Starting phenix.real_space_refine
on Fri May  9 21:04:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kdn_37140/05_2025/8kdn_37140.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kdn_37140/05_2025/8kdn_37140.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kdn_37140/05_2025/8kdn_37140.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kdn_37140/05_2025/8kdn_37140.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kdn_37140/05_2025/8kdn_37140.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kdn_37140/05_2025/8kdn_37140.cif"
  }
  resolution = 4.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.010
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      22      5.16       5
     C    2635      2.51       5
     N     615      2.21       5
     O     658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3930
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 409
          Classifications: {'peptide': 52}
          Link IDs: {'PTRANS': 2, 'TRANS': 49}
    Chain: "B"
      Number of atoms: 3509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3509
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 23, 'TRANS': 430}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 2.80, per 1000 atoms: 0.71
  Number of scatterers: 3930
  At special positions: 0
  Unit cell: (76.725, 85.932, 79.794, 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      22     16.00
     O     658      8.00
     N     615      7.00
     C    2635      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 210 " - pdb=" SG  CYS B 164 " distance=2.11

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 491.0 milliseconds
  

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  934

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 0 sheets defined
      86.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 165 through 173
      removed outlier: 4.327A  pdb=" N   LYS A 171 " --> pdb=" O   GLU A 167 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   VAL A 172 " --> pdb=" O   GLU A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 207
      removed outlier: 4.001A  pdb=" N   TRP A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 65
      removed outlier: 3.685A  pdb=" N   ILE B  59 " --> pdb=" O   GLY B  55 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   GLY B  65 " --> pdb=" O   GLY B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 72 through 80
      removed outlier: 4.397A  pdb=" N   GLU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 110
      removed outlier: 3.907A  pdb=" N   GLY B  93 " --> pdb=" O   TRP B  89 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU B 105 " --> pdb=" O   LEU B 101 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU B 106 " --> pdb=" O   CYS B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 125
      removed outlier: 3.663A  pdb=" N   VAL B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 139
      removed outlier: 3.581A  pdb=" N   LYS B 132 " --> pdb=" O   PRO B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 157
      removed outlier: 3.616A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR B 155 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 161
    Processing helix  chain 'B' and resid 167 through 188
    Processing helix  chain 'B' and resid 189 through 221
    Processing helix  chain 'B' and resid 239 through 255
      removed outlier: 4.510A  pdb=" N   LEU B 245 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY B 250 " --> pdb=" O   ALA B 246 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   PHE B 252 " --> pdb=" O   TYR B 248 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 267
      removed outlier: 4.192A  pdb=" N   LEU B 260 " --> pdb=" O   TRP B 257 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ASN B 261 " --> pdb=" O   ASN B 258 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   THR B 264 " --> pdb=" O   ASN B 261 " (cutoff:3.500A)
      removed outlier: 5.728A  pdb=" N   GLU B 265 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 269 through 300
      Proline residue:  B 275  - end of helix
      Proline residue:  B 283  - end of helix
      removed outlier: 3.594A  pdb=" N   PHE B 297 " --> pdb=" O   ASN B 293 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   THR B 299 " --> pdb=" O   ALA B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 308
    Processing helix  chain 'B' and resid 310 through 320
    Processing helix  chain 'B' and resid 325 through 356
      removed outlier: 3.563A  pdb=" N   ARG B 348 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 365
      removed outlier: 3.531A  pdb=" N   LEU B 363 " --> pdb=" O   PRO B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 387
      removed outlier: 3.578A  pdb=" N   LEU B 377 " --> pdb=" O   PRO B 373 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   TYR B 387 " --> pdb=" O   MET B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 390
      No H-bonds generated for 'chain 'B' and resid 388 through 390'
    Processing helix  chain 'B' and resid 393 through 422
      removed outlier: 3.838A  pdb=" N   ILE B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   PHE B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   PHE B 403 " --> pdb=" O   PHE B 399 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ASN B 404 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   TRP B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 454
      removed outlier: 3.874A  pdb=" N   LEU B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER B 450 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 467
      removed outlier: 3.550A  pdb=" N   THR B 463 " --> pdb=" O   GLY B 459 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER B 467 " --> pdb=" O   THR B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 476
      removed outlier: 4.145A  pdb=" N   VAL B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 501
      removed outlier: 3.707A  pdb=" N   GLY B 488 " --> pdb=" O   TRP B 484 " (cutoff:3.500A)

