Starting phenix.real_space_refine
on Mon Apr 28 08:18:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ldr_63006/04_2025/9ldr_63006.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ldr_63006/04_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_63006/04_2025/9ldr_63006.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ldr_63006/04_2025/9ldr_63006.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ldr_63006/04_2025/9ldr_63006.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ldr_63006/04_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 4.78, per 1000 atoms: 0.66
  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: 2.03
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.74
  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: 1.92

  Time building geometry restraints manager: 2.22 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:             1.770
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.140
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.040
-------------------------------------------------------------------------------
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  : 0.796 
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: 0.2056
  time to fit residues: 34.0814
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  : 0.798 
-------------------------------------------------------------------------------
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 = 0.3785 r_free = 0.3785 target = 0.153603 restraints weight = 13956.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.155873 restraints weight = 11930.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
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  : 0.755 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8566 (m-80) cc_final: 0.8132 (m-80)
REVERT: A  209 MET cc_start: 0.2410 (mmt) cc_final: 0.1344 (mmt)
REVERT: A  231 TRP cc_start: 0.7367 (m-90) cc_final: 0.7085 (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: 0.5518 (ptm160)
REVERT: B  485 MET cc_start: 0.5559 (pmm) cc_final: 0.5287 (ppp)
REVERT: B  555 ILE cc_start: 0.8385 (pt) cc_final: 0.7882 (mt)
  outliers start: 17
  outliers final: 10
  residues processed: 108
  average time/residue: 0.1787
  time to fit residues: 26.6102
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  : 0.783 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   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:    0.8980
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.2382

-------------------------------------------------------------------------------
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 = 0.4352 r_free = 0.4352 target = 0.211551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.159980 restraints weight = 9040.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.160053 restraints weight = 10800.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.160905 restraints weight = 10590.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7455  Z= 0.153
  Angle     :  0.634  10.980  10143  Z= 0.316
  Chirality :  0.039   0.159   1164
  Planarity :  0.004   0.054   1273
  Dihedral  :  5.094  53.753   1002
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.12 %
    Favored  : 79.85 %
  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: -0.66 (0.27), residues: 930
  helix:  1.01 (0.24), residues: 485
  sheet: -1.64 (0.53), residues: 71
  loop : -2.20 (0.29), residues: 374

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        0.05867 (  380)
  hydrogen bonds       : angle       4.61911 ( 1089)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       1.79863 (    2)
  covalent geometry    : bond        0.00351 ( 7454)
  covalent geometry    : angle       0.63355 (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
  113 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.7254 (tp30) cc_final: 0.6962 (tp30)
REVERT: A  150 TYR cc_start: 0.8539 (m-80) cc_final: 0.8160 (m-80)
REVERT: A  209 MET cc_start: 0.2509 (mmt) cc_final: 0.1383 (mmt)
REVERT: A  231 TRP cc_start: 0.7343 (m-90) cc_final: 0.6999 (m100)
REVERT: A  493 GLN cc_start: 0.9242 (tp-100) cc_final: 0.8939 (tm-30)
REVERT: B  181 ARG cc_start: 0.6084 (mmm160) cc_final: 0.5482 (ptm160)
REVERT: B  405 TYR cc_start: 0.8309 (t80) cc_final: 0.7850 (t80)
  outliers start: 16
  outliers final: 13
  residues processed: 106
  average time/residue: 0.1866
  time to fit residues: 27.0895
Evaluate side-chains
  96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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  393 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:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 83 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 85 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    1.6166

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.194898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.152739 restraints weight = 8729.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.151227 restraints weight = 16338.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.152421 restraints weight = 16135.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7455  Z= 0.170
  Angle     :  0.632   9.862  10143  Z= 0.317
  Chirality :  0.040   0.141   1164
  Planarity :  0.004   0.054   1273
  Dihedral  :  4.958  52.858   1002
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.26 %
    Favored  : 77.69 %
  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: -0.37 (0.28), residues: 930
  helix:  1.20 (0.24), residues: 489
  sheet: -1.45 (0.54), residues: 71
  loop : -2.04 (0.30), residues: 370

