)
  covalent geometry    : bond        0.00275 ( 4930)
  covalent geometry    : angle       0.50464 ( 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
  80 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.737 
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: 0.7539 (m-80) cc_final: 0.7047 (m-80)
REVERT: A 1269 LYS cc_start: 0.8787 (tptt) cc_final: 0.8055 (tptt)
  outliers start: 6
  outliers final: 5
  residues processed: 78
  average time/residue: 0.4195
  time to fit residues: 41.4690
Evaluate side-chains
  76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
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 1266 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.4801 r_free = 0.4801 target = 0.202697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.172180 restraints weight = 36840.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.181118 restraints weight = 21433.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.187203 restraints weight = 13420.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.4607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5013
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4931  Z= 0.153
  Angle     :  0.545   8.964   6675  Z= 0.282
  Chirality :  0.039   0.146    767
  Planarity :  0.004   0.045    840
  Dihedral  :  3.709  14.635    651
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.27 %
    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:  0.85 (0.35), residues: 592
  helix:  1.72 (0.32), residues: 258
  sheet: -0.85 (0.67), residues: 55
  loop : -0.17 (0.40), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1238 
 HIS   0.005   0.001   HIS A1024 
 PHE   0.014   0.001   PHE A 382 
 TYR   0.014   0.001   TYR A1009 
 ARG   0.002   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04562 (  219)
  hydrogen bonds       : angle       4.85432 (  642)
  SS BOND              : bond        0.00178 (    1)
  SS BOND              : angle       0.20419 (    2)
  covalent geometry    : bond        0.00323 ( 4930)
  covalent geometry    : angle       0.54546 ( 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
  81 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.734 
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 1269 LYS cc_start: 0.8792 (tptt) cc_final: 0.8056 (tptt)
  outliers start: 8
  outliers final: 7
  residues processed: 77
  average time/residue: 0.3960
  time to fit residues: 38.2888
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  : 0.717 
-------------------------------------------------------------------------------
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 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:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.4752 r_free = 0.4752 target = 0.197644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.165671 restraints weight = 33246.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.174645 restraints weight = 19467.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.180772 restraints weight = 12378.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5235
moved from start:          0.3293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4931  Z= 0.198
  Angle     :  0.586   5.338   6675  Z= 0.313
  Chirality :  0.041   0.149    767
  Planarity :  0.005   0.043    840
  Dihedral  :  4.153  17.621    651
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.22 %
    Favored  : 87.07 %
  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:  0.16 (0.34), residues: 592
  helix:  1.29 (0.31), residues: 259
  sheet: -1.28 (0.66), residues: 55
  loop : -0.70 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1238 
 HIS   0.006   0.001   HIS A1286 
 PHE   0.024   0.002   PHE A1244 
 TYR   0.011   0.002   TYR A1245 
 ARG   0.004   0.001   ARG A 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04857 (  219)
  hydrogen bonds       : angle       4.97610 (  642)
  SS BOND              : bond        0.00302 (    1)
  SS BOND              : angle       0.31822 (    2)
  covalent geometry    : bond        0.00409 ( 4930)
  covalent geometry    : angle       0.58564 ( 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
  85 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.802 
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: 0.8694 (mm-30) cc_final: 0.8443 (mm-30)
REVERT: A  462 PHE cc_start: 0.7524 (m-80) cc_final: 0.7313 (m-80)
REVERT: A 1269 LYS cc_start: 0.8823 (tptt) cc_final: 0.8090 (tptt)
REVERT: A 1316 LYS cc_start: 0.8599 (mptt) cc_final: 0.8213 (tptp)
  outliers start: 9
  outliers final: 7
  residues processed: 82
  average time/residue: 0.4182
  time to fit residues: 43.1135
Evaluate side-chains
  79 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
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  570 ASP
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4769 r_free = 0.4769 target = 0.198926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.166484 restraints weight = 34809.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.175799 restraints weight = 20314.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.182090 restraints weight = 12818.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.4590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5167
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4931  Z= 0.123
  Angle     :  0.510   5.142   6675  Z= 0.266
  Chirality :  0.039   0.139    767
  Planarity :  0.004   0.043    840
  Dihedral  :  3.924  15.817    651
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.36 %
    Favored  : 86.31 %
  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:  0.36 (0.35), residues: 592
  helix:  1.50 (0.32), residues: 259
  sheet: -1.29 (0.66), residues: 55
  loop : -0.60 (0.38), 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   0.010   0.001   PHE A 382 
 TYR   0.016   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04094 (  219)
