Starting phenix.real_space_refine
on Tue Mar  3 11:53:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n98_24252/03_2026/7n98_24252.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n98_24252/03_2026/7n98_24252.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n98_24252/03_2026/7n98_24252.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n98_24252/03_2026/7n98_24252.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n98_24252/03_2026/7n98_24252.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n98_24252/03_2026/7n98_24252.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2412      2.51       5
     N     572      2.21       5
     O     621      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3625
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 473, 3625
          Classifications: {'peptide': 473}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 22, 'TRANS': 450}
          Unresolved non-hydrogen bonds: 100
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 77
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 72
  Time building chain proxies: 1.08, per 1000 atoms: 0.30
  Number of scatterers: 3625
  At special positions: 0
  Unit cell: (79.12, 71.38, 85.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     621      8.00
     N     572      7.00
     C    2412      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 216 " - pdb=" SG  CYS A 464 " 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: 0.29
  Conformation dependent library (CDL) restraints added in 140.6 milliseconds
  

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  888

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 1 sheets defined
      74.6% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 51
      removed outlier: 3.917A  pdb=" N   GLY A  51 " --> pdb=" O   CYS A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 4.275A  pdb=" N   GLN A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS A  60 " --> pdb=" O   GLN A  56 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE A  64 " --> pdb=" O   CYS A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 73
    Processing helix  chain 'A' and resid 77 through 105
      removed outlier: 3.712A  pdb=" N   ASP A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ALA A  93 " --> pdb=" O   ARG A  89 " (cutoff:3.500A)
      Proline residue:  A  97  - end of helix
      removed outlier: 3.724A  pdb=" N   SER A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LYS A 105 " --> pdb=" O   PHE A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 120
      removed outlier: 3.521A  pdb=" N   ILE A 119 " --> pdb=" O   MET A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 133
      removed outlier: 4.653A  pdb=" N   ILE A 127 " --> pdb=" O   PRO A 123 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   TRP A 133 " --> pdb=" O   TYR A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 148
    Processing helix  chain 'A' and resid 148 through 172
      removed outlier: 3.810A  pdb=" N   LEU A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   PHE A 154 " --> pdb=" O   TRP A 150 " (cutoff:3.500A)
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 173 through 175
      No H-bonds generated for 'chain 'A' and resid 173 through 175'
    Processing helix  chain 'A' and resid 179 through 209
      removed outlier: 4.145A  pdb=" N   ASP A 184 " --> pdb=" O   GLN A 180 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR A 189 " --> pdb=" O   SER A 185 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL A 193 " --> pdb=" O   TYR A 189 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 195 " --> pdb=" O   MET A 191 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR A 202 " --> pdb=" O   THR A 198 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ALA A 203 " --> pdb=" O   VAL A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 266
      removed outlier: 3.740A  pdb=" N   LEU A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 293
      removed outlier: 3.688A  pdb=" N   MET A 293 " --> pdb=" O   LEU A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 323
      removed outlier: 3.505A  pdb=" N   ALA A 303 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   LEU A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   CYS A 323 " --> pdb=" O   PHE A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 344
      removed outlier: 3.883A  pdb=" N   LEU A 338 " --> pdb=" O   GLN A 334 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ALA A 344 " --> pdb=" O   ILE A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 357
      removed outlier: 3.768A  pdb=" N   LEU A 355 " --> pdb=" O   TRP A 351 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ARG A 357 " --> pdb=" O   TRP A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 379
      Proline residue:  A 373  - end of helix