    292 hydrogen bonds defined for protein.
    852 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: 1.03

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 664
        1.33 -     1.45: 1057
        1.45 -     1.58: 2279
        1.58 -     1.70: 2
        1.70 -     1.82: 31
  Bond restraints: 4033
  Sorted by residual:
  bond pdb=" CB  SER B 338 "
       pdb=" OG  SER B 338 "
    ideal  model  delta    sigma   weight residual
    1.417  1.488 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" C   VAL B 166 "
       pdb=" N   PRO B 167 "
    ideal  model  delta    sigma   weight residual
    1.332  1.365 -0.033 1.12e-02 7.97e+03 8.50e+00
  bond pdb=" C   SER B 143 "
       pdb=" O   SER B 143 "
    ideal  model  delta    sigma   weight residual
    1.237  1.203  0.034 1.19e-02 7.06e+03 8.12e+00
  bond pdb=" CA  LEU B 274 "
       pdb=" C   LEU B 274 "
    ideal  model  delta    sigma   weight residual
    1.521  1.551 -0.030 1.08e-02 8.57e+03 7.71e+00
  bond pdb=" C   LEU B 180 "
       pdb=" O   LEU B 180 "
    ideal  model  delta    sigma   weight residual
    1.237  1.205  0.031 1.16e-02 7.43e+03 7.35e+00
  ... (remaining 4028 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 4131
        1.78 -     3.56: 1131
        3.56 -     5.34: 207
        5.34 -     7.11: 32
        7.11 -     8.89: 4
  Bond angle restraints: 5505
  Sorted by residual:
  angle pdb=" CA  ASP B 116 "
        pdb=" CB  ASP B 116 "
        pdb=" CG  ASP B 116 "
      ideal   model   delta    sigma   weight residual
     112.60  118.63   -6.03 1.00e+00 1.00e+00 3.64e+01
  angle pdb=" CA  PHE B 200 "
        pdb=" CB  PHE B 200 "
        pdb=" CG  PHE B 200 "
      ideal   model   delta    sigma   weight residual
     113.80  107.96    5.84 1.00e+00 1.00e+00 3.41e+01
  angle pdb=" C   PHE B 389 "
        pdb=" CA  PHE B 389 "
        pdb=" CB  PHE B 389 "
      ideal   model   delta    sigma   weight residual
     111.74  119.36   -7.62 1.37e+00 5.33e-01 3.09e+01
  angle pdb=" CA  PHE B 445 "
        pdb=" CB  PHE B 445 "
        pdb=" CG  PHE B 445 "
      ideal   model   delta    sigma   weight residual
     113.80  119.22   -5.42 1.00e+00 1.00e+00 2.94e+01
  angle pdb=" N   TYR B 259 "
        pdb=" CA  TYR B 259 "
        pdb=" C   TYR B 259 "
      ideal   model   delta    sigma   weight residual
     111.36  116.60   -5.24 1.09e+00 8.42e-01 2.31e+01
  ... (remaining 5500 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 2151
       17.97 -    35.94: 151
       35.94 -    53.91: 20
       53.91 -    71.88: 3
       71.88 -    89.85: 4
  Dihedral angle restraints: 2329
    sinusoidal: 876
      harmonic: 1453
  Sorted by residual:
  dihedral pdb=" CA  PRO B 455 "
           pdb=" C   PRO B 455 "
           pdb=" N   VAL B 456 "
           pdb=" CA  VAL B 456 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.56  -29.44     0      5.00e+00 4.00e-02 3.47e+01
  dihedral pdb=" CA  TRP B 477 "
           pdb=" C   TRP B 477 "
           pdb=" N   TRP B 478 "
           pdb=" CA  TRP B 478 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.28  -27.72     0      5.00e+00 4.00e-02 3.07e+01
  dihedral pdb=" CA  ILE B 139 "
           pdb=" C   ILE B 139 "
           pdb=" N   ILE B 140 "
           pdb=" CA  ILE B 140 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.56  -25.44     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 2326 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 430
       0.072 -    0.145: 173
       0.145 -    0.217: 51
       0.217 -    0.290: 10
       0.290 -    0.362: 1
  Chirality restraints: 665
  Sorted by residual:
  chirality pdb=" CA  SER B 113 "
            pdb=" N   SER B 113 "
            pdb=" C   SER B 113 "
            pdb=" CB  SER B 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.27e+00
  chirality pdb=" CB  ILE B 147 "
            pdb=" CA  ILE B 147 "
            pdb=" CG1 ILE B 147 "
            pdb=" CG2 ILE B 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" CA  THR B 194 "
            pdb=" N   THR B 194 "
            pdb=" C   THR B 194 "
            pdb=" CB  THR B 194 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 662 not shown)