  hydrogen bonds       : angle       4.68263 (  642)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.01423 (    2)
  covalent geometry    : bond        0.00270 ( 4930)
  covalent geometry    : angle       0.50998 ( 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
  84 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.760 
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: 0.8756 (mm-30) cc_final: 0.8467 (mm-30)
REVERT: A  462 PHE cc_start: 0.7484 (m-80) cc_final: 0.7244 (m-80)
REVERT: A 1269 LYS cc_start: 0.8780 (tptt) cc_final: 0.8061 (tptt)
  outliers start: 7
  outliers final: 7
  residues processed: 82
  average time/residue: 0.4011
  time to fit residues: 41.4585
Evaluate side-chains
  82 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
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 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:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A1193 GLN
A1298 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4728 r_free = 0.4728 target = 0.194284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.161728 restraints weight = 34108.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.170793 restraints weight = 19974.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.176857 restraints weight = 12675.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.4536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5327
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   4931  Z= 0.189
  Angle     :  0.566   4.526   6675  Z= 0.303
  Chirality :  0.040   0.136    767
  Planarity :  0.005   0.045    840
  Dihedral  :  4.260  17.241    651
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 12.93 %
    Favored  : 85.55 %
  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:  0.03 (0.35), residues: 592
  helix:  1.28 (0.31), residues: 259
  sheet: -1.52 (0.68), residues: 55
  loop : -0.83 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1238 
 HIS   0.005   0.001   HIS A1090 
 PHE   0.012   0.002   PHE A 440 
 TYR   0.008   0.002   TYR A1009 
 ARG   0.003   0.000   ARG A 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04514 (  219)
  hydrogen bonds       : angle       4.90111 (  642)
  SS BOND              : bond        0.00252 (    1)
  SS BOND              : angle       0.50134 (    2)
  covalent geometry    : bond        0.00396 ( 4930)
  covalent geometry    : angle       0.56570 ( 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
  87 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.685 
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: 0.8754 (mm-30) cc_final: 0.8493 (mm-30)
REVERT: A  462 PHE cc_start: 0.7511 (m-80) cc_final: 0.7192 (m-80)
REVERT: A 1269 LYS cc_start: 0.8787 (tptt) cc_final: 0.8108 (tptt)
  outliers start: 8
  outliers final: 8
  residues processed: 84
  average time/residue: 0.3952
  time to fit residues: 41.5444
Evaluate side-chains
  84 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
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  447 CYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 11 optimal weight:    8.9990
   chunk 35 optimal weight:    0.1980
   chunk 51 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.7922

-------------------------------------------------------------------------------
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 = 0.4744 r_free = 0.4744 target = 0.195775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.163123 restraints weight = 34415.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.172338 restraints weight = 20000.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.178577 restraints weight = 12636.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.4553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5268
moved from start:          0.4156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4931  Z= 0.131
  Angle     :  0.526   4.804   6675  Z= 0.277
  Chirality :  0.039   0.136    767
  Planarity :  0.004   0.047    840
  Dihedral  :  4.123  16.013    651
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.93 %
    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:  0.25 (0.35), residues: 592
  helix:  1.46 (0.31), residues: 259
  sheet: -1.39 (0.68), residues: 55
  loop : -0.71 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A1024 
 PHE   0.010   0.001   PHE A 440 
 TYR   0.016   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04055 (  219)
  hydrogen bonds       : angle       4.66783 (  642)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       0.14702 (    2)
  covalent geometry    : bond        0.00286 ( 4930)
  covalent geometry    : angle       0.52578 ( 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
  89 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.711 
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: A  318 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8451 (mm-30)
REVERT: A  462 PHE cc_start: 0.7490 (m-80) cc_final: 0.7185 (m-80)
REVERT: A 1269 LYS cc_start: 0.8769 (tptt) cc_final: 0.8088 (tptt)
  outliers start: 11
  outliers final: 11
  residues processed: 84
  average time/residue: 0.3863
  time to fit residues: 40.9460
Evaluate side-chains
  86 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
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 1042 LEU
Chi-restraints excluded: chain A residue 1061 VAL
Chi-restraints excluded: chain A residue 1062 CYS
Chi-restraints excluded: chain A residue 1181 LEU
Chi-restraints excluded: chain A residue 1266 THR
Chi-restraints excluded: chain A residue 1278 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:    0.0770
   chunk 60 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0980
   chunk 49 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0270
   overall best weight:    0.1796

-------------------------------------------------------------------------------
