Starting phenix.real_space_refine
on Sun May 11 01:37:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ldr_63006/05_2025/9ldr_63006.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ldr_63006/05_2025/9ldr_63006.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ldr_63006/05_2025/9ldr_63006.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ldr_63006/05_2025/9ldr_63006.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ldr_63006/05_2025/9ldr_63006.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ldr_63006/05_2025/9ldr_63006.cif"
  }
  resolution = 3.58
  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=   0.003 sd=   0.070
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      30      5.16       5
     C    4743      2.51       5
     N    1190      2.21       5
     O    1311      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 61 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: 7274
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 463, 3595
          Classifications: {'peptide': 463}
          Link IDs: {'PTRANS': 21, 'TRANS': 441}
    Chain: "B"
      Number of atoms: 3670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3670
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 22, 'TRANS': 448}
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 4.59, per 1000 atoms: 0.63
  Number of scatterers: 7274
  At special positions: 0
  Unit cell: (109.44, 106.02, 78.66, 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      30     16.00
     O    1311      8.00
     N    1190      7.00
     C    4743      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 159 " - pdb=" SG  CYS B 211 " 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: 1.63
  Conformation dependent library (CDL) restraints added in 923.5 milliseconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 5 sheets defined
      58.7% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 59
    Processing helix  chain 'A' and resid 77 through 106
    Processing helix  chain 'A' and resid 111 through 120
      removed outlier: 3.503A  pdb=" N   ILE A 115 " --> pdb=" O   SER A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 134
    Processing helix  chain 'A' and resid 134 through 152
      removed outlier: 3.874A  pdb=" N   THR A 138 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLY A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE A 152 " --> pdb=" O   ALA A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 156
    Processing helix  chain 'A' and resid 163 through 184
      removed outlier: 3.964A  pdb=" N   TYR A 184 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 214
    Processing helix  chain 'A' and resid 232 through 245
      removed outlier: 4.527A  pdb=" N   LEU A 238 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 248
      No H-bonds generated for 'chain 'A' and resid 246 through 248'
    Processing helix  chain 'A' and resid 253 through 260
      removed outlier: 3.589A  pdb=" N   VAL A 256 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 5.893A  pdb=" N   GLU A 258 " --> pdb=" O   PHE A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 293
      Proline residue:  A 268  - end of helix
      Proline residue:  A 276  - end of helix
    Processing helix  chain 'A' and resid 294 through 299
    Processing helix  chain 'A' and resid 303 through 312
    Processing helix  chain 'A' and resid 318 through 349
      removed outlier: 3.656A  pdb=" N   ILE A 322 " --> pdb=" O   TRP A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 381
    Processing helix  chain 'A' and resid 385 through 392
      removed outlier: 3.914A  pdb=" N   GLN A 388 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   ILE A 390 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 415
      removed outlier: 3.519A  pdb=" N   GLU A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 446
      Proline residue:  A 443  - end of helix
      removed outlier: 3.653A  pdb=" N   THR A 446 " --> pdb=" O   VAL A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 460
      removed outlier: 3.590A  pdb=" N   SER A 451 " --> pdb=" O   ASP A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 469
      removed outlier: 3.580A  pdb=" N   TYR A 465 " --> pdb=" O   GLY A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 496
      removed outlier: 3.729A  pdb=" N   ARG A 481 " --> pdb=" O   PRO A 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 174
    Processing helix  chain 'B' and resid 176 through 207
      removed outlier: 3.656A  pdb=" N   VAL B 180 " --> pdb=" O   SER B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 236
      removed outlier: 3.871A  pdb=" N   GLN B 235 " --> pdb=" O   LEU B 231 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLY B 236 " --> pdb=" O   GLN B 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 231 through 236'
    Processing helix  chain 'B' and resid 241 through 246
    Processing helix  chain 'B' and resid 248 through 255
    Processing helix  chain 'B' and resid 287 through 301
    Processing helix  chain 'B' and resid 325 through 342