  Planarity restraints: 660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 141 "    0.316 9.50e-02 1.11e+02   1.42e-01 1.27e+01
        pdb=" NE  ARG B 141 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 141 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 141 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 141 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 348 "    0.314 9.50e-02 1.11e+02   1.41e-01 1.22e+01
        pdb=" NE  ARG B 348 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 348 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 348 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 348 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 182 "    0.269 9.50e-02 1.11e+02   1.21e-01 9.11e+00
        pdb=" NE  ARG A 182 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 182 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 182 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 182 "    0.012 2.00e-02 2.50e+03
  ... (remaining 657 not shown)

  Histogram of nonbonded interaction distances:
        2.61 -     3.07: 2508
        3.07 -     3.53: 4300
        3.53 -     3.98: 6293
        3.98 -     4.44: 7251
        4.44 -     4.90: 11235
  Nonbonded interactions: 31587
  Sorted by model distance:
  nonbonded pdb=" O   VAL B 288 "
            pdb=" OG1 THR B 292 "
     model   vdw
     2.610 3.040
  nonbonded pdb=" OH  TYR B 103 "
            pdb=" OD1 ASP B 116 "
     model   vdw
     2.614 3.040
  nonbonded pdb=" NH2 ARG A 182 "
            pdb=" O   LYS B 498 "
     model   vdw
     2.633 3.120
  nonbonded pdb=" OG  SER B 395 "
            pdb=" OE1 GLU B 457 "
     model   vdw
     2.635 3.040
  nonbonded pdb=" O   ALA B 295 "
            pdb=" OG1 THR B 298 "
     model   vdw
     2.635 3.040
  ... (remaining 31582 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             0.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.600
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6349
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      :  0.011   0.077   4034  Z= 0.703
  Angle     :  1.682   8.893   5507  Z= 1.133
  Chirality :  0.084   0.362    665
  Planarity :  0.012   0.142    660
  Dihedral  : 13.038  89.853   1392
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 0.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  4.45 %
    Favored  : 94.38 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.31), residues: 500
  helix: -1.67 (0.21), residues: 378
  sheet:  None (None), residues: 0
  loop : -1.70 (0.58), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP B 257 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.024   0.005   PHE B  69 
 TYR   0.021   0.005   TYR B 146 
 ARG   0.011   0.001   ARG B 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17033 (  292)
  hydrogen bonds       : angle       8.07243 (  852)
  SS BOND              : bond        0.07680 (    1)
  SS BOND              : angle       4.38125 (    2)
  covalent geometry    : bond        0.01104 ( 4033)
  covalent geometry    : angle       1.67985 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 169
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   60 VAL cc_start: 0.7315 (t) cc_final: 0.7075 (p)
REVERT: B  111 SER cc_start: 0.8071 (p) cc_final: 0.7536 (m)
REVERT: B  141 ARG cc_start: 0.6753 (tpp-160) cc_final: 0.6444 (tpp-160)
REVERT: B  239 ASP cc_start: 0.6811 (t0) cc_final: 0.6364 (t0)
REVERT: B  249 SER cc_start: 0.8405 (m) cc_final: 0.8157 (p)
REVERT: B  272 ARG cc_start: 0.5694 (ttt180) cc_final: 0.5404 (tpt170)
REVERT: B  297 PHE cc_start: 0.7492 (m-80) cc_final: 0.7155 (m-80)
REVERT: B  298 THR cc_start: 0.8119 (p) cc_final: 0.7838 (p)
REVERT: B  315 PHE cc_start: 0.8096 (t80) cc_final: 0.7843 (t80)
REVERT: B  318 TYR cc_start: 0.9131 (t80) cc_final: 0.8884 (t80)
REVERT: B  319 HIS cc_start: 0.6702 (m-70) cc_final: 0.5654 (m-70)
REVERT: B  365 MET cc_start: 0.8073 (mmt) cc_final: 0.7718 (mmt)
REVERT: B  367 HIS cc_start: 0.7775 (t-90) cc_final: 0.7168 (t-90)
REVERT: B  369 GLN cc_start: 0.8257 (mm-40) cc_final: 0.8028 (mp10)
REVERT: B  391 LYS cc_start: 0.7614 (tptm) cc_final: 0.7241 (mmtt)
REVERT: B  394 PHE cc_start: 0.6433 (t80) cc_final: 0.6163 (t80)
REVERT: B  500 MET cc_start: 0.5676 (mmt) cc_final: 0.4931 (mtm)
  outliers start: 5
  outliers final: 1
  residues processed: 170
  average time/residue: 0.1564
  time to fit residues: 33.3383
Evaluate side-chains
  116 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 23 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 293 ASN ** 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 = 0.3433 r_free = 0.3433 target = 0.122520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.099046 restraints weight = 6332.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.102339 restraints weight = 3595.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.104534 restraints weight = 2493.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4034  Z= 0.138
  Angle     :  0.646   6.619   5507  Z= 0.332
  Chirality :  0.043   0.179    665
  Planarity :  0.004   0.031    660
  Dihedral  :  5.294  21.047    534
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.36), residues: 500
  helix:  0.89 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -1.00 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 452 
 HIS   0.002   0.001   HIS B 420 
 PHE   0.018   0.002   PHE B 200 
 TYR   0.020   0.001   TYR B 103 