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   0.015   0.002   PHE A 337 
 TYR   0.018   0.002   TYR A 163 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06144 (  380)
  hydrogen bonds       : angle       4.56075 ( 1089)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       1.88637 (    2)
  covalent geometry    : bond        0.00404 ( 7454)
  covalent geometry    : angle       0.63179 (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
  115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.7285 (tp30) cc_final: 0.6998 (tp30)
REVERT: A  150 TYR cc_start: 0.8541 (m-80) cc_final: 0.8190 (m-80)
REVERT: A  209 MET cc_start: 0.2652 (mmt) cc_final: 0.1508 (mmt)
REVERT: B  181 ARG cc_start: 0.5991 (mmm160) cc_final: 0.5613 (ptm160)
  outliers start: 24
  outliers final: 16
  residues processed: 108
  average time/residue: 0.1739
  time to fit residues: 26.3212
Evaluate side-chains
  99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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  617 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 38 optimal weight:    0.0970
   chunk 40 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0060
   chunk 60 optimal weight:    8.9990
   chunk 21 optimal weight:    0.3980
   chunk 49 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
A 254 ASN
A 493 GLN
B 539 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.201036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.157056 restraints weight = 8568.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.155140 restraints weight = 12716.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.156501 restraints weight = 11982.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7455  Z= 0.113
  Angle     :  0.576   9.287  10143  Z= 0.286
  Chirality :  0.037   0.129   1164
  Planarity :  0.004   0.051   1273
  Dihedral  :  4.678  51.354   1002
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.52 %
    Favored  : 77.57 %
  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:  0.11 (0.28), residues: 930
  helix:  1.71 (0.24), residues: 482
  sheet: -1.20 (0.55), residues: 71
  loop : -1.92 (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   0.011   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        0.04648 (  380)
  hydrogen bonds       : angle       4.25263 ( 1089)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       1.46217 (    2)
  covalent geometry    : bond        0.00238 ( 7454)
  covalent geometry    : angle       0.57605 (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
  123 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 GLU cc_start: 0.7205 (tp30) cc_final: 0.6955 (tp30)
REVERT: A  150 TYR cc_start: 0.8478 (m-80) cc_final: 0.7956 (m-80)
REVERT: A  209 MET cc_start: 0.2154 (mmt) cc_final: 0.1052 (mmt)
REVERT: B  405 TYR cc_start: 0.8180 (t80) cc_final: 0.7974 (t80)
REVERT: B  529 ASP cc_start: 0.6981 (t0) cc_final: 0.6722 (t0)
  outliers start: 23
  outliers final: 15
  residues processed: 116
  average time/residue: 0.1770
  time to fit residues: 28.8946
Evaluate side-chains
  104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
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  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  379 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:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 8 optimal weight:    0.1980
   chunk 82 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0270
   chunk 88 optimal weight:    1.9990
   chunk 90 optimal weight:   30.0000
   overall best weight:    0.5040