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 = 0.4788 r_free = 0.4788 target = 0.200332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.169072 restraints weight = 33625.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.178029 restraints weight = 19127.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.184223 restraints weight = 11938.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.4622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5109
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4931  Z= 0.100
  Angle     :  0.496   4.452   6675  Z= 0.258
  Chirality :  0.039   0.141    767
  Planarity :  0.004   0.046    840
  Dihedral  :  3.775  13.993    651
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 13.88 %
    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:  0.74 (0.36), residues: 592
  helix:  1.86 (0.31), residues: 259
  sheet: -1.22 (0.68), residues: 55
  loop : -0.42 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A1209 
 HIS   0.004   0.001   HIS A1286 
 PHE   0.008   0.001   PHE A 462 
 TYR   0.017   0.001   TYR A1009 
 ARG   0.004   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03526 (  219)
  hydrogen bonds       : angle       4.32649 (  642)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       0.34017 (    2)
  covalent geometry    : bond        0.00225 ( 4930)
  covalent geometry    : angle       0.49620 ( 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
  87 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.814 
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: A  318 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8416 (mm-30)
REVERT: A  462 PHE cc_start: 0.7466 (m-80) cc_final: 0.7165 (m-80)
REVERT: A 1269 LYS cc_start: 0.8695 (tptt) cc_final: 0.7987 (tptt)
  outliers start: 6
  outliers final: 5
  residues processed: 84
  average time/residue: 0.3956
  time to fit residues: 42.0802
Evaluate side-chains
  84 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   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:    0.6980
   chunk 32 optimal weight:    0.1980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4760 r_free = 0.4760 target = 0.198146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.165590 restraints weight = 33586.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.174696 restraints weight = 19372.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4575 r_free = 0.4575 target = 0.181015 restraints weight = 12263.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.4599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5213
moved from start:          0.4356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4931  Z= 0.116
  Angle     :  0.508   5.763   6675  Z= 0.266
  Chirality :  0.039   0.179    767
  Planarity :  0.004   0.046    840
  Dihedral  :  3.816  14.072    651
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  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:  0.69 (0.35), residues: 592
  helix:  1.84 (0.31), residues: 259
  sheet: -1.21 (0.68), residues: 55
  loop : -0.49 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1238 
 HIS   0.003   0.001   HIS A1024 
 PHE   0.016   0.001   PHE A1244 
 TYR   0.014   0.001   TYR A1009 
 ARG   0.003   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03704 (  219)
  hydrogen bonds       : angle       4.39656 (  642)
  SS BOND              : bond        0.00138 (    1)
  SS BOND              : angle       0.51396 (    2)
  covalent geometry    : bond        0.00256 ( 4930)
  covalent geometry    : angle       0.50837 ( 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
  83 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.798 
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: A  318 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8375 (mm-30)
REVERT: A  462 PHE cc_start: 0.7383 (m-80) cc_final: 0.7119 (m-80)
REVERT: A 1269 LYS cc_start: 0.8780 (tptt) cc_final: 0.8092 (tptt)
  outliers start: 5
  outliers final: 5
  residues processed: 81
  average time/residue: 0.3940
  time to fit residues: 40.1890
Evaluate side-chains
  83 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
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
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:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 10 optimal weight:    0.3980
   chunk 30 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4755 r_free = 0.4755 target = 0.197170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.164148 restraints weight = 33639.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.173343 restraints weight = 19635.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.179756 restraints weight = 12521.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.4596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5228
moved from start:          0.4483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4931  Z= 0.111
  Angle     :  0.501   5.388   6675  Z= 0.262
  Chirality :  0.039   0.164    767
  Planarity :  0.004   0.046    840
  Dihedral  :  3.839  14.486    651
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 14.26 %
    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:  0.71 (0.35), residues: 592
  helix:  1.82 (0.31), residues: 264
  sheet: -1.17 (0.68), residues: 55
  loop : -0.49 (0.40), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A1024 
 PHE   0.013   0.001   PHE A1244 
 TYR   0.015   0.001   TYR A1009 
 ARG   0.004   0.000   ARG A1022 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03635 (  219)
  hydrogen bonds       : angle       4.38364 (  642)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       0.24819 (    2)
  covalent geometry    : bond        0.00246 ( 4930)
  covalent geometry    : angle       0.50155 ( 6673)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3940.01 seconds
wall clock time: 68 minutes 34.54 seconds (4114.54 seconds total)