 ARG   0.002   0.000   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  292)
  hydrogen bonds       : angle       4.64472 (  852)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.88239 (    2)
  covalent geometry    : bond        0.00289 ( 4033)
  covalent geometry    : angle       0.64566 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8226 (pm20) cc_final: 0.7624 (pm20)
REVERT: B  194 THR cc_start: 0.7650 (p) cc_final: 0.7409 (p)
REVERT: B  205 LEU cc_start: 0.8455 (mt) cc_final: 0.8173 (mt)
REVERT: B  254 TYR cc_start: 0.8208 (m-80) cc_final: 0.7663 (m-80)
REVERT: B  259 TYR cc_start: 0.7373 (m-10) cc_final: 0.6928 (m-10)
REVERT: B  297 PHE cc_start: 0.8084 (m-80) cc_final: 0.7478 (m-80)
REVERT: B  335 CYS cc_start: 0.9061 (m) cc_final: 0.8703 (m)
REVERT: B  365 MET cc_start: 0.7760 (mmt) cc_final: 0.7120 (mmp)
REVERT: B  394 PHE cc_start: 0.7685 (t80) cc_final: 0.7073 (t80)
REVERT: B  398 ASN cc_start: 0.7919 (m-40) cc_final: 0.7216 (m-40)
REVERT: B  415 MET cc_start: 0.9147 (tmm) cc_final: 0.8679 (ttp)
REVERT: B  500 MET cc_start: 0.6498 (mmt) cc_final: 0.5502 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1246
  time to fit residues: 22.6664
Evaluate side-chains
  104 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 31 optimal weight:    0.1980
   chunk 4 optimal weight:    8.9990
   chunk 8 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 497 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.123093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.099576 restraints weight = 6396.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.102934 restraints weight = 3582.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.105125 restraints weight = 2462.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4034  Z= 0.128
  Angle     :  0.612   6.813   5507  Z= 0.304
  Chirality :  0.041   0.158    665
  Planarity :  0.004   0.034    660
  Dihedral  :  4.677  18.877    534
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.37), residues: 500
  helix:  1.51 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop : -0.89 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 405 
 HIS   0.003   0.001   HIS B 319 
 PHE   0.015   0.001   PHE B 200 
 TYR   0.014   0.001   TYR B 289 
 ARG   0.001   0.000   ARG A 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03600 (  292)
  hydrogen bonds       : angle       4.17959 (  852)
  SS BOND              : bond        0.00064 (    1)
  SS BOND              : angle       0.75386 (    2)
  covalent geometry    : bond        0.00291 ( 4033)
  covalent geometry    : angle       0.61169 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8370 (pm20) cc_final: 0.7779 (pm20)
REVERT: B  178 CYS cc_start: 0.8550 (t) cc_final: 0.8336 (t)
REVERT: B  194 THR cc_start: 0.7766 (p) cc_final: 0.7460 (p)
REVERT: B  254 TYR cc_start: 0.8186 (m-80) cc_final: 0.7634 (m-80)
REVERT: B  265 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6845 (mt-10)
REVERT: B  297 PHE cc_start: 0.8293 (m-80) cc_final: 0.7998 (m-80)
REVERT: B  319 HIS cc_start: 0.7622 (m-70) cc_final: 0.7350 (m90)
REVERT: B  394 PHE cc_start: 0.7641 (t80) cc_final: 0.7341 (t80)
REVERT: B  398 ASN cc_start: 0.7940 (m-40) cc_final: 0.7476 (m-40)
REVERT: B  500 MET cc_start: 0.6601 (mmt) cc_final: 0.5391 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.1267
  time to fit residues: 19.9204
Evaluate side-chains
  93 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
B 261 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.117805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.094429 restraints weight = 6612.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.097595 restraints weight = 3775.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.099483 restraints weight = 2645.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.4287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4034  Z= 0.225
  Angle     :  0.707   7.602   5507  Z= 0.351
  Chirality :  0.045   0.149    665
  Planarity :  0.005   0.038    660
  Dihedral  :  4.778  18.974    534
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.36), residues: 500
  helix:  1.33 (0.25), residues: 382
  sheet:  None (None), residues: 0
  loop : -0.52 (0.59), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 417 
 HIS   0.002   0.001   HIS B 420 
 PHE   0.024   0.002   PHE B 473 
 TYR   0.030   0.002   TYR B 289 
 ARG   0.003   0.001   ARG B 348 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04142 (  292)
  hydrogen bonds       : angle       4.51327 (  852)
  SS BOND              : bond        0.00009 (    1)
  SS BOND              : angle       1.11997 (    2)
  covalent geometry    : bond        0.00538 ( 4033)
  covalent geometry    : angle       0.70648 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8416 (pm20) cc_final: 0.8100 (pm20)
REVERT: B  178 CYS cc_start: 0.8495 (t) cc_final: 0.8236 (t)
REVERT: B  254 TYR cc_start: 0.8382 (m-80) cc_final: 0.7858 (m-80)
REVERT: B  259 TYR cc_start: 0.8074 (m-10) cc_final: 0.7869 (m-10)
REVERT: B  335 CYS cc_start: 0.9082 (m) cc_final: 0.8671 (m)
REVERT: B  500 MET cc_start: 0.6865 (mmt) cc_final: 0.5740 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1226
  time to fit residues: 17.0205
Evaluate side-chains
  90 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0170
   chunk 37 optimal weight:    0.2980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6622