      removed outlier: 3.813A  pdb=" N   ALA A 379 " --> pdb=" O   LEU A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 409
      removed outlier: 3.535A  pdb=" N   VAL A 390 " --> pdb=" O   ILE A 386 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA A 401 " --> pdb=" O   VAL A 397 " (cutoff:3.500A)
      Proline residue:  A 406  - end of helix
    Processing helix  chain 'A' and resid 409 through 420
      removed outlier: 3.699A  pdb=" N   VAL A 413 " --> pdb=" O   MET A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 456
      removed outlier: 4.058A  pdb=" N   PHE A 431 " --> pdb=" O   THR A 427 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   PHE A 432 " --> pdb=" O   GLU A 428 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER A 433 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   LEU A 447 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY A 448 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 493
      removed outlier: 3.956A  pdb=" N   LYS A 475 " --> pdb=" O   LYS A 471 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   ALA A 481 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
      Proline residue:  A 482  - end of helix
    Processing helix  chain 'A' and resid 498 through 509
      removed outlier: 4.732A  pdb=" N   LYS A 507 " --> pdb=" O   ARG A 503 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   LYS A 508 " --> pdb=" O   ARG A 504 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 218

    214 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: 0.45

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1088
        1.34 -     1.46: 750
        1.46 -     1.58: 1857
        1.58 -     1.69: 0
        1.69 -     1.81: 30
  Bond restraints: 3725
  Sorted by residual:
  bond pdb=" N   LYS A 440 "
       pdb=" CA  LYS A 440 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.25e+00
  bond pdb=" N   ALA A  53 "
       pdb=" CA  ALA A  53 "
    ideal  model  delta    sigma   weight residual
    1.463  1.456  0.007 6.90e-03 2.10e+04 1.16e+00
  bond pdb=" C   GLY A  52 "
       pdb=" N   ALA A  53 "
    ideal  model  delta    sigma   weight residual
    1.341  1.323  0.017 1.65e-02 3.67e+03 1.09e+00
  bond pdb=" C   VAL A 135 "
       pdb=" N   PRO A 136 "
    ideal  model  delta    sigma   weight residual
    1.332  1.324  0.008 8.20e-03 1.49e+04 1.01e+00
  bond pdb=" N   PRO A 136 "
       pdb=" CA  PRO A 136 "
    ideal  model  delta    sigma   weight residual
    1.473  1.465  0.008 8.50e-03 1.38e+04 8.95e-01
  ... (remaining 3720 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 4806
        1.37 -     2.75: 222
        2.75 -     4.12: 34
        4.12 -     5.49: 19
        5.49 -     6.87: 2
  Bond angle restraints: 5083
  Sorted by residual:
  angle pdb=" N   VAL A 372 "
        pdb=" CA  VAL A 372 "
        pdb=" C   VAL A 372 "
      ideal   model   delta    sigma   weight residual
     108.88  115.75   -6.87 2.16e+00 2.14e-01 1.01e+01
  angle pdb=" C   MET A 409 "
        pdb=" N   LEU A 410 "
        pdb=" CA  LEU A 410 "
      ideal   model   delta    sigma   weight residual
     120.09  123.82   -3.73 1.25e+00 6.40e-01 8.89e+00
  angle pdb=" C   GLY A  52 "
        pdb=" N   ALA A  53 "
        pdb=" CA  ALA A  53 "
      ideal   model   delta    sigma   weight residual
     119.83  122.80   -2.97 1.11e+00 8.12e-01 7.16e+00
  angle pdb=" N   LYS A 440 "
        pdb=" CA  LYS A 440 "
        pdb=" C   LYS A 440 "
      ideal   model   delta    sigma   weight residual
     111.28  108.53    2.75 1.09e+00 8.42e-01 6.39e+00
  angle pdb=" C   ALA A  53 "
        pdb=" CA  ALA A  53 "
        pdb=" CB  ALA A  53 "
      ideal   model   delta    sigma   weight residual
     113.57  109.70    3.87 1.57e+00 4.06e-01 6.09e+00
  ... (remaining 5078 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.76: 1934
       15.76 -    31.52: 165
       31.52 -    47.28: 43
       47.28 -    63.04: 11
       63.04 -    78.81: 4
  Dihedral angle restraints: 2157
    sinusoidal: 780
      harmonic: 1377
  Sorted by residual:
  dihedral pdb=" CA  GLU A 382 "
           pdb=" C   GLU A 382 "
           pdb=" N   ARG A 383 "
           pdb=" CA  ARG A 383 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.40   23.60     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  VAL A 372 "
           pdb=" C   VAL A 372 "
           pdb=" N   PRO A 373 "
           pdb=" CA  PRO A 373 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.21  -22.79     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ALA A  53 "
           pdb=" C   ALA A  53 "
           pdb=" N   PRO A  54 "
           pdb=" CA  PRO A  54 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.58  -21.42     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 2154 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 407
       0.041 -    0.082: 143
       0.082 -    0.123: 41
       0.123 -    0.164: 5