      removed outlier: 3.835A  pdb=" N   THR B 329 " --> pdb=" O   ASP B 325 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU B 336 " --> pdb=" O   LYS B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 354
    Processing helix  chain 'B' and resid 356 through 372
      removed outlier: 3.641A  pdb=" N   PHE B 360 " --> pdb=" O   ASP B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 393
      removed outlier: 3.504A  pdb=" N   ILE B 389 " --> pdb=" O   ASP B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 427
      removed outlier: 3.521A  pdb=" N   LYS B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR B 427 " --> pdb=" O   TYR B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 445
    Processing helix  chain 'B' and resid 450 through 458
    Processing helix  chain 'B' and resid 505 through 509
      removed outlier: 3.654A  pdb=" N   THR B 509 " --> pdb=" O   ALA B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 515
      removed outlier: 4.037A  pdb=" N   GLU B 515 " --> pdb=" O   LYS B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 534
      removed outlier: 3.541A  pdb=" N   GLU B 534 " --> pdb=" O   GLN B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 539
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.665A  pdb=" N   SER B 589 " --> pdb=" O   ALA B 586 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 225 through 226
    Processing sheet with id=AA2, first strand: chain 'B' and resid 307 through 308
      removed outlier: 6.893A  pdb=" N   LEU B 307 " --> pdb=" O   GLN B 347 " (cutoff:3.500A)
      removed outlier: 8.813A  pdb=" N   ARG B 349 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 7.123A  pdb=" N   LEU B 377 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
      removed outlier: 8.307A  pdb=" N   THR B 402 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   ALA B 379 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 541 through 544
      removed outlier: 3.732A  pdb=" N   HIS B 557 " --> pdb=" O   ASP B 541 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   HIS B 543 " --> pdb=" O   ILE B 555 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   TYR B 554 " --> pdb=" O   VAL B 566 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 575 through 576
    Processing sheet with id=AA5, first strand: chain 'B' and resid 593 through 594

    380 hydrogen bonds defined for protein.
    1089 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: 1.78

  Time building geometry restraints manager: 1.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1372
        1.33 -     1.45: 1855
        1.45 -     1.57: 4182
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 7454
  Sorted by residual:
  bond pdb=" CA  GLN B 235 "
       pdb=" C   GLN B 235 "
    ideal  model  delta    sigma   weight residual
    1.522  1.476  0.046 1.38e-02 5.25e+03 1.13e+01
  bond pdb=" CA  ASN B 241 "
       pdb=" C   ASN B 241 "
    ideal  model  delta    sigma   weight residual
    1.533  1.504  0.029 9.60e-03 1.09e+04 9.00e+00
  bond pdb=" CA  PHE A 122 "
       pdb=" C   PHE A 122 "
    ideal  model  delta    sigma   weight residual
    1.524  1.499  0.025 1.24e-02 6.50e+03 4.02e+00
  bond pdb=" CA  LEU B 406 "
       pdb=" C   LEU B 406 "
    ideal  model  delta    sigma   weight residual
    1.522  1.496  0.027 1.34e-02 5.57e+03 3.98e+00
  bond pdb=" CA  LYS B 258 "
       pdb=" C   LYS B 258 "
    ideal  model  delta    sigma   weight residual
    1.530  1.508  0.021 1.11e-02 8.12e+03 3.63e+00
  ... (remaining 7449 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 9625
        1.70 -     3.41: 435
        3.41 -     5.11: 60
        5.11 -     6.82: 13
        6.82 -     8.52: 8
  Bond angle restraints: 10141
  Sorted by residual:
  angle pdb=" N   GLY A 120 "
        pdb=" CA  GLY A 120 "
        pdb=" C   GLY A 120 "
      ideal   model   delta    sigma   weight residual
     112.33  120.85   -8.52 1.21e+00 6.83e-01 4.96e+01
  angle pdb=" N   GLY B 240 "
        pdb=" CA  GLY B 240 "
        pdb=" C   GLY B 240 "
      ideal   model   delta    sigma   weight residual
     111.36  103.62    7.74 1.17e+00 7.31e-01 4.37e+01
  angle pdb=" N   PHE A 122 "
        pdb=" CA  PHE A 122 "
        pdb=" C   PHE A 122 "
      ideal   model   delta    sigma   weight residual
     110.97  104.13    6.84 1.09e+00 8.42e-01 3.94e+01
  angle pdb=" N   GLU B 414 "
        pdb=" CA  GLU B 414 "
        pdb=" C   GLU B 414 "
      ideal   model   delta    sigma   weight residual
     113.38  106.46    6.92 1.23e+00 6.61e-01 3.17e+01
  angle pdb=" N   GLY B 236 "
        pdb=" CA  GLY B 236 "
        pdb=" C   GLY B 236 "
      ideal   model   delta    sigma   weight residual
     115.32  108.25    7.07 1.48e+00 4.57e-01 2.28e+01
  ... (remaining 10136 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 3804
       17.10 -    34.19: 449
       34.19 -    51.29: 82
       51.29 -    68.39: 24
       68.39 -    85.48: 9
  Dihedral angle restraints: 4368
    sinusoidal: 1684
      harmonic: 2684
  Sorted by residual:
  dihedral pdb=" CA  CYS B 211 "
           pdb=" C   CYS B 211 "
           pdb=" N   ARG B 212 "
