Starting phenix.real_space_refine
on Wed Sep 17 08:38:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ldr_63006/09_2025/9ldr_63006.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ldr_63006/09_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_63006/09_2025/9ldr_63006.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ldr_63006/09_2025/9ldr_63006.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ldr_63006/09_2025/9ldr_63006.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ldr_63006/09_2025/9ldr_63006.cif"
  }
  resolution = 3.58
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.78, per 1000 atoms: 0.24
  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: 0.63
  Conformation dependent library (CDL) restraints added in 378.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.28
  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: 1.03

  Time building geometry restraints manager: 0.84 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:             1.160
  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:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.390
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.004   0.000   ARG A 418 
 TYR   0.026   0.002   TYR A 163 
 PHE   0.022   0.002   PHE A 245 
 TRP   0.012   0.001   TRP B 194 
 HIS   0.003   0.001   HIS B 266 

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

*********************** 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  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6781 (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: 0.5436 (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: 0.0928
  time to fit residues: 15.4687
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  : 0.248 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0270
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
A 140 GLN
A 286 ASN
B 221 HIS
B 365 GLN
B 557 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.214374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.162066 restraints weight = 9006.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.158150 restraints weight = 10922.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.160310 restraints weight = 9479.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.161993 restraints weight = 6370.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.162504 restraints weight = 5966.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1562

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= 0.137
  Angle     :  0.630   7.741  10143  Z= 0.316
  Chirality :  0.039   0.131   1164
  Planarity :  0.004   0.053   1273
  Dihedral  :  6.055  68.579   1005
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.69 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.27), residues: 930
  helix:  0.53 (0.23), residues: 494
  sheet: -1.93 (0.51), residues: 71
  loop : -2.38 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 412 
 TYR   0.017   0.001   TYR A 163 
 PHE   0.013   0.001   PHE A 337 
 TRP   0.012   0.001   TRP A 398 
 HIS   0.004   0.001   HIS B 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7454)
  covalent geometry    : angle       0.62940 (10141)
  SS BOND              : bond        0.00096 (    1)
  SS BOND              : angle       1.66306 (    2)
  hydrogen bonds       : bond        0.05626 (  380)
  hydrogen bonds       : angle       4.74853 ( 1089)

*********************** 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
  120 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6708 (tt0)
REVERT: A  150 TYR cc_start: 0.8582 (m-80) cc_final: 0.8194 (m-80)
REVERT: A  209 MET cc_start: 0.2439 (mmt) cc_final: 0.1432 (mmt)
REVERT: A  231 TRP cc_start: 0.7274 (m-90) cc_final: 0.6981 (m100)
REVERT: A  493 GLN cc_start: 0.9225 (tp-100) cc_final: 0.8917 (tm-30)
REVERT: B  181 ARG cc_start: 0.6072 (mmm160) cc_final: 0.5395 (ptm160)
REVERT: B  405 TYR cc_start: 0.8267 (t80) cc_final: 0.8005 (t80)
REVERT: B  485 MET cc_start: 0.5639 (pmm) cc_final: 0.5414 (ppp)
REVERT: B  555 ILE cc_start: 0.8499 (pt) cc_final: 0.7967 (mt)
  outliers start: 15
  outliers final: 8
  residues processed: 112
  average time/residue: 0.0810
  time to fit residues: 12.6754
Evaluate side-chains
  93 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  211 LEU
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 45 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
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 = 0.4321 r_free = 0.4321 target = 0.208324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.157661 restraints weight = 9088.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.153977 restraints weight = 13245.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.156451 restraints weight = 12013.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.156392 restraints weight = 7344.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.157448 restraints weight = 6595.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   7455  Z= 0.197
  Angle     :  0.659  10.809  10143  Z= 0.334
  Chirality :  0.041   0.153   1164
  Planarity :  0.005   0.055   1273
  Dihedral  :  5.881  61.790   1005
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.36 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.27), residues: 930
  helix:  0.95 (0.24), residues: 487
  sheet: -1.62 (0.54), residues: 71
  loop : -2.14 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 363 
 TYR   0.019   0.002   TYR A 163 
 PHE   0.019   0.002   PHE A 337 
 TRP   0.013   0.001   TRP A 398 
 HIS   0.004   0.001   HIS B 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 ( 7454)
  covalent geometry    : angle       0.65848 (10141)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       2.06445 (    2)
  hydrogen bonds       : bond        0.06720 (  380)
  hydrogen bonds       : angle       4.76039 ( 1089)