       0.164 -    0.205: 2
  Chirality restraints: 598
  Sorted by residual:
  chirality pdb=" CB  ILE A 486 "
            pdb=" CA  ILE A 486 "
            pdb=" CG1 ILE A 486 "
            pdb=" CG2 ILE A 486 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  PRO A  54 "
            pdb=" N   PRO A  54 "
            pdb=" C   PRO A  54 "
            pdb=" CB  PRO A  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.02e-01
  chirality pdb=" CA  PRO A 425 "
            pdb=" N   PRO A 425 "
            pdb=" C   PRO A 425 "
            pdb=" CB  PRO A 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.47e-01
  ... (remaining 595 not shown)

  Planarity restraints: 627
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 466 "    0.043 5.00e-02 4.00e+02   6.44e-02 6.64e+00
        pdb=" N   PRO A 467 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 467 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 467 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  53 "   -0.033 5.00e-02 4.00e+02   4.96e-02 3.94e+00
        pdb=" N   PRO A  54 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A  54 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  54 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 496 "    0.032 5.00e-02 4.00e+02   4.78e-02 3.65e+00
        pdb=" N   PRO A 497 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 497 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 497 "    0.027 5.00e-02 4.00e+02
  ... (remaining 624 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 584
        2.75 -     3.29: 3814
        3.29 -     3.83: 5785
        3.83 -     4.36: 6120
        4.36 -     4.90: 10383
  Nonbonded interactions: 26686
  Sorted by model distance:
  nonbonded pdb=" CE  MET A 409 "
            pdb=" CD2 LEU A 495 "
     model   vdw
     2.217 3.880
  nonbonded pdb=" O   PHE A 358 "
            pdb=" OG1 THR A 362 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OD1 ASN A 318 "
            pdb=" OG  SER A 450 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ILE A 176 "
            pdb=" OG  SER A 177 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" OE2 GLU A 500 "
            pdb=" NH2 ARG A 503 "
     model   vdw
     2.337 3.120
  ... (remaining 26681 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:             0.430
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.640
  Find NCS groups from input model:        0.020
  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:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
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      :  0.004   0.040   3726  Z= 0.194
  Angle     :  0.720   6.867   5085  Z= 0.403
  Chirality :  0.046   0.205    598
  Planarity :  0.006   0.064    627
  Dihedral  : 13.694  78.806   1266
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.54 %
    Favored  : 99.20 %
  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 are not related in a simple way.
  whole: -1.56 (0.40), residues: 471
  helix: -0.05 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop : -3.04 (0.50), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 190 
 TYR   0.013   0.002   TYR A 435 
 PHE   0.016   0.002   PHE A 285 
 TRP   0.016   0.002   TRP A 407 
 HIS   0.002   0.001   HIS A 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 3725)
  covalent geometry    : angle       0.72033 ( 5083)
  SS BOND              : bond        0.00503 (    1)
  SS BOND              : angle       0.81683 (    2)
  hydrogen bonds       : bond        0.15925 (  214)
  hydrogen bonds       : angle       5.54293 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.8549 (mttt) cc_final: 0.7984 (tttm)
REVERT: A  361 LYS cc_start: 0.8623 (tmtt) cc_final: 0.8340 (tptp)
REVERT: A  503 ARG cc_start: 0.8368 (mtm180) cc_final: 0.7986 (ptm160)
  outliers start: 1
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0477
  time to fit residues: 6.3675
Evaluate side-chains
  81 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 318 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.121657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.097596 restraints weight = 7230.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.101045 restraints weight = 3681.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.103328 restraints weight = 2357.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.105070 restraints weight = 1751.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.105857 restraints weight = 1416.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3726  Z= 0.152
  Angle     :  0.635   6.855   5085  Z= 0.331
  Chirality :  0.045   0.168    598
  Planarity :  0.006   0.055    627
  Dihedral  :  4.952  23.933    501
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.67 %
    Favored  : 85.25 %
  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 are not related in a simple way.