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

Flipped N/Q/H residues before XYZ refinement:
** B 261 ASN ** 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 = 0.3464 r_free = 0.3464 target = 0.124975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.101193 restraints weight = 6501.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.104590 restraints weight = 3653.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.106843 restraints weight = 2538.844|
|-----------------------------------------------------------------------------|
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.4750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4034  Z= 0.114
  Angle     :  0.599   6.435   5507  Z= 0.290
  Chirality :  0.040   0.151    665
  Planarity :  0.004   0.037    660
  Dihedral  :  4.256  17.642    534
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.37), residues: 500
  helix:  1.75 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.29 (0.62), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 405 
 HIS   0.001   0.001   HIS B 367 
 PHE   0.014   0.001   PHE B  95 
 TYR   0.018   0.001   TYR B 103 
 ARG   0.001   0.000   ARG B 421 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03350 (  292)
  hydrogen bonds       : angle       3.96513 (  852)
  SS BOND              : bond        0.00111 (    1)
  SS BOND              : angle       0.48187 (    2)
  covalent geometry    : bond        0.00247 ( 4033)
  covalent geometry    : angle       0.59886 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8407 (pm20) cc_final: 0.8093 (pm20)
REVERT: B  178 CYS cc_start: 0.8540 (t) cc_final: 0.8315 (t)
REVERT: B  254 TYR cc_start: 0.8217 (m-80) cc_final: 0.7712 (m-80)
REVERT: B  305 MET cc_start: 0.8546 (mtt) cc_final: 0.8301 (mmm)
REVERT: B  319 HIS cc_start: 0.8138 (m-70) cc_final: 0.7781 (m-70)
REVERT: B  365 MET cc_start: 0.8171 (mmp) cc_final: 0.7842 (mmp)
REVERT: B  407 CYS cc_start: 0.7171 (t) cc_final: 0.6562 (t)
REVERT: B  432 ASN cc_start: 0.6973 (t0) cc_final: 0.6731 (t0)
REVERT: B  500 MET cc_start: 0.6922 (mmt) cc_final: 0.5782 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1269
  time to fit residues: 18.9754
Evaluate side-chains
  91 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 1 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:   10.0000
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B 398 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.124711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.101053 restraints weight = 6349.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.104430 restraints weight = 3537.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.106412 restraints weight = 2450.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.4984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4034  Z= 0.114
  Angle     :  0.595   7.460   5507  Z= 0.286
  Chirality :  0.039   0.153    665
  Planarity :  0.004   0.035    660
  Dihedral  :  4.118  18.326    534
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.37), residues: 500
  helix:  1.95 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.31 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 405 
 HIS   0.002   0.000   HIS B 319 
 PHE   0.013   0.001   PHE B  95 
 TYR   0.018   0.001   TYR B 103 
 ARG   0.001   0.000   ARG B 421 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03179 (  292)
  hydrogen bonds       : angle       3.91574 (  852)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       0.38492 (    2)
  covalent geometry    : bond        0.00258 ( 4033)
  covalent geometry    : angle       0.59475 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8420 (pm20) cc_final: 0.7819 (pm20)
REVERT: B  105 GLU cc_start: 0.5723 (tp30) cc_final: 0.5204 (tp30)
REVERT: B  136 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7703 (mm-30)
REVERT: B  178 CYS cc_start: 0.8548 (t) cc_final: 0.8342 (t)