           pdb=" CA  ARG B 212 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.44  -21.56     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" CA  SER A 219 "
           pdb=" C   SER A 219 "
           pdb=" N   GLU A 220 "
           pdb=" CA  GLU A 220 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.91  -20.09     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  GLY A 314 "
           pdb=" C   GLY A 314 "
           pdb=" N   MET A 315 "
           pdb=" CA  MET A 315 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.46   19.54     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 4365 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 651
       0.032 -    0.064: 347
       0.064 -    0.096: 117
       0.096 -    0.127: 40
       0.127 -    0.159: 9
  Chirality restraints: 1164
  Sorted by residual:
  chirality pdb=" CG  LEU B 406 "
            pdb=" CB  LEU B 406 "
            pdb=" CD1 LEU B 406 "
            pdb=" CD2 LEU B 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.34e-01
  chirality pdb=" CA  HIS B 237 "
            pdb=" N   HIS B 237 "
            pdb=" C   HIS B 237 "
            pdb=" CB  HIS B 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.23e-01
  chirality pdb=" CA  PHE A 195 "
            pdb=" N   PHE A 195 "
            pdb=" C   PHE A 195 "
            pdb=" CB  PHE A 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.98e-01
  ... (remaining 1161 not shown)

  Planarity restraints: 1273
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 405 "    0.018 2.00e-02 2.50e+03   3.62e-02 1.31e+01
        pdb=" C   TYR B 405 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   TYR B 405 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LEU B 406 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 234 "    0.013 2.00e-02 2.50e+03   2.61e-02 6.83e+00
        pdb=" C   PHE B 234 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   PHE B 234 "    0.017 2.00e-02 2.50e+03
        pdb=" N   GLN B 235 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 153 "    0.035 5.00e-02 4.00e+02   5.25e-02 4.40e+00
        pdb=" N   PRO A 154 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 154 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 154 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1270 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 729
        2.73 -     3.27: 7624
        3.27 -     3.81: 11906
        3.81 -     4.36: 13710
        4.36 -     4.90: 23495
  Nonbonded interactions: 57464
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 220 "
            pdb=" OE1 GLU A 220 "
     model   vdw
     2.184 3.120
  nonbonded pdb=" NH1 ARG B 452 "
            pdb=" O   THR B 600 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" O   ASP B 493 "
            pdb=" OG  SER B 496 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" ND2 ASN A  57 "
            pdb=" OG1 THR A 252 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   LEU A 484 "
            pdb=" OG1 THR A 488 "
     model   vdw
     2.257 3.040
  ... (remaining 57459 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:             0.810
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.580
  Find NCS groups from input model:        0.100
  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:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
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      :  0.007   0.046   7455  Z= 0.295
  Angle     :  0.839   8.524  10143  Z= 0.502
  Chirality :  0.045   0.159   1164
  Planarity :  0.005   0.052   1273
  Dihedral  : 15.478  85.481   2641
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 14.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  8.11 %
    Favored  : 90.11 %
  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: -2.99 (0.24), residues: 930
  helix: -1.23 (0.21), residues: 492
  sheet: -2.48 (0.53), residues: 64
  loop : -2.86 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 194 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.022   0.002   PHE A 245 
 TYR   0.026   0.002   TYR A 163 
 ARG   0.004   0.000   ARG A 418 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15051 (  380)
  hydrogen bonds       : angle       6.71092 ( 1089)
  SS BOND              : bond        0.00287 (    1)
  SS BOND              : angle       2.54082 (    2)
  covalent geometry    : bond        0.00651 ( 7454)
  covalent geometry    : angle       0.83850 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6780 (tt0)
REVERT: A  150 TYR cc_start: 0.8597 (m-80) cc_final: 0.8149 (m-80)
REVERT: A  220 GLU cc_start: 0.6998 (pm20) cc_final: 0.5279 (pm20)
REVERT: A  231 TRP cc_start: 0.7480 (m-90) cc_final: 0.7093 (m100)
REVERT: A  493 GLN cc_start: 0.9248 (tp-100) cc_final: 0.8996 (tm-30)
REVERT: B  181 ARG cc_start: 0.6142 (mmm160) cc_final: 0.5527 (ptm160)
REVERT: B  337 PHE cc_start: 0.8116 (t80) cc_final: 0.7882 (t80)
REVERT: B  373 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6784 (mm-30)
  outliers start: 14
  outliers final: 2
  residues processed: 125
  average time/residue: 0.1938