  whole: -1.11 (0.40), residues: 471
  helix:  0.29 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop : -3.01 (0.52), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 190 
 TYR   0.016   0.001   TYR A  55 
 PHE   0.029   0.002   PHE A 134 
 TRP   0.008   0.001   TRP A  91 
 HIS   0.001   0.000   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3725)
  covalent geometry    : angle       0.63468 ( 5083)
  SS BOND              : bond        0.00623 (    1)
  SS BOND              : angle       1.39401 (    2)
  hydrogen bonds       : bond        0.05327 (  214)
  hydrogen bonds       : angle       4.33561 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 ILE cc_start: 0.8184 (tp) cc_final: 0.7954 (tp)
REVERT: A  137 ASP cc_start: 0.7387 (t0) cc_final: 0.6999 (t0)
REVERT: A  300 LYS cc_start: 0.8578 (mttt) cc_final: 0.7931 (tttm)
REVERT: A  361 LYS cc_start: 0.8527 (tmtt) cc_final: 0.7946 (tptp)
REVERT: A  381 MET cc_start: 0.5079 (ttt) cc_final: 0.4637 (ttm)
REVERT: A  409 MET cc_start: 0.8055 (ttt) cc_final: 0.7767 (mtp)
REVERT: A  503 ARG cc_start: 0.8364 (mtm180) cc_final: 0.7894 (ptm160)
  outliers start: 4
  outliers final: 3
  residues processed: 92
  average time/residue: 0.0429
  time to fit residues: 5.3554
Evaluate side-chains
  85 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  299 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 32 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.123772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.099637 restraints weight = 7103.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.103156 restraints weight = 3707.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.105603 restraints weight = 2389.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.107107 restraints weight = 1764.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.108373 restraints weight = 1443.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3726  Z= 0.134
  Angle     :  0.603   8.266   5085  Z= 0.308
  Chirality :  0.044   0.167    598
  Planarity :  0.005   0.049    627
  Dihedral  :  4.682  22.644    501
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 19.84 %
    Favored  : 78.82 %
  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 are not related in a simple way.
  whole: -0.89 (0.40), residues: 471
  helix:  0.49 (0.30), residues: 319
  sheet:  None (None), residues: 0
  loop : -2.99 (0.51), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 190 
 TYR   0.009   0.001   TYR A  55 
 PHE   0.033   0.001   PHE A 134 
 TRP   0.010   0.001   TRP A  91 
 HIS   0.001   0.000   HIS A  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3725)
  covalent geometry    : angle       0.60333 ( 5083)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.79575 (    2)
  hydrogen bonds       : bond        0.04500 (  214)
  hydrogen bonds       : angle       3.96786 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 ASP cc_start: 0.7247 (t0) cc_final: 0.6808 (t0)
REVERT: A  300 LYS cc_start: 0.8530 (mttt) cc_final: 0.7937 (tttm)
REVERT: A  361 LYS cc_start: 0.8552 (tmtt) cc_final: 0.8055 (tptp)
REVERT: A  381 MET cc_start: 0.4913 (ttt) cc_final: 0.4495 (ttm)
REVERT: A  504 ARG cc_start: 0.8867 (mtm110) cc_final: 0.8656 (mtm110)
REVERT: A  508 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8361 (mmtm)
  outliers start: 5
  outliers final: 2
  residues processed: 95
  average time/residue: 0.0552
  time to fit residues: 6.8376
Evaluate side-chains
  85 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  478 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0970
   chunk 31 optimal weight:    0.0670
   chunk 6 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    0.4516

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.125399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.101101 restraints weight = 6948.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.104583 restraints weight = 3650.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.107065 restraints weight = 2369.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.108759 restraints weight = 1751.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.109803 restraints weight = 1419.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3726  Z= 0.125
  Angle     :  0.603   8.693   5085  Z= 0.300
  Chirality :  0.043   0.164    598
  Planarity :  0.005   0.045    627
  Dihedral  :  4.481  22.122    501
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 21.45 %
    Favored  : 75.87 %
  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 are not related in a simple way.
