Starting phenix.real_space_refine
on Sat Aug 23 11:27:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oef_16825/08_2025/8oef_16825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oef_16825/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oef_16825/08_2025/8oef_16825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oef_16825/08_2025/8oef_16825.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oef_16825/08_2025/8oef_16825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oef_16825/08_2025/8oef_16825.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'GLU:plan': 13, 'ARG:plan': 3, 'ASP:plan': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 103
  Time building chain proxies: 1.63, per 1000 atoms: 0.17
  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: 0.57
  Conformation dependent library (CDL) restraints added in 124.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.15
  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: 1.49

  Time building geometry restraints manager: 0.78 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:             1.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.060
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     7.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.070
-------------------------------------------------------------------------------
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 : 5.68
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.008   0.000   ARG A1022 
 TYR   0.014   0.001   TYR A 481 
 PHE   0.013   0.001   PHE A 382 
 TRP   0.005   0.001   TRP A 485 
 HIS   0.010   0.001   HIS A1090 

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

*********************** 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  : 0.244 
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: 0.1635
  time to fit residues: 13.9136
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  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4823 r_free = 0.4823 target = 0.205441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.176916 restraints weight = 36843.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.185673 restraints weight = 21566.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.191222 restraints weight = 13521.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.194931 restraints weight = 8944.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.197522 restraints weight = 6198.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.4718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4812
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4931  Z= 0.180
  Angle     :  0.577   4.924   6675  Z= 0.309
  Chirality :  0.040   0.159    767
  Planarity :  0.004   0.047    840
  Dihedral  :  3.596  15.137    651
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 10.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.35), residues: 592
  helix:  1.38 (0.31), residues: 264
  sheet: -1.13 (0.62), residues: 60
  loop :  0.10 (0.41), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1022 
 TYR   0.014   0.001   TYR A1009 
 PHE   0.015   0.002   PHE A 615 
 TRP   0.010   0.001   TRP A 555 
 HIS   0.006   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 4930)
  covalent geometry    : angle       0.57654 ( 6673)
  SS BOND              : bond        0.00340 (    1)
  SS BOND              : angle       0.90762 (    2)
  hydrogen bonds       : bond        0.06234 (  219)
  hydrogen bonds       : angle       5.56726 (  642)

*********************** 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
  79 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.195 
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: 0.7677 (m-80) cc_final: 0.7204 (m-80)
REVERT: A 1244 PHE cc_start: 0.4364 (t80) cc_final: 0.3748 (t80)
REVERT: A 1269 LYS cc_start: 0.8790 (tptt) cc_final: 0.8090 (tptt)
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 0.1790
  time to fit residues: 16.8542
Evaluate side-chains
  73 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  308 LEU
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 1157 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0980
   overall best weight:    0.5582

-------------------------------------------------------------------------------
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 = 0.4837 r_free = 0.4837 target = 0.206595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.176254 restraints weight = 37109.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.185468 restraints weight = 21439.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.191542 restraints weight = 13364.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4712 r_free = 0.4712 target = 0.195511 restraints weight = 8778.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.198406 restraints weight = 6030.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.4732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4768
moved from start:          0.1777

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= 0.113
  Angle     :  0.484   4.584   6675  Z= 0.251
  Chirality :  0.039   0.146    767
  Planarity :  0.004   0.049    840
  Dihedral  :  3.455  13.111    651
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.08 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.35), residues: 592
  helix:  1.83 (0.32), residues: 258
  sheet: -0.76 (0.64), residues: 55
  loop :  0.03 (0.40), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 583 
 TYR   0.005   0.001   TYR A 481 
 PHE   0.012   0.001   PHE A 382 
 TRP   0.009   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 4930)
  covalent geometry    : angle       0.48449 ( 6673)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       0.03793 (    2)
  hydrogen bonds       : bond        0.05138 (  219)
  hydrogen bonds       : angle       4.92616 (  642)