  time to fit residues: 32.1071
Evaluate side-chains
  96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain B residue  162 PHE
Chi-restraints excluded: chain B residue  237 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:   40.0000
   chunk 70 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
A 254 ASN
A 286 ASN
B 221 HIS
** B 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.208457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.156993 restraints weight = 9010.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.153582 restraints weight = 13957.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.155867 restraints weight = 11967.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   7455  Z= 0.207
  Angle     :  0.687   7.614  10143  Z= 0.351
  Chirality :  0.042   0.150   1164
  Planarity :  0.005   0.057   1273
  Dihedral  :  6.311  75.546   1005
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.45 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.26), residues: 930
  helix:  0.17 (0.23), residues: 495
  sheet: -2.08 (0.53), residues: 65
  loop : -2.43 (0.29), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 398 
 HIS   0.004   0.001   HIS B 266 
 PHE   0.019   0.002   PHE A 337 
 TYR   0.022   0.002   TYR A 163 
 ARG   0.005   0.001   ARG A 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07033 (  380)
  hydrogen bonds       : angle       5.04511 ( 1089)
  SS BOND              : bond        0.00109 (    1)
  SS BOND              : angle       2.12687 (    2)
  covalent geometry    : bond        0.00498 ( 7454)
  covalent geometry    : angle       0.68604 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8567 (m-80) cc_final: 0.8133 (m-80)
REVERT: A  209 MET cc_start: 0.2408 (mmt) cc_final: 0.1342 (mmt)
REVERT: A  231 TRP cc_start: 0.7367 (m-90) cc_final: 0.7084 (m100)
REVERT: A  493 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8954 (tm-30)
REVERT: B  181 ARG cc_start: 0.6127 (mmm160) cc_final: 0.5516 (ptm160)
REVERT: B  485 MET cc_start: 0.5561 (pmm) cc_final: 0.5289 (ppp)
REVERT: B  555 ILE cc_start: 0.8387 (pt) cc_final: 0.7883 (mt)
  outliers start: 17
  outliers final: 10
  residues processed: 108
  average time/residue: 0.1867
  time to fit residues: 27.9408
Evaluate side-chains
  97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue  162 PHE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  551 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 54 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   chunk 64 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 82 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0370
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.0860

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

Flipped N/Q/H residues before XYZ refinement:
B 557 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.212283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.159109 restraints weight = 9033.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.155675 restraints weight = 12433.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.158263 restraints weight = 10107.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7455  Z= 0.144
  Angle     :  0.626  10.738  10143  Z= 0.312
  Chirality :  0.039   0.131   1164
  Planarity :  0.004   0.054   1273
  Dihedral  :  5.065  53.614   1002
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.87 %
    Favored  : 80.10 %
  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 (0.27), residues: 930
  helix:  1.11 (0.24), residues: 479
  sheet: -1.64 (0.53), residues: 71
  loop : -2.24 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 398 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.014   0.001   PHE A 337 
 TYR   0.018   0.001   TYR A 163 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05685 (  380)
  hydrogen bonds       : angle       4.58447 ( 1089)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       1.73774 (    2)
  covalent geometry    : bond        0.00327 ( 7454)
  covalent geometry    : angle       0.62592 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.7251 (tp30) cc_final: 0.6959 (tp30)
REVERT: A  150 TYR cc_start: 0.8561 (m-80) cc_final: 0.8192 (m-80)
REVERT: A  209 MET cc_start: 0.2473 (mmt) cc_final: 0.1445 (mmt)
REVERT: A  231 TRP cc_start: 0.7344 (m-90) cc_final: 0.6964 (m100)
REVERT: B  181 ARG cc_start: 0.6074 (mmm160) cc_final: 0.5423 (ptm160)
REVERT: B  405 TYR cc_start: 0.8331 (t80) cc_final: 0.7799 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1882
  time to fit residues: 27.5291
Evaluate side-chains
  96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue  162 PHE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  551 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 81 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 85 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0770
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    1.3744

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