  whole: -0.61 (0.40), residues: 471
  helix:  0.67 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -2.84 (0.52), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 503 
 TYR   0.016   0.001   TYR A  55 
 PHE   0.033   0.002   PHE A 134 
 TRP   0.007   0.001   TRP A  91 
 HIS   0.001   0.000   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 3725)
  covalent geometry    : angle       0.60258 ( 5083)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.42298 (    2)
  hydrogen bonds       : bond        0.03921 (  214)
  hydrogen bonds       : angle       3.68265 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 ASP cc_start: 0.7146 (t0) cc_final: 0.6657 (t0)
REVERT: A  164 CYS cc_start: 0.9303 (t) cc_final: 0.9073 (t)
REVERT: A  300 LYS cc_start: 0.8518 (mttt) cc_final: 0.7937 (tttm)
REVERT: A  361 LYS cc_start: 0.8530 (tmtt) cc_final: 0.7982 (tptp)
REVERT: A  381 MET cc_start: 0.4871 (ttt) cc_final: 0.4348 (ttm)
REVERT: A  409 MET cc_start: 0.7963 (ttt) cc_final: 0.7649 (mtp)
  outliers start: 10
  outliers final: 5
  residues processed: 101
  average time/residue: 0.0458
  time to fit residues: 6.1610
Evaluate side-chains
  89 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 CYS
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  355 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0370
   chunk 36 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6058

-------------------------------------------------------------------------------
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 = 0.3679 r_free = 0.3679 target = 0.125802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.101147 restraints weight = 6890.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.104638 restraints weight = 3661.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.107109 restraints weight = 2388.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.108421 restraints weight = 1777.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.109822 restraints weight = 1478.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3726  Z= 0.126
  Angle     :  0.606   8.127   5085  Z= 0.301
  Chirality :  0.044   0.195    598
  Planarity :  0.005   0.046    627
  Dihedral  :  4.399  22.171    501
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 23.86 %
    Favored  : 73.19 %
  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 are not related in a simple way.
  whole: -0.42 (0.41), residues: 471
  helix:  0.80 (0.30), residues: 322
  sheet:  None (None), residues: 0
  loop : -2.76 (0.53), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 504 
 TYR   0.009   0.001   TYR A  55 
 PHE   0.030   0.001   PHE A 134 
 TRP   0.012   0.001   TRP A  91 
 HIS   0.001   0.000   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3725)
  covalent geometry    : angle       0.60584 ( 5083)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.36084 (    2)
  hydrogen bonds       : bond        0.03894 (  214)
  hydrogen bonds       : angle       3.60268 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 ASP cc_start: 0.7136 (t0) cc_final: 0.6607 (t0)
REVERT: A  164 CYS cc_start: 0.9302 (t) cc_final: 0.9085 (t)
REVERT: A  300 LYS cc_start: 0.8546 (mttt) cc_final: 0.7952 (tttm)
REVERT: A  361 LYS cc_start: 0.8559 (tmtt) cc_final: 0.8047 (tptp)
REVERT: A  381 MET cc_start: 0.4814 (ttt) cc_final: 0.4306 (ttm)
REVERT: A  409 MET cc_start: 0.7988 (ttt) cc_final: 0.7706 (mtp)
REVERT: A  508 LYS cc_start: 0.8674 (mmtm) cc_final: 0.8358 (mmtm)
  outliers start: 11
  outliers final: 5
  residues processed: 97
  average time/residue: 0.0401
  time to fit residues: 5.2695
Evaluate side-chains
  95 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 90
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  486 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 18 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0270
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.126056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.101166 restraints weight = 7047.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.104700 restraints weight = 3690.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.107250 restraints weight = 2390.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.108981 restraints weight = 1769.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.109955 restraints weight = 1433.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3726  Z= 0.122
  Angle     :  0.585   8.021   5085  Z= 0.293
  Chirality :  0.043   0.195    598
  Planarity :  0.005   0.046    627
  Dihedral  :  4.339  22.193    501
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 24.66 %
    Favored  : 72.12 %
  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 are not related in a simple way.