*********************** 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
  82 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.178 
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 1156 LYS cc_start: 0.9030 (tttm) cc_final: 0.8665 (tttm)
REVERT: A 1269 LYS cc_start: 0.8736 (tptt) cc_final: 0.7997 (tptt)
  outliers start: 8
  outliers final: 7
  residues processed: 78
  average time/residue: 0.1698
  time to fit residues: 16.7280
Evaluate side-chains
  76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
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 1017 ILE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 48 optimal weight:    0.2980
   chunk 16 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 472 GLN
** A1024 HIS ** 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 = 0.4820 r_free = 0.4820 target = 0.204563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.174054 restraints weight = 36766.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.183102 restraints weight = 21297.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.189310 restraints weight = 13280.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4695 r_free = 0.4695 target = 0.193451 restraints weight = 8740.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.196334 restraints weight = 5992.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.4712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4830
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4931  Z= 0.116
  Angle     :  0.488   4.655   6675  Z= 0.254
  Chirality :  0.039   0.144    767
  Planarity :  0.004   0.045    840
  Dihedral  :  3.535  13.911    651
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.70 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.05 (0.36), residues: 592
  helix:  1.84 (0.32), residues: 259
  sheet: -0.81 (0.66), residues: 55
  loop :  0.00 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1165 
 TYR   0.015   0.001   TYR A1009 
 PHE   0.013   0.001   PHE A 382 
 TRP   0.010   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4930)
  covalent geometry    : angle       0.48844 ( 6673)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       0.11664 (    2)
  hydrogen bonds       : bond        0.04332 (  219)
  hydrogen bonds       : angle       4.76424 (  642)

*********************** 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: 8
    poor density    : 70
  time to evaluate  : 0.150 
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 1156 LYS cc_start: 0.9012 (tttm) cc_final: 0.8649 (tttm)
REVERT: A 1269 LYS cc_start: 0.8744 (tptt) cc_final: 0.8017 (tptt)
  outliers start: 8
  outliers final: 7
  residues processed: 74
  average time/residue: 0.1410
  time to fit residues: 13.3003
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  : 0.170 
-------------------------------------------------------------------------------
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 1017 ILE
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 38 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 8 optimal weight:    0.5980
   chunk 26 optimal weight:    0.4980
   chunk 3 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4822 r_free = 0.4822 target = 0.204867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.174688 restraints weight = 36653.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.183562 restraints weight = 21272.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.189537 restraints weight = 13304.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.193798 restraints weight = 8853.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.196642 restraints weight = 6044.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.4716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4822
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4931  Z= 0.101
  Angle     :  0.472   4.478   6675  Z= 0.241
  Chirality :  0.039   0.142    767
  Planarity :  0.004   0.042    840
  Dihedral  :  3.473  13.812    651
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.09
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.36), residues: 592
  helix:  2.03 (0.32), residues: 259
  sheet: -0.81 (0.67), residues: 55
  loop :  0.03 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1165 
 TYR   0.008   0.001   TYR A1009 
 PHE   0.019   0.001   PHE A1244 
 TRP   0.008   0.001   TRP A1238 
 HIS   0.003   0.001   HIS A1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 4930)
  covalent geometry    : angle       0.47187 ( 6673)
  SS BOND              : bond        0.00280 (    1)
  SS BOND              : angle       1.05894 (    2)
  hydrogen bonds       : bond        0.03928 (  219)
  hydrogen bonds       : angle       4.57185 (  642)

*********************** 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
  83 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.200 
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 1156 LYS cc_start: 0.8989 (tttm) cc_final: 0.8620 (tttm)
REVERT: A 1269 LYS cc_start: 0.8761 (tptt) cc_final: 0.8019 (tptt)
  outliers start: 9
  outliers final: 9
  residues processed: 79
  average time/residue: 0.1509
  time to fit residues: 15.1835
Evaluate side-chains
  80 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
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 1017 ILE
Chi-restraints excluded: chain A residue 1030 GLU
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 15 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0060
   chunk 16 optimal weight:    0.2980
   chunk 38 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.5396

-------------------------------------------------------------------------------
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 = 0.4814 r_free = 0.4814 target = 0.204376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.173621 restraints weight = 36152.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.182509 restraints weight = 21037.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4641 r_free = 0.4641 target = 0.188729 restraints weight = 13194.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.192932 restraints weight = 8704.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.195691 restraints weight = 5963.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.4702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4852
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4931  Z= 0.108
  Angle     :  0.492   6.058   6675  Z= 0.252
  Chirality :  0.039   0.141    767
  Planarity :  0.004   0.040    840
  Dihedral  :  3.530  14.522    651
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.36), residues: 592
  helix:  2.00 (0.32), residues: 259
  sheet: -0.80 (0.69), residues: 55
  loop : -0.00 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1088 
 TYR   0.014   0.001   TYR A1009 
 PHE   0.019   0.001   PHE A1244 
 TRP   0.008   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 4930)
  covalent geometry    : angle       0.49207 ( 6673)
  SS BOND              : bond        0.00169 (    1)
  SS BOND              : angle       0.34798 (    2)
  hydrogen bonds       : bond        0.03862 (  219)
  hydrogen bonds       : angle       4.49822 (  642)