B 365 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.196188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.154103 restraints weight = 8721.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.152537 restraints weight = 15508.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.153783 restraints weight = 14281.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7455  Z= 0.154
  Angle     :  0.620   9.586  10143  Z= 0.310
  Chirality :  0.039   0.136   1164
  Planarity :  0.004   0.053   1273
  Dihedral  :  4.906  52.682   1002
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 18.76 %
    Favored  : 78.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.28), residues: 930
  helix:  1.31 (0.24), residues: 488
  sheet: -1.44 (0.54), residues: 71
  loop : -2.03 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 398 
 HIS   0.004   0.001   HIS B 557 
 PHE   0.014   0.001   PHE A 337 
 TYR   0.017   0.001   TYR A 163 
 ARG   0.005   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05822 (  380)
  hydrogen bonds       : angle       4.51319 ( 1089)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       1.79206 (    2)
  covalent geometry    : bond        0.00361 ( 7454)
  covalent geometry    : angle       0.62001 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.7215 (tp30) cc_final: 0.6925 (tp30)
REVERT: A  150 TYR cc_start: 0.8492 (m-80) cc_final: 0.8094 (m-80)
REVERT: A  209 MET cc_start: 0.2452 (mmt) cc_final: 0.1268 (mmt)
REVERT: B  181 ARG cc_start: 0.5963 (mmm160) cc_final: 0.5586 (ptm160)
REVERT: B  555 ILE cc_start: 0.8211 (pt) cc_final: 0.7800 (mt)
  outliers start: 25
  outliers final: 17
  residues processed: 107
  average time/residue: 0.1825
  time to fit residues: 27.1244
Evaluate side-chains
  102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  104 THR
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue  162 PHE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 40 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 60 optimal weight:    8.9990
   chunk 21 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 254 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.199463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.155903 restraints weight = 8591.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.154487 restraints weight = 13278.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.155711 restraints weight = 12117.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7455  Z= 0.121
  Angle     :  0.577   9.452  10143  Z= 0.288
  Chirality :  0.038   0.128   1164
  Planarity :  0.004   0.051   1273
  Dihedral  :  4.707  51.359   1002
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.77 %
    Favored  : 77.19 %
  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:  0.05 (0.28), residues: 930
  helix:  1.66 (0.24), residues: 482
  sheet: -1.27 (0.55), residues: 71
  loop : -1.94 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 398 
 HIS   0.004   0.001   HIS B 557 
 PHE   0.012   0.001   PHE A 432 
 TYR   0.015   0.001   TYR A 163 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04983 (  380)
  hydrogen bonds       : angle       4.30817 ( 1089)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       1.55045 (    2)
  covalent geometry    : bond        0.00263 ( 7454)
  covalent geometry    : angle       0.57687 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.7223 (tp30) cc_final: 0.6971 (tp30)
REVERT: A  150 TYR cc_start: 0.8500 (m-80) cc_final: 0.8080 (m-80)
REVERT: A  209 MET cc_start: 0.2210 (mmt) cc_final: 0.1203 (mmm)
REVERT: B  405 TYR cc_start: 0.8160 (t80) cc_final: 0.7833 (t80)
REVERT: B  529 ASP cc_start: 0.6935 (t0) cc_final: 0.6678 (t0)
  outliers start: 24
  outliers final: 17
  residues processed: 114
  average time/residue: 0.1703
  time to fit residues: 27.4345
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  182 CYS
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  241 ASN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 88 optimal weight:    0.6980
   chunk 90 optimal weight:   30.0000
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 365 GLN
B 539 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.200538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.155841 restraints weight = 8592.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.153873 restraints weight = 13468.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.155311 restraints weight = 12349.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7455  Z= 0.119
  Angle     :  0.585   9.309  10143  Z= 0.288
  Chirality :  0.038   0.127   1164
  Planarity :  0.004   0.051   1273
  Dihedral  :  4.420  50.264   1000
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.55 %
    Favored  : 75.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.28), residues: 930
  helix:  1.82 (0.24), residues: 483
  sheet: -1.14 (0.55), residues: 71
  loop : -1.87 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 398 
 HIS   0.004   0.001   HIS B 557 
 PHE   0.016   0.001   PHE B 285 
 TYR   0.033   0.001   TYR B 554 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04723 (  380)
  hydrogen bonds       : angle       4.19915 ( 1089)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       1.46852 (    2)