  whole: -0.23 (0.41), residues: 471
  helix:  0.95 (0.30), residues: 322
  sheet:  None (None), residues: 0
  loop : -2.69 (0.53), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 504 
 TYR   0.019   0.001   TYR A  55 
 PHE   0.031   0.001   PHE A 134 
 TRP   0.008   0.001   TRP A  91 
 HIS   0.001   0.000   HIS A 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 3725)
  covalent geometry    : angle       0.58539 ( 5083)
  SS BOND              : bond        0.00032 (    1)
  SS BOND              : angle       0.37489 (    2)
  hydrogen bonds       : bond        0.03720 (  214)
  hydrogen bonds       : angle       3.50333 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 ASP cc_start: 0.6973 (t0) cc_final: 0.6459 (t0)
REVERT: A  164 CYS cc_start: 0.9285 (t) cc_final: 0.9081 (t)
REVERT: A  300 LYS cc_start: 0.8569 (mttt) cc_final: 0.7956 (tttm)
REVERT: A  361 LYS cc_start: 0.8532 (tmtt) cc_final: 0.8069 (tptp)
REVERT: A  381 MET cc_start: 0.4790 (ttt) cc_final: 0.4260 (ttm)
REVERT: A  409 MET cc_start: 0.7971 (ttt) cc_final: 0.7703 (mtp)
REVERT: A  508 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8360 (mmtm)
  outliers start: 12
  outliers final: 8
  residues processed: 102
  average time/residue: 0.0431
  time to fit residues: 6.0035
Evaluate side-chains
  99 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  486 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.121494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.096721 restraints weight = 7221.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.100001 restraints weight = 3867.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.102363 restraints weight = 2561.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.103938 restraints weight = 1924.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.104901 restraints weight = 1581.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3726  Z= 0.163
  Angle     :  0.628   7.722   5085  Z= 0.318
  Chirality :  0.045   0.193    598
  Planarity :  0.005   0.045    627
  Dihedral  :  4.492  22.603    501
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 26.54 %
    Favored  : 69.71 %
  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 are not related in a simple way.
  whole: -0.29 (0.41), residues: 471
  helix:  0.95 (0.30), residues: 323
  sheet:  None (None), residues: 0
  loop : -2.86 (0.51), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 383 
 TYR   0.011   0.001   TYR A  55 
 PHE   0.033   0.002   PHE A 134 
 TRP   0.011   0.001   TRP A  91 
 HIS   0.002   0.001   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 3725)
  covalent geometry    : angle       0.62769 ( 5083)
  SS BOND              : bond        0.00081 (    1)
  SS BOND              : angle       0.48903 (    2)
  hydrogen bonds       : bond        0.04575 (  214)
  hydrogen bonds       : angle       3.72939 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A  137 ASP cc_start: 0.7006 (t0) cc_final: 0.6468 (t0)
REVERT: A  164 CYS cc_start: 0.9304 (t) cc_final: 0.9084 (t)
REVERT: A  300 LYS cc_start: 0.8542 (mttt) cc_final: 0.7907 (tttm)
REVERT: A  334 GLN cc_start: 0.8084 (pt0) cc_final: 0.7652 (mt0)
REVERT: A  361 LYS cc_start: 0.8551 (tmtt) cc_final: 0.8036 (tptp)
REVERT: A  381 MET cc_start: 0.4804 (ttt) cc_final: 0.4295 (ttm)
REVERT: A  409 MET cc_start: 0.8254 (ttt) cc_final: 0.8006 (mtp)
REVERT: A  458 ASN cc_start: 0.7168 (m110) cc_final: 0.6945 (m110)
  outliers start: 14
  outliers final: 9
  residues processed: 92
  average time/residue: 0.0446
  time to fit residues: 5.5681
Evaluate side-chains
  89 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  316 GLU
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  478 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 28 optimal weight:    0.0980
   chunk 14 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.124750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.099646 restraints weight = 7110.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.103172 restraints weight = 3719.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.105751 restraints weight = 2394.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.107200 restraints weight = 1765.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.108559 restraints weight = 1453.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3726  Z= 0.128