*********************** 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: 21
    poor density    : 92
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8570 (m-80) cc_final: 0.8247 (m-80)
REVERT: A  209 MET cc_start: 0.2583 (mmt) cc_final: 0.1352 (mmt)
REVERT: A  220 GLU cc_start: 0.6322 (pm20) cc_final: 0.5553 (pm20)
REVERT: A  231 TRP cc_start: 0.7369 (m-90) cc_final: 0.7042 (m100)
REVERT: A  493 GLN cc_start: 0.9230 (tp-100) cc_final: 0.8984 (tm-30)
REVERT: B  181 ARG cc_start: 0.5998 (mmm160) cc_final: 0.5327 (ptm160)
  outliers start: 21
  outliers final: 14
  residues processed: 102
  average time/residue: 0.0848
  time to fit residues: 11.7687
Evaluate side-chains
  96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
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  359 ILE
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  500 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  551 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0670
   chunk 53 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 90 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.6118

-------------------------------------------------------------------------------
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 = 0.4379 r_free = 0.4379 target = 0.214723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.162241 restraints weight = 9106.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.158346 restraints weight = 11405.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.161230 restraints weight = 9705.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.161330 restraints weight = 6077.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.162553 restraints weight = 5725.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7455  Z= 0.121
  Angle     :  0.577   9.342  10143  Z= 0.289
  Chirality :  0.038   0.132   1164
  Planarity :  0.004   0.051   1273
  Dihedral  :  4.815  52.076   1002
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.74 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.28), residues: 930
  helix:  1.52 (0.24), residues: 482
  sheet: -1.37 (0.54), residues: 71
  loop : -2.00 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 363 
 TYR   0.016   0.001   TYR A 163 
 PHE   0.011   0.001   PHE A 432 
 TRP   0.010   0.001   TRP A 398 
 HIS   0.004   0.001   HIS B 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7454)
  covalent geometry    : angle       0.57664 (10141)
  SS BOND              : bond        0.00048 (    1)
  SS BOND              : angle       1.52954 (    2)
  hydrogen bonds       : bond        0.04912 (  380)
  hydrogen bonds       : angle       4.34175 ( 1089)

*********************** 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
  121 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8553 (m-80) cc_final: 0.8156 (m-80)
REVERT: A  209 MET cc_start: 0.2113 (mmt) cc_final: 0.1007 (mmt)
REVERT: A  220 GLU cc_start: 0.6061 (pm20) cc_final: 0.4852 (pm20)
REVERT: A  231 TRP cc_start: 0.7349 (m-90) cc_final: 0.7030 (m100)
REVERT: A  315 MET cc_start: 0.7501 (tpp) cc_final: 0.7292 (mmm)
REVERT: B  405 TYR cc_start: 0.8386 (t80) cc_final: 0.7905 (t80)
  outliers start: 26
  outliers final: 14
  residues processed: 110
  average time/residue: 0.0821
  time to fit residues: 12.6304
Evaluate side-chains
  98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
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  245 PHE
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  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  241 ASN
Chi-restraints excluded: chain B residue  242 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 1 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 86 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 84 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.5990

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.195692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.151634 restraints weight = 8753.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.149062 restraints weight = 15332.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.150028 restraints weight = 14514.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.152365 restraints weight = 9411.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.152396 restraints weight = 7590.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7455  Z= 0.168
  Angle     :  0.628   9.788  10143  Z= 0.315
  Chirality :  0.040   0.138   1164
  Planarity :  0.004   0.052   1273
  Dihedral  :  4.807  51.616   1002
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.90 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.28), residues: 930
  helix:  1.43 (0.24), residues: 490
  sheet: -1.26 (0.56), residues: 71
  loop : -1.89 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 363 
 TYR   0.016   0.002   TYR A 163 
 PHE   0.016   0.002   PHE A 337 
 TRP   0.011   0.001   TRP A 398 
 HIS   0.004   0.001   HIS B 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 7454)
  covalent geometry    : angle       0.62778 (10141)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       1.84677 (    2)
  hydrogen bonds       : bond        0.05964 (  380)
  hydrogen bonds       : angle       4.47761 ( 1089)

*********************** 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
  111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8534 (m-80) cc_final: 0.8162 (m-80)
REVERT: A  209 MET cc_start: 0.2481 (mmt) cc_final: 0.1292 (mmt)
REVERT: A  220 GLU cc_start: 0.5960 (pm20) cc_final: 0.4827 (pm20)
REVERT: B  181 ARG cc_start: 0.5903 (mmm160) cc_final: 0.5470 (ptm160)
REVERT: B  405 TYR cc_start: 0.8236 (t80) cc_final: 0.7988 (t80)
REVERT: B  529 ASP cc_start: 0.7063 (t0) cc_final: 0.6743 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 105
  average time/residue: 0.0825
  time to fit residues: 12.0377
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  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 TYR
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  379 ILE
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain B residue  162 PHE
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  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 6 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 92 optimal weight:    9.9990
   chunk 40 optimal weight:    0.0970
   chunk 70 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 60 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7178