REVERT: B  194 THR cc_start: 0.7366 (p) cc_final: 0.7059 (p)
REVERT: B  205 LEU cc_start: 0.8394 (mt) cc_final: 0.8173 (mt)
REVERT: B  254 TYR cc_start: 0.8273 (m-80) cc_final: 0.7775 (m-80)
REVERT: B  265 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6791 (mt-10)
REVERT: B  305 MET cc_start: 0.8638 (mtt) cc_final: 0.8371 (mmm)
REVERT: B  319 HIS cc_start: 0.8082 (m-70) cc_final: 0.7782 (m-70)
REVERT: B  365 MET cc_start: 0.8283 (mmp) cc_final: 0.8017 (mmp)
REVERT: B  383 MET cc_start: 0.9185 (mmm) cc_final: 0.8943 (tpt)
REVERT: B  500 MET cc_start: 0.6917 (mmt) cc_final: 0.5846 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1328
  time to fit residues: 18.9915
Evaluate side-chains
  88 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 9 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 46 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 38 optimal weight:    0.2980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B 261 ASN ** 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 = 0.3482 r_free = 0.3482 target = 0.126067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.102760 restraints weight = 6322.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.105918 restraints weight = 3555.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.108197 restraints weight = 2472.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.5126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4034  Z= 0.111
  Angle     :  0.585   6.736   5507  Z= 0.282
  Chirality :  0.039   0.153    665
  Planarity :  0.004   0.035    660
  Dihedral  :  4.020  18.623    534
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.37), residues: 500
  helix:  2.03 (0.26), residues: 388
  sheet:  None (None), residues: 0
  loop : -0.24 (0.61), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 257 
 HIS   0.001   0.000   HIS B 319 
 PHE   0.019   0.001   PHE B 474 
 TYR   0.028   0.001   TYR B 103 
 ARG   0.001   0.000   ARG B 427 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03082 (  292)
  hydrogen bonds       : angle       3.86009 (  852)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.35440 (    2)
  covalent geometry    : bond        0.00249 ( 4033)
  covalent geometry    : angle       0.58485 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8449 (pm20) cc_final: 0.7895 (pm20)
REVERT: B  136 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7276 (mm-30)
REVERT: B  178 CYS cc_start: 0.8644 (t) cc_final: 0.8388 (t)
REVERT: B  205 LEU cc_start: 0.8269 (mt) cc_final: 0.8062 (mt)
REVERT: B  254 TYR cc_start: 0.7922 (m-80) cc_final: 0.7358 (m-80)
REVERT: B  319 HIS cc_start: 0.8120 (m-70) cc_final: 0.7806 (m-70)
REVERT: B  383 MET cc_start: 0.9162 (mmm) cc_final: 0.8937 (tpt)
REVERT: B  500 MET cc_start: 0.6927 (mmt) cc_final: 0.5837 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1248
  time to fit residues: 17.1793
Evaluate side-chains
  88 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 44 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 11 optimal weight:    0.3980
   chunk 4 optimal weight:    0.4980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 261 ASN ** 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 = 0.3491 r_free = 0.3491 target = 0.126628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.103407 restraints weight = 6255.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.106649 restraints weight = 3517.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.108834 restraints weight = 2438.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.5270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4034  Z= 0.111
  Angle     :  0.586   6.381   5507  Z= 0.282
  Chirality :  0.039   0.148    665
  Planarity :  0.004   0.034    660
  Dihedral  :  3.959  17.269    534
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.38), residues: 500
  helix:  2.19 (0.26), residues: 387
  sheet:  None (None), residues: 0
  loop : -0.24 (0.61), residues: 113