  Angle     :  0.607   7.883   5085  Z= 0.304
  Chirality :  0.044   0.220    598
  Planarity :  0.005   0.047    627
  Dihedral  :  4.469  22.823    501
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 27.35 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.41), residues: 471
  helix:  1.00 (0.30), residues: 323
  sheet:  None (None), residues: 0
  loop : -2.70 (0.54), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 504 
 TYR   0.019   0.001   TYR A  55 
 PHE   0.037   0.002   PHE A 329 
 TRP   0.009   0.001   TRP A  91 
 HIS   0.001   0.000   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3725)
  covalent geometry    : angle       0.60697 ( 5083)
  SS BOND              : bond        0.00041 (    1)
  SS BOND              : angle       0.33170 (    2)
  hydrogen bonds       : bond        0.03944 (  214)
  hydrogen bonds       : angle       3.53114 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 THR cc_start: 0.9557 (t) cc_final: 0.9294 (p)
REVERT: A  137 ASP cc_start: 0.6991 (t0) cc_final: 0.6464 (t0)
REVERT: A  164 CYS cc_start: 0.9305 (t) cc_final: 0.9099 (t)
REVERT: A  300 LYS cc_start: 0.8484 (mttt) cc_final: 0.7885 (tttm)
REVERT: A  334 GLN cc_start: 0.8026 (pt0) cc_final: 0.7591 (mt0)
REVERT: A  361 LYS cc_start: 0.8533 (tmtt) cc_final: 0.8057 (tptp)
REVERT: A  381 MET cc_start: 0.4855 (ttt) cc_final: 0.4339 (ttm)
REVERT: A  409 MET cc_start: 0.8160 (ttt) cc_final: 0.7900 (mtp)
REVERT: A  458 ASN cc_start: 0.7053 (m110) cc_final: 0.6831 (m110)
REVERT: A  508 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8248 (mmtm)
  outliers start: 10
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0487
  time to fit residues: 6.3551
Evaluate side-chains
  101 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  421 HIS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  486 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.124869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.099774 restraints weight = 7069.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.103267 restraints weight = 3677.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.105782 restraints weight = 2381.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.107355 restraints weight = 1770.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.108613 restraints weight = 1451.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3726  Z= 0.134
  Angle     :  0.612   7.688   5085  Z= 0.306
  Chirality :  0.044   0.215    598
  Planarity :  0.005   0.048    627
  Dihedral  :  4.464  22.564    501
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 27.35 %
    Favored  : 69.71 %
  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 are not related in a simple way.
  whole: -0.09 (0.41), residues: 471
  helix:  1.05 (0.30), residues: 324
  sheet:  None (None), residues: 0
  loop : -2.67 (0.54), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 190 
 TYR   0.010   0.001   TYR A  55 
 PHE   0.033   0.001   PHE A 134 
 TRP   0.007   0.001   TRP A 407 
 HIS   0.002   0.000   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3725)
  covalent geometry    : angle       0.61254 ( 5083)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.34616 (    2)
  hydrogen bonds       : bond        0.03988 (  214)
  hydrogen bonds       : angle       3.53049 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 THR cc_start: 0.9561 (t) cc_final: 0.9260 (p)
REVERT: A  137 ASP cc_start: 0.7088 (t0) cc_final: 0.6570 (t0)
REVERT: A  164 CYS cc_start: 0.9306 (t) cc_final: 0.9103 (t)
REVERT: A  300 LYS cc_start: 0.8487 (mttt) cc_final: 0.7891 (tttm)
REVERT: A  334 GLN cc_start: 0.8037 (pt0) cc_final: 0.7623 (mt0)
REVERT: A  361 LYS cc_start: 0.8540 (tmtt) cc_final: 0.8069 (tptp)
REVERT: A  381 MET cc_start: 0.4872 (ttt) cc_final: 0.4366 (ttm)
REVERT: A  409 MET cc_start: 0.8217 (ttt) cc_final: 0.7970 (mtp)
REVERT: A  458 ASN cc_start: 0.7292 (m110) cc_final: 0.7082 (m110)
REVERT: A  508 LYS cc_start: 0.8655 (mmtm) cc_final: 0.8277 (mmtm)
  outliers start: 11
  outliers final: 8
  residues processed: 100
  average time/residue: 0.0449
  time to fit residues: 6.0971
Evaluate side-chains
  96 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  202 THR
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  421 HIS