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.200142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.156236 restraints weight = 8709.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.153760 restraints weight = 12892.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.155667 restraints weight = 11312.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.154450 restraints weight = 8616.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.154887 restraints weight = 8386.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7455  Z= 0.119
  Angle     :  0.593   9.116  10143  Z= 0.292
  Chirality :  0.038   0.130   1164
  Planarity :  0.004   0.050   1273
  Dihedral  :  4.601  50.632   1002
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 21.67 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.28), residues: 930
  helix:  1.80 (0.24), residues: 482
  sheet: -1.19 (0.54), residues: 71
  loop : -1.81 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 363 
 TYR   0.015   0.001   TYR A 163 
 PHE   0.015   0.001   PHE B 285 
 TRP   0.009   0.001   TRP A 398 
 HIS   0.003   0.001   HIS B 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7454)
  covalent geometry    : angle       0.59252 (10141)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       1.51120 (    2)
  hydrogen bonds       : bond        0.04804 (  380)
  hydrogen bonds       : angle       4.23390 ( 1089)

*********************** 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
  115 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8503 (m-80) cc_final: 0.8085 (m-80)
REVERT: A  209 MET cc_start: 0.2236 (mmt) cc_final: 0.1180 (mmm)
REVERT: B  405 TYR cc_start: 0.8219 (t80) cc_final: 0.7986 (t80)
REVERT: B  529 ASP cc_start: 0.7137 (t0) cc_final: 0.6854 (t0)
REVERT: B  555 ILE cc_start: 0.8285 (pp) cc_final: 0.7611 (mt)
  outliers start: 19
  outliers final: 13
  residues processed: 108
  average time/residue: 0.0743
  time to fit residues: 11.3664
Evaluate side-chains
  103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  245 PHE
Chi-restraints excluded: chain A residue  379 ILE
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  412 THR
Chi-restraints excluded: chain B residue  495 SER
Chi-restraints excluded: chain B residue  612 LEU
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 78 optimal weight:   20.0000
   chunk 21 optimal weight:    0.0470
   chunk 6 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 41 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 91 optimal weight:    9.9990
   chunk 12 optimal weight:    0.0170
   overall best weight:    0.4116

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

Flipped N/Q/H residues before XYZ refinement:
A 235 ASN
** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 539 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.203183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.158485 restraints weight = 8604.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.155830 restraints weight = 12279.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.157319 restraints weight = 11560.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.154689 restraints weight = 9214.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.155906 restraints weight = 8449.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7455  Z= 0.108
  Angle     :  0.575   8.568  10143  Z= 0.281
  Chirality :  0.037   0.130   1164
  Planarity :  0.004   0.050   1273
  Dihedral  :  4.298  49.109   1000
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.42 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.29), residues: 930
  helix:  1.96 (0.25), residues: 483
  sheet: -1.06 (0.55), residues: 71
  loop : -1.64 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.012   0.001   TYR A 163 
 PHE   0.013   0.001   PHE B 285 
 TRP   0.010   0.001   TRP A 398 
 HIS   0.004   0.001   HIS A 218 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 7454)
  covalent geometry    : angle       0.57468 (10141)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       1.38294 (    2)
  hydrogen bonds       : bond        0.04230 (  380)
  hydrogen bonds       : angle       4.11462 ( 1089)

*********************** 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: 20
    poor density    : 95
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8443 (m-80) cc_final: 0.7870 (m-80)
REVERT: A  209 MET cc_start: 0.2229 (mmt) cc_final: 0.1113 (mmm)
REVERT: B  405 TYR cc_start: 0.8186 (t80) cc_final: 0.7925 (t80)
REVERT: B  529 ASP cc_start: 0.7206 (t0) cc_final: 0.6958 (t0)
REVERT: B  555 ILE cc_start: 0.8322 (pp) cc_final: 0.7635 (mt)
  outliers start: 20
  outliers final: 17
  residues processed: 108
  average time/residue: 0.0850
  time to fit residues: 12.6461
Evaluate side-chains
  100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 MET
Chi-restraints excluded: chain A residue   58 MET
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  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  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
Chi-restraints excluded: chain B residue  241 ASN
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 59 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 14 optimal weight:    0.1980
   chunk 74 optimal weight:    3.9990
   chunk 9 optimal weight:    0.5980
   chunk 87 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.4170 r_free = 0.4170 target = 0.198052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.153729 restraints weight = 8650.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.151281 restraints weight = 15166.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.152583 restraints weight = 14243.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.154367 restraints weight = 9586.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.154635 restraints weight = 8335.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7455  Z= 0.152
  Angle     :  0.625   9.407  10143  Z= 0.306
  Chirality :  0.040   0.145   1164
  Planarity :  0.004   0.053   1273
  Dihedral  :  4.356  48.541   1000
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.80 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.28), residues: 930
  helix:  1.82 (0.25), residues: 484
  sheet: -1.08 (0.55), residues: 71
  loop : -1.65 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 363 
 TYR   0.013   0.001   TYR A 163 
 PHE   0.014   0.001   PHE A 337 
 TRP   0.009   0.001   TRP A 398 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7454)
  covalent geometry    : angle       0.62508 (10141)
  SS BOND              : bond        0.00110 (    1)
  SS BOND              : angle       1.61817 (    2)
  hydrogen bonds       : bond        0.05296 (  380)
  hydrogen bonds       : angle       4.24566 ( 1089)