*********************** 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
  82 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.193 
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 1156 LYS cc_start: 0.8990 (tttm) cc_final: 0.8615 (tttm)
REVERT: A 1244 PHE cc_start: 0.4403 (t80) cc_final: 0.4122 (t80)
REVERT: A 1269 LYS cc_start: 0.8758 (tptt) cc_final: 0.8006 (tptt)
  outliers start: 9
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1337
  time to fit residues: 13.5454
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  : 0.161 
-------------------------------------------------------------------------------
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 1017 ILE
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 3 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0570
   chunk 34 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.4800 r_free = 0.4800 target = 0.202943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.172216 restraints weight = 36139.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.181021 restraints weight = 20984.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.187154 restraints weight = 13208.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.191393 restraints weight = 8766.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.194151 restraints weight = 6044.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.4684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4914
moved from start:          0.3089

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= 0.117
  Angle     :  0.492   4.318   6675  Z= 0.254
  Chirality :  0.039   0.148    767
  Planarity :  0.004   0.039    840
  Dihedral  :  3.618  14.466    651
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 11.22 %
    Favored  : 86.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.35), residues: 592
  helix:  1.99 (0.31), residues: 259
  sheet: -0.98 (0.68), residues: 55
  loop : -0.11 (0.40), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 441 
 TYR   0.012   0.001   TYR A1009 
 PHE   0.014   0.001   PHE A1244 
 TRP   0.009   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4930)
  covalent geometry    : angle       0.49192 ( 6673)
  SS BOND              : bond        0.00213 (    1)
  SS BOND              : angle       0.29783 (    2)
  hydrogen bonds       : bond        0.03762 (  219)
  hydrogen bonds       : angle       4.46159 (  642)

*********************** 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
  82 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.262 
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: 0.8714 (mm-30) cc_final: 0.8433 (mm-30)
REVERT: A  566 PHE cc_start: 0.6771 (t80) cc_final: 0.6360 (t80)
REVERT: A 1156 LYS cc_start: 0.8991 (tttm) cc_final: 0.8616 (tttm)
REVERT: A 1269 LYS cc_start: 0.8777 (tptt) cc_final: 0.8025 (tptt)
  outliers start: 10
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1473
  time to fit residues: 14.7165
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  : 0.253 
-------------------------------------------------------------------------------
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 1017 ILE
Chi-restraints excluded: chain A residue 1030 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
** A1024 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1111 HIS
A1193 GLN
A1298 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.198027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.168045 restraints weight = 34378.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.176339 restraints weight = 20175.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.182085 restraints weight = 12868.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.186083 restraints weight = 8678.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.188945 restraints weight = 6121.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.4673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5088
moved from start:          0.3652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4931  Z= 0.160
  Angle     :  0.550   4.636   6675  Z= 0.290
  Chirality :  0.040   0.148    767
  Planarity :  0.004   0.040    840
  Dihedral  :  3.932  14.214    651
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.22 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.35), residues: 592
  helix:  1.70 (0.31), residues: 259
  sheet: -1.19 (0.68), residues: 55
  loop : -0.45 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 441 
 TYR   0.025   0.002   TYR A1009 
 PHE   0.014   0.002   PHE A1244 
 TRP   0.018   0.002   TRP A1238 
 HIS   0.006   0.001   HIS A 309 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 4930)
  covalent geometry    : angle       0.55016 ( 6673)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       0.26146 (    2)
  hydrogen bonds       : bond        0.04241 (  219)
  hydrogen bonds       : angle       4.66314 (  642)

*********************** 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
  88 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.155 
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: 0.8736 (mm-30) cc_final: 0.8459 (mm-30)
REVERT: A  462 PHE cc_start: 0.7238 (m-80) cc_final: 0.6993 (m-80)
REVERT: A 1269 LYS cc_start: 0.8803 (tptt) cc_final: 0.8059 (tptt)
  outliers start: 12
  outliers final: 10
  residues processed: 83
  average time/residue: 0.1486
  time to fit residues: 15.6866
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  : 0.219 
-------------------------------------------------------------------------------
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 1017 ILE
Chi-restraints excluded: chain A residue 1030 GLU
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 31 optimal weight:    2.9990
   chunk 2 optimal weight:    0.4980
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4783 r_free = 0.4783 target = 0.199570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.167402 restraints weight = 33883.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.176310 restraints weight = 19746.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.182621 restraints weight = 12482.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.186944 restraints weight = 8334.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.189984 restraints weight = 5815.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.4704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5024
moved from start:          0.3801