Chi-restraints excluded: chain A residue  486 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 33 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0870
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.4958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.127597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.102165 restraints weight = 7232.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.105839 restraints weight = 3720.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.108407 restraints weight = 2385.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.110043 restraints weight = 1762.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.111347 restraints weight = 1443.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3726  Z= 0.123
  Angle     :  0.609   8.189   5085  Z= 0.300
  Chirality :  0.043   0.210    598
  Planarity :  0.005   0.048    627
  Dihedral  :  4.387  22.184    501
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 29.22 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.41), residues: 471
  helix:  1.10 (0.29), residues: 329
  sheet:  None (None), residues: 0
  loop : -2.72 (0.56), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 190 
 TYR   0.023   0.001   TYR A  55 
 PHE   0.033   0.001   PHE A 134 
 TRP   0.009   0.001   TRP A 407 
 HIS   0.002   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3725)
  covalent geometry    : angle       0.60927 ( 5083)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.39154 (    2)
  hydrogen bonds       : bond        0.03503 (  214)
  hydrogen bonds       : angle       3.40025 (  642)

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

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

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  942 Ramachandran restraints generated.
    471 Oldfield, 0 Emsley, 471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 THR cc_start: 0.9559 (t) cc_final: 0.9273 (p)
REVERT: A  137 ASP cc_start: 0.7064 (t0) cc_final: 0.6548 (t0)
REVERT: A  300 LYS cc_start: 0.8510 (mttt) cc_final: 0.7891 (tttm)
REVERT: A  334 GLN cc_start: 0.7971 (pt0) cc_final: 0.7556 (mt0)
REVERT: A  361 LYS cc_start: 0.8505 (tmtt) cc_final: 0.8020 (tptp)
REVERT: A  381 MET cc_start: 0.4823 (ttt) cc_final: 0.4293 (ttm)
REVERT: A  409 MET cc_start: 0.8195 (ttt) cc_final: 0.7965 (mtp)
REVERT: A  508 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8289 (mmtm)
  outliers start: 6
  outliers final: 6
  residues processed: 98
  average time/residue: 0.0464
  time to fit residues: 6.0988
Evaluate side-chains
  98 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 VAL
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 THR
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  421 HIS
Chi-restraints excluded: chain A residue  486 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3677 r_free = 0.3677 target = 0.125949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.100768 restraints weight = 7013.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.104347 restraints weight = 3643.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.106814 restraints weight = 2355.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.108413 restraints weight = 1748.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.109640 restraints weight = 1433.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3726  Z= 0.131
  Angle     :  0.613   8.100   5085  Z= 0.304
  Chirality :  0.044   0.198    598
  Planarity :  0.005   0.048    627
  Dihedral  :  4.391  22.095    501
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 29.76 %
    Favored  : 68.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.41), residues: 471
  helix:  1.20 (0.29), residues: 329
  sheet:  None (None), residues: 0
  loop : -2.74 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 190 
 TYR   0.018   0.001   TYR A  55 
 PHE   0.032   0.001   PHE A 134 
 TRP   0.008   0.001   TRP A  91 
 HIS   0.002   0.000   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3725)
  covalent geometry    : angle       0.61354 ( 5083)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       0.36028 (    2)
  hydrogen bonds       : bond        0.03725 (  214)
  hydrogen bonds       : angle       3.44609 (  642)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 799.18 seconds
wall clock time: 14 minutes 25.89 seconds (865.89 seconds total)