  covalent geometry    : bond        0.00263 ( 7454)
  covalent geometry    : angle       0.58440 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8476 (m-80) cc_final: 0.7921 (m-80)
REVERT: A  209 MET cc_start: 0.2190 (mmt) cc_final: 0.1127 (mmm)
REVERT: A  315 MET cc_start: 0.7233 (tpp) cc_final: 0.7009 (mmm)
REVERT: B  405 TYR cc_start: 0.8192 (t80) cc_final: 0.7852 (t80)
REVERT: B  529 ASP cc_start: 0.7081 (t0) cc_final: 0.6817 (t0)
  outliers start: 20
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1841
  time to fit residues: 28.1662
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  182 CYS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  241 ASN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 85 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0770
   chunk 45 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 68 optimal weight:   10.0000
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 235 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.202161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.159694 restraints weight = 8505.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.157983 restraints weight = 13413.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.159252 restraints weight = 12376.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7455  Z= 0.113
  Angle     :  0.582   9.131  10143  Z= 0.283
  Chirality :  0.038   0.141   1164
  Planarity :  0.004   0.051   1273
  Dihedral  :  4.314  49.077   1000
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.29 %
    Favored  : 75.92 %
  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:  0.41 (0.29), residues: 930
  helix:  1.91 (0.25), residues: 483
  sheet: -1.06 (0.55), residues: 71
  loop : -1.73 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 398 
 HIS   0.002   0.001   HIS B 266 
 PHE   0.012   0.001   PHE B 285 
 TYR   0.012   0.001   TYR A 163 
 ARG   0.005   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04467 (  380)
  hydrogen bonds       : angle       4.13037 ( 1089)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       1.40591 (    2)
  covalent geometry    : bond        0.00245 ( 7454)
  covalent geometry    : angle       0.58154 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8452 (m-80) cc_final: 0.7910 (m-80)
REVERT: A  209 MET cc_start: 0.2204 (mmt) cc_final: 0.1133 (mmm)
REVERT: B  529 ASP cc_start: 0.7039 (t0) cc_final: 0.6773 (t0)
REVERT: B  555 ILE cc_start: 0.8167 (pp) cc_final: 0.7533 (mt)
  outliers start: 22
  outliers final: 15
  residues processed: 106
  average time/residue: 0.1793
  time to fit residues: 26.6270
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  182 CYS
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0670
   chunk 44 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0570
   chunk 48 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 71 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 88 optimal weight:    0.0970
   overall best weight:    0.3034

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.204554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.159234 restraints weight = 8612.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.158083 restraints weight = 12530.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.159353 restraints weight = 11964.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7455  Z= 0.105
  Angle     :  0.591   9.280  10143  Z= 0.284
  Chirality :  0.038   0.167   1164
  Planarity :  0.004   0.051   1273
  Dihedral  :  4.189  48.025   1000
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 22.81 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.29), residues: 930
  helix:  2.03 (0.25), residues: 485
  sheet: -1.02 (0.56), residues: 71
  loop : -1.63 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 398 
 HIS   0.002   0.001   HIS B 266 
 PHE   0.011   0.001   PHE B 285 
 TYR   0.023   0.001   TYR B 405 
 ARG   0.003   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (  380)
  hydrogen bonds       : angle       4.01742 ( 1089)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       1.31242 (    2)
  covalent geometry    : bond        0.00219 ( 7454)
  covalent geometry    : angle       0.59042 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8414 (m-80) cc_final: 0.7821 (m-80)
REVERT: A  209 MET cc_start: 0.2103 (mmt) cc_final: 0.1040 (mmm)
REVERT: B  529 ASP cc_start: 0.7152 (t0) cc_final: 0.6890 (t0)
REVERT: B  555 ILE cc_start: 0.8277 (pp) cc_final: 0.7554 (mt)
REVERT: B  565 LEU cc_start: 0.8387 (tp) cc_final: 0.8115 (tp)
  outliers start: 14
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1716
  time to fit residues: 24.4174
Evaluate side-chains
  97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 76 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 43 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0050
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