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= 0.115
  Angle     :  0.508   4.431   6675  Z= 0.265
  Chirality :  0.040   0.183    767
  Planarity :  0.004   0.043    840
  Dihedral  :  3.791  14.005    651
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.79 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.35), residues: 592
  helix:  1.96 (0.31), residues: 259
  sheet: -1.15 (0.68), residues: 55
  loop : -0.37 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 441 
 TYR   0.013   0.001   TYR A1009 
 PHE   0.009   0.001   PHE A 440 
 TRP   0.011   0.001   TRP A1238 
 HIS   0.004   0.001   HIS A1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 4930)
  covalent geometry    : angle       0.50857 ( 6673)
  SS BOND              : bond        0.00113 (    1)
  SS BOND              : angle       0.11755 (    2)
  hydrogen bonds       : bond        0.03779 (  219)
  hydrogen bonds       : angle       4.47221 (  642)

*********************** 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
  84 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.156 
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: 0.8792 (mm-30) cc_final: 0.8489 (mm-30)
REVERT: A 1269 LYS cc_start: 0.8703 (tptt) cc_final: 0.7983 (tptt)
  outliers start: 11
  outliers final: 11
  residues processed: 79
  average time/residue: 0.1504
  time to fit residues: 15.1216
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  : 0.153 
-------------------------------------------------------------------------------
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 1030 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 30 optimal weight:    0.0870
   chunk 21 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    1.0962

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.196143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.165648 restraints weight = 34792.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.173961 restraints weight = 20861.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.179736 restraints weight = 13510.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.183612 restraints weight = 9213.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.186452 restraints weight = 6615.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.4634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5174
moved from start:          0.4239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4931  Z= 0.165
  Angle     :  0.568   5.525   6675  Z= 0.301
  Chirality :  0.040   0.169    767
  Planarity :  0.005   0.037    840
  Dihedral  :  4.088  17.928    651
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.55 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.34), residues: 592
  helix:  1.65 (0.30), residues: 259
  sheet: -1.38 (0.67), residues: 55
  loop : -0.66 (0.38), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 441 
 TYR   0.012   0.001   TYR A1009 
 PHE   0.011   0.001   PHE A1180 
 TRP   0.017   0.002   TRP A1238 
 HIS   0.004   0.001   HIS A1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 4930)
  covalent geometry    : angle       0.56811 ( 6673)
  SS BOND              : bond        0.00202 (    1)
  SS BOND              : angle       0.38981 (    2)
  hydrogen bonds       : bond        0.04186 (  219)
  hydrogen bonds       : angle       4.64601 (  642)

********************** 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
  88 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.253 
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: 0.8707 (mm-30) cc_final: 0.8403 (mm-30)
REVERT: A 1269 LYS cc_start: 0.8799 (tptt) cc_final: 0.8085 (tptt)
  outliers start: 9
  outliers final: 9
  residues processed: 84
  average time/residue: 0.1734
  time to fit residues: 18.6776
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  : 0.280 
-------------------------------------------------------------------------------
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 1017 ILE
Chi-restraints excluded: chain A residue 1030 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 22 optimal weight:    7.9990
   chunk 48 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4759 r_free = 0.4759 target = 0.197341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.165325 restraints weight = 34042.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.174056 restraints weight = 20135.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.180214 restraints weight = 12905.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.184508 restraints weight = 8735.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.187535 restraints weight = 6161.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.4660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5104
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4931  Z= 0.122
  Angle     :  0.534   5.394   6675  Z= 0.281
  Chirality :  0.040   0.150    767
  Planarity :  0.004   0.041    840
  Dihedral  :  3.952  14.935    651
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 13.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.35), residues: 592
  helix:  1.81 (0.30), residues: 259
  sheet: -1.26 (0.67), residues: 55
  loop : -0.54 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1022 
 TYR   0.012   0.001   TYR A1009 
 PHE   0.008   0.001   PHE A1180 
 TRP   0.012   0.001   TRP A 485 
 HIS   0.004   0.001   HIS A1024 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4930)
  covalent geometry    : angle       0.53417 ( 6673)
  SS BOND              : bond        0.00077 (    1)
  SS BOND              : angle       0.07580 (    2)
  hydrogen bonds       : bond        0.03811 (  219)
  hydrogen bonds       : angle       4.45323 (  642)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2006.64 seconds
wall clock time: 34 minutes 43.64 seconds (2083.64 seconds total)