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 405 
 HIS   0.001   0.000   HIS B 319 
 PHE   0.019   0.001   PHE B 474 
 TYR   0.022   0.001   TYR B 103 
 ARG   0.001   0.000   ARG B 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03081 (  292)
  hydrogen bonds       : angle       3.83181 (  852)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.32834 (    2)
  covalent geometry    : bond        0.00249 ( 4033)
  covalent geometry    : angle       0.58637 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.451 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8447 (pm20) cc_final: 0.7917 (pm20)
REVERT: A  209 ARG cc_start: 0.6318 (mmt180) cc_final: 0.5892 (mmm-85)
REVERT: B  105 GLU cc_start: 0.6007 (tm-30) cc_final: 0.5312 (tp30)
REVERT: B  178 CYS cc_start: 0.8584 (t) cc_final: 0.8317 (t)
REVERT: B  205 LEU cc_start: 0.8221 (mt) cc_final: 0.8010 (mt)
REVERT: B  254 TYR cc_start: 0.7956 (m-80) cc_final: 0.7454 (m-80)
REVERT: B  319 HIS cc_start: 0.8109 (m-70) cc_final: 0.7495 (m-70)
REVERT: B  362 ILE cc_start: 0.8590 (mt) cc_final: 0.8326 (mt)
REVERT: B  365 MET cc_start: 0.7973 (mmp) cc_final: 0.7625 (mmp)
REVERT: B  383 MET cc_start: 0.9138 (mmm) cc_final: 0.8925 (tpt)
REVERT: B  404 ASN cc_start: 0.7968 (m-40) cc_final: 0.7745 (m110)
REVERT: B  500 MET cc_start: 0.6942 (mmt) cc_final: 0.5906 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1170
  time to fit residues: 17.7195
Evaluate side-chains
  93 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0970
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 261 ASN ** 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 = 0.3468 r_free = 0.3468 target = 0.125012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.101681 restraints weight = 6368.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.104850 restraints weight = 3617.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.107079 restraints weight = 2531.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.5290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4034  Z= 0.129
  Angle     :  0.626   6.975   5507  Z= 0.302
  Chirality :  0.041   0.140    665
  Planarity :  0.004   0.033    660
  Dihedral  :  4.063  17.095    534
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.38), residues: 500
  helix:  2.09 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.26 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 257 
 HIS   0.002   0.001   HIS B 319 
 PHE   0.023   0.002   PHE B 439 
 TYR   0.022   0.001   TYR B 103 
 ARG   0.001   0.000   ARG A 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03358 (  292)
  hydrogen bonds       : angle       3.91365 (  852)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.39158 (    2)
  covalent geometry    : bond        0.00304 ( 4033)
  covalent geometry    : angle       0.62633 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8556 (pm20) cc_final: 0.7959 (pm20)
REVERT: A  209 ARG cc_start: 0.6397 (mmt180) cc_final: 0.5942 (mmm-85)
REVERT: B  178 CYS cc_start: 0.8586 (t) cc_final: 0.8301 (t)
REVERT: B  205 LEU cc_start: 0.8347 (mt) cc_final: 0.8145 (mt)
REVERT: B  254 TYR cc_start: 0.8076 (m-80) cc_final: 0.7538 (m-80)
REVERT: B  265 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6938 (mp0)
REVERT: B  291 LEU cc_start: 0.8395 (mm) cc_final: 0.8142 (mm)
REVERT: B  365 MET cc_start: 0.8220 (mmp) cc_final: 0.7928 (mmp)
REVERT: B  383 MET cc_start: 0.9169 (mmm) cc_final: 0.8950 (tpt)
REVERT: B  394 PHE cc_start: 0.7173 (t80) cc_final: 0.6746 (t80)
REVERT: B  500 MET cc_start: 0.7008 (mmt) cc_final: 0.6056 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1179
  time to fit residues: 16.6237
Evaluate side-chains
  91 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.125611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.102786 restraints weight = 6311.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.106041 restraints weight = 3563.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.108165 restraints weight = 2464.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.5462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4034  Z= 0.115
  Angle     :  0.617   7.115   5507  Z= 0.296
  Chirality :  0.041   0.151    665
  Planarity :  0.004   0.032    660
  Dihedral  :  3.989  17.518    534
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.38), residues: 500
  helix:  2.13 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.27 (0.61), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 257 
 HIS   0.008   0.002   HIS B 367 
 PHE   0.028   0.002   PHE B 439 
 TYR   0.025   0.001   TYR B 103 
 ARG   0.001   0.000   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03235 (  292)
  hydrogen bonds       : angle       3.84736 (  852)
  SS BOND              : bond        0.00089 (    1)
  SS BOND              : angle       0.32354 (    2)
  covalent geometry    : bond        0.00260 ( 4033)
  covalent geometry    : angle       0.61745 ( 5505)