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

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

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 = 0.202208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.157344 restraints weight = 8585.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.155720 restraints weight = 13134.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.157233 restraints weight = 12904.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7455  Z= 0.111
  Angle     :  0.576   8.957  10143  Z= 0.283
  Chirality :  0.038   0.128   1164
  Planarity :  0.004   0.051   1273
  Dihedral  :  4.381  50.113   1000
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  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:  0.35 (0.28), residues: 930
  helix:  1.89 (0.25), residues: 483
  sheet: -1.12 (0.55), residues: 71
  loop : -1.80 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   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        0.04410 (  380)
  hydrogen bonds       : angle       4.14319 ( 1089)
  SS BOND              : bond        0.00002 (    1)
  SS BOND              : angle       1.42555 (    2)
  covalent geometry    : bond        0.00238 ( 7454)
  covalent geometry    : angle       0.57533 (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
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8450 (m-80) cc_final: 0.7916 (m-80)
REVERT: A  209 MET cc_start: 0.2149 (mmt) cc_final: 0.1120 (mmm)
REVERT: A  315 MET cc_start: 0.7220 (tpp) cc_final: 0.6992 (mmm)
REVERT: B  405 TYR cc_start: 0.8197 (t80) cc_final: 0.7856 (t80)
REVERT: B  529 ASP cc_start: 0.7105 (t0) cc_final: 0.6850 (t0)
REVERT: B  555 ILE cc_start: 0.8241 (pp) cc_final: 0.7585 (mt)
  outliers start: 20
  outliers final: 17
  residues processed: 106
  average time/residue: 0.1717
  time to fit residues: 25.5713
Evaluate side-chains
  104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
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  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  241 ASN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  457 MET
Chi-restraints excluded: chain B residue  495 SER
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:    3.9990
   chunk 32 optimal weight:    0.0370
   chunk 17 optimal weight:    0.3980
   chunk 62 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0670
   chunk 45 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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 = 0.4223 r_free = 0.4223 target = 0.204146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.157668 restraints weight = 8558.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.152826 restraints weight = 15547.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.155156 restraints weight = 13857.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7455  Z= 0.107
  Angle     :  0.577   9.496  10143  Z= 0.278
  Chirality :  0.037   0.128   1164
  Planarity :  0.004   0.049   1273
  Dihedral  :  4.245  48.450   1000
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 21.04 %
    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:  0.50 (0.29), residues: 930
  helix:  1.99 (0.25), residues: 484
  sheet: -1.10 (0.55), residues: 71
  loop : -1.68 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 398 
 HIS   0.003   0.001   HIS B 557 
 PHE   0.014   0.001   PHE B 285 
 TYR   0.010   0.001   TYR A 163 
 ARG   0.005   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04077 (  380)
  hydrogen bonds       : angle       4.04836 ( 1089)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       1.31396 (    2)
  covalent geometry    : bond        0.00226 ( 7454)
  covalent geometry    : angle       0.57725 (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
  115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8427 (m-80) cc_final: 0.7855 (m-80)
REVERT: A  209 MET cc_start: 0.2082 (mmt) cc_final: 0.1034 (mmm)
REVERT: A  315 MET cc_start: 0.7253 (tpp) cc_final: 0.7021 (mmm)
REVERT: B  405 TYR cc_start: 0.8269 (t80) cc_final: 0.7891 (t80)
REVERT: B  529 ASP cc_start: 0.7270 (t0) cc_final: 0.7008 (t0)
REVERT: B  555 ILE cc_start: 0.8269 (pp) cc_final: 0.7564 (mt)
  outliers start: 24
  outliers final: 19
  residues processed: 108
  average time/residue: 0.1956
  time to fit residues: 29.6876
Evaluate side-chains
  104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
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  206 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  355 LEU
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  457 MET
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:    7.9990
   chunk 35 optimal weight:    0.0050
   chunk 44 optimal weight:    6.9990
   chunk 6 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 71 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.6394

-------------------------------------------------------------------------------
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 = 0.4212 r_free = 0.4212 target = 0.202821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.158528 restraints weight = 8672.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.157180 restraints weight = 12968.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.158795 restraints weight = 12353.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.2952

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     :  0.593   8.344  10143  Z= 0.287
  Chirality :  0.038   0.172   1164
  Planarity :  0.004   0.051   1273
  Dihedral  :  4.176  47.565   1000
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 21.55 %
    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:  0.55 (0.29), residues: 930
  helix:  2.03 (0.25), residues: 484
  sheet: -1.11 (0.55), residues: 71
  loop : -1.64 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 398 
 HIS   0.003   0.001   HIS B 557 
 PHE   0.012   0.001   PHE B 285 
 TYR   0.010   0.001   TYR A 163 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04322 (  380)
  hydrogen bonds       : angle       4.03183 ( 1089)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       1.35479 (    2)
  covalent geometry    : bond        0.00249 ( 7454)
  covalent geometry    : angle       0.59299 (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
  108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8443 (m-80) cc_final: 0.7804 (m-80)
REVERT: A  209 MET cc_start: 0.2233 (mmt) cc_final: 0.1176 (mmm)
REVERT: A  315 MET cc_start: 0.7149 (tpp) cc_final: 0.6947 (mmm)
REVERT: B  529 ASP cc_start: 0.7256 (t0) cc_final: 0.7041 (t0)
  outliers start: 24
  outliers final: 20
  residues processed: 100
  average time/residue: 0.2041
  time to fit residues: 30.8493
Evaluate side-chains
  103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 GLU
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  206 ILE
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  245 PHE
Chi-restraints excluded: chain A residue  355 LEU
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  192 LEU
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain B residue  412 THR
Chi-restraints excluded: chain B residue  457 MET
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:    0.0000
   chunk 76 optimal weight:    0.0020
   chunk 81 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.9394