** A 266 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 = 0.4217 r_free = 0.4217 target = 0.203273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.163877 restraints weight = 8630.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.157933 restraints weight = 11024.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.148961 restraints weight = 10455.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7455  Z= 0.112
  Angle     :  0.596   9.121  10143  Z= 0.286
  Chirality :  0.038   0.150   1164
  Planarity :  0.004   0.052   1273
  Dihedral  :  4.135  46.917   1000
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 22.31 %
    Favored  : 75.54 %
  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:  0.59 (0.29), residues: 930
  helix:  2.04 (0.25), residues: 485
  sheet: -1.03 (0.56), residues: 71
  loop : -1.62 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 398 
 HIS   0.002   0.001   HIS B 266 
 PHE   0.011   0.001   PHE B 285 
 TYR   0.019   0.001   TYR B 405 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04264 (  380)
  hydrogen bonds       : angle       3.98686 ( 1089)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       1.32475 (    2)
  covalent geometry    : bond        0.00247 ( 7454)
  covalent geometry    : angle       0.59528 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8417 (m-80) cc_final: 0.7933 (m-80)
REVERT: A  209 MET cc_start: 0.2211 (mmt) cc_final: 0.1112 (mmm)
REVERT: B  529 ASP cc_start: 0.7628 (t0) cc_final: 0.7344 (t0)
REVERT: B  555 ILE cc_start: 0.8496 (pp) cc_final: 0.7783 (mt)
  outliers start: 17
  outliers final: 15
  residues processed: 101
  average time/residue: 0.1688
  time to fit residues: 24.0073
Evaluate side-chains
  94 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0470
   chunk 42 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.203300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.158962 restraints weight = 8769.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.155629 restraints weight = 14837.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.157495 restraints weight = 12841.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7455  Z= 0.117
  Angle     :  0.622  12.219  10143  Z= 0.297
  Chirality :  0.040   0.312   1164
  Planarity :  0.004   0.074   1273
  Dihedral  :  4.118  45.705   1000
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 22.56 %
    Favored  : 75.29 %
  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:  0.56 (0.29), residues: 930
  helix:  1.94 (0.25), residues: 491
  sheet: -1.03 (0.56), residues: 71
  loop : -1.60 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 398 
 HIS   0.002   0.001   HIS B 266 
 PHE   0.011   0.001   PHE A 432 
 TYR   0.020   0.001   TYR B 405 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04319 (  380)
  hydrogen bonds       : angle       4.03993 ( 1089)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       1.32345 (    2)
  covalent geometry    : bond        0.00265 ( 7454)
  covalent geometry    : angle       0.62180 (10141)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8404 (m-80) cc_final: 0.7897 (m-80)
REVERT: A  209 MET cc_start: 0.2314 (mmt) cc_final: 0.1299 (mmm)
REVERT: B  529 ASP cc_start: 0.7253 (t0) cc_final: 0.7018 (t0)
REVERT: B  555 ILE cc_start: 0.8322 (pp) cc_final: 0.7648 (mt)
  outliers start: 17
  outliers final: 15
  residues processed: 95
  average time/residue: 0.1718
  time to fit residues: 23.1447
Evaluate side-chains
  95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  374 CYS
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0270
   chunk 26 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0570
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.4956

-------------------------------------------------------------------------------
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 = 0.4227 r_free = 0.4227 target = 0.204436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.160214 restraints weight = 8567.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.158251 restraints weight = 12821.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.160309 restraints weight = 11535.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   7455  Z= 0.113
  Angle     :  0.627  13.089  10143  Z= 0.296
  Chirality :  0.039   0.262   1164
  Planarity :  0.004   0.059   1273
  Dihedral  :  4.097  44.429   1000
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 22.56 %
    Favored  : 75.29 %
  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:  0.61 (0.29), residues: 930
  helix:  2.03 (0.25), residues: 486
  sheet: -1.08 (0.55), residues: 71
  loop : -1.56 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 398 
 HIS   0.002   0.001   HIS B 266 
 PHE   0.011   0.001   PHE A 432 
 TYR   0.020   0.001   TYR B 405 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04146 (  380)
  hydrogen bonds       : angle       4.00994 ( 1089)
  SS BOND              : bond        0.00032 (    1)
  SS BOND              : angle       1.19362 (    2)
  covalent geometry    : bond        0.00252 ( 7454)
  covalent geometry    : angle       0.62670 (10141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2178.64 seconds
wall clock time: 38 minutes 59.39 seconds (2339.39 seconds total)