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

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

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1000 Ramachandran restraints generated.
    500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8573 (pm20) cc_final: 0.7747 (pm20)
REVERT: A  209 ARG cc_start: 0.6470 (mmt180) cc_final: 0.6046 (mmm-85)
REVERT: B  133 LEU cc_start: 0.8896 (tp) cc_final: 0.8670 (tt)
REVERT: B  178 CYS cc_start: 0.8577 (t) cc_final: 0.8304 (t)
REVERT: B  205 LEU cc_start: 0.8275 (mt) cc_final: 0.8068 (mt)
REVERT: B  254 TYR cc_start: 0.8030 (m-80) cc_final: 0.7457 (m-80)
REVERT: B  265 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6910 (mp0)
REVERT: B  291 LEU cc_start: 0.8297 (mm) cc_final: 0.8075 (mm)
REVERT: B  383 MET cc_start: 0.9141 (mmm) cc_final: 0.8934 (tpt)
REVERT: B  394 PHE cc_start: 0.7153 (t80) cc_final: 0.6709 (t80)
REVERT: B  500 MET cc_start: 0.6917 (mmt) cc_final: 0.6052 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1162
  time to fit residues: 15.7370
Evaluate side-chains
  92 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0050
   chunk 32 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.4000

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

Flipped N/Q/H residues before XYZ refinement:
** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 367 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 = 0.3467 r_free = 0.3467 target = 0.124709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.101155 restraints weight = 6433.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.104394 restraints weight = 3681.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.106419 restraints weight = 2579.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.5483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4034  Z= 0.132
  Angle     :  0.641   6.918   5507  Z= 0.314
  Chirality :  0.042   0.140    665
  Planarity :  0.004   0.032    660
  Dihedral  :  4.126  17.312    534
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.38), residues: 500
  helix:  1.92 (0.26), residues: 393
  sheet:  None (None), residues: 0
  loop : -0.25 (0.64), residues: 107

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 257 
 HIS   0.002   0.001   HIS B 319 
 PHE   0.025   0.002   PHE B 439 
 TYR   0.022   0.001   TYR B 103 
 ARG   0.002   0.000   ARG B 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03470 (  292)
  hydrogen bonds       : angle       3.90593 (  852)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.39644 (    2)
  covalent geometry    : bond        0.00312 ( 4033)
  covalent geometry    : angle       0.64155 ( 5505)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1404.88 seconds
wall clock time: 25 minutes 53.07 seconds (1553.07 seconds total)