-------------------------------------------------------------------------------
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 = 0.4198 r_free = 0.4198 target = 0.201225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.157644 restraints weight = 8699.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.154739 restraints weight = 16350.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.156535 restraints weight = 14220.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7455  Z= 0.128
  Angle     :  0.615  10.354  10143  Z= 0.297
  Chirality :  0.039   0.236   1164
  Planarity :  0.004   0.053   1273
  Dihedral  :  4.196  46.504   1000
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.67 %
    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:  0.47 (0.29), residues: 930
  helix:  1.90 (0.25), residues: 491
  sheet: -1.09 (0.56), residues: 71
  loop : -1.67 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 398 
 HIS   0.003   0.001   HIS B 266 
 PHE   0.012   0.001   PHE A 337 
 TYR   0.012   0.001   TYR A 163 
 ARG   0.005   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04781 (  380)
  hydrogen bonds       : angle       4.08016 ( 1089)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       1.47368 (    2)
  covalent geometry    : bond        0.00293 ( 7454)
  covalent geometry    : angle       0.61504 (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
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.699 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8455 (m-80) cc_final: 0.7951 (m-80)
REVERT: A  209 MET cc_start: 0.2323 (mmt) cc_final: 0.1222 (mmm)
REVERT: B  198 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7698 (mm)
REVERT: B  555 ILE cc_start: 0.8245 (pp) cc_final: 0.7564 (mt)
  outliers start: 23
  outliers final: 21
  residues processed: 103
  average time/residue: 0.1988
  time to fit residues: 28.8902
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 GLU
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  355 LEU
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 A residue  494 LEU
Chi-restraints excluded: chain B residue  192 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  457 MET
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:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 19 optimal weight:    9.9990
   chunk 42 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.201673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.158148 restraints weight = 8734.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.157445 restraints weight = 13230.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.158635 restraints weight = 12989.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7557
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7455  Z= 0.122
  Angle     :  0.636  12.953  10143  Z= 0.303
  Chirality :  0.040   0.364   1164
  Planarity :  0.004   0.071   1273
  Dihedral  :  4.172  45.275   1000
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.55 %
    Favored  : 75.67 %
  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:  0.51 (0.29), residues: 930
  helix:  1.92 (0.25), residues: 491
  sheet: -1.12 (0.56), residues: 71
  loop : -1.62 (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   0.012   0.001   PHE A 432 
 TYR   0.019   0.001   TYR B 405 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04623 (  380)
  hydrogen bonds       : angle       4.09417 ( 1089)
  SS BOND              : bond        0.00063 (    1)
  SS BOND              : angle       1.39030 (    2)
  covalent geometry    : bond        0.00275 ( 7454)
  covalent geometry    : angle       0.63613 (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
  111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8455 (m-80) cc_final: 0.7903 (m-80)
REVERT: A  209 MET cc_start: 0.2331 (mmt) cc_final: 0.1252 (mmm)
REVERT: B  246 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7242 (mmmt)
REVERT: B  555 ILE cc_start: 0.8259 (pp) cc_final: 0.7569 (mt)
  outliers start: 22
  outliers final: 19
  residues processed: 103
  average time/residue: 0.1960
  time to fit residues: 28.4403
Evaluate side-chains
  104 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
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  355 LEU
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  192 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  457 MET
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:    0.5980
   chunk 2 optimal weight:    0.0770
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 70 optimal weight:   10.0000
   chunk 58 optimal weight:    9.9990
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 = 0.4212 r_free = 0.4212 target = 0.202921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.159117 restraints weight = 8667.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.157222 restraints weight = 13412.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.158771 restraints weight = 12360.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7455  Z= 0.115
  Angle     :  0.614  12.642  10143  Z= 0.294
  Chirality :  0.039   0.340   1164
  Planarity :  0.004   0.059   1273
  Dihedral  :  4.091  43.754   1000
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.67 %
    Favored  : 75.79 %
  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:  1.97 (0.25), residues: 491
  sheet: -1.12 (0.56), residues: 71
  loop : -1.57 (0.32), 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   0.012   0.001   PHE B 285 
 TYR   0.020   0.001   TYR B 405 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04377 (  380)
  hydrogen bonds       : angle       4.03622 ( 1089)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       1.35439 (    2)
  covalent geometry    : bond        0.00256 ( 7454)
  covalent geometry    : angle       0.61407 (10141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2390.24 seconds
wall clock time: 43 minutes 54.30 seconds (2634.30 seconds total)