*********************** 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
  112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8478 (m-80) cc_final: 0.8028 (m-80)
REVERT: A  209 MET cc_start: 0.2332 (mmt) cc_final: 0.1201 (mmm)
REVERT: B  405 TYR cc_start: 0.8225 (t80) cc_final: 0.7930 (t80)
REVERT: B  529 ASP cc_start: 0.7330 (t0) cc_final: 0.7097 (t0)
REVERT: B  555 ILE cc_start: 0.8389 (pp) cc_final: 0.7656 (mt)
  outliers start: 23
  outliers final: 19
  residues processed: 103
  average time/residue: 0.0778
  time to fit residues: 11.4509
Evaluate side-chains
  108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
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  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  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  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
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  612 LEU
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 39 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.4186 r_free = 0.4186 target = 0.199819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.156178 restraints weight = 8557.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.152680 restraints weight = 15477.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.154388 restraints weight = 13992.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.154285 restraints weight = 9305.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.154953 restraints weight = 9143.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7455  Z= 0.129
  Angle     :  0.614   9.228  10143  Z= 0.301
  Chirality :  0.039   0.169   1164
  Planarity :  0.004   0.052   1273
  Dihedral  :  4.305  47.881   1000
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 22.43 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.29), residues: 930
  helix:  1.85 (0.25), residues: 484
  sheet: -1.04 (0.56), residues: 71
  loop : -1.59 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 363 
 TYR   0.043   0.002   TYR B 554 
 PHE   0.013   0.001   PHE A 432 
 TRP   0.009   0.001   TRP A 398 
 HIS   0.003   0.001   HIS B 557 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7454)
  covalent geometry    : angle       0.61362 (10141)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       1.46523 (    2)
  hydrogen bonds       : bond        0.04924 (  380)
  hydrogen bonds       : angle       4.19741 ( 1089)

*********************** 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
  110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8500 (m-80) cc_final: 0.8033 (m-80)
REVERT: A  209 MET cc_start: 0.2301 (mmt) cc_final: 0.1200 (mmm)
REVERT: A  315 MET cc_start: 0.7126 (tpp) cc_final: 0.6879 (mmm)
REVERT: B  405 TYR cc_start: 0.8206 (t80) cc_final: 0.7915 (t80)
REVERT: B  529 ASP cc_start: 0.7297 (t0) cc_final: 0.7059 (t0)
  outliers start: 19
  outliers final: 19
  residues processed: 103
  average time/residue: 0.0778
  time to fit residues: 11.5124
Evaluate side-chains
  105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
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  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  192 LEU
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
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  612 LEU
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 67 optimal weight:    1.9990
   chunk 76 optimal weight:    0.0770
   chunk 79 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0010
   chunk 46 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.8146

-------------------------------------------------------------------------------
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 = 0.4194 r_free = 0.4194 target = 0.200764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.157820 restraints weight = 8661.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.154430 restraints weight = 15931.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.155871 restraints weight = 12939.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.156028 restraints weight = 9481.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.156358 restraints weight = 10235.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7455  Z= 0.125
  Angle     :  0.621  10.390  10143  Z= 0.303
  Chirality :  0.039   0.170   1164
  Planarity :  0.004   0.071   1273
  Dihedral  :  4.249  46.598   1000
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.31 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.29), residues: 930
  helix:  1.87 (0.25), residues: 485
  sheet: -1.06 (0.55), residues: 71
  loop : -1.52 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 363 
 TYR   0.013   0.001   TYR A 163 
 PHE   0.012   0.001   PHE A 432 
 TRP   0.012   0.001   TRP B 338 
 HIS   0.003   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7454)
  covalent geometry    : angle       0.62106 (10141)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       1.42841 (    2)
  hydrogen bonds       : bond        0.04766 (  380)
  hydrogen bonds       : angle       4.13522 ( 1089)

********************** 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
  109 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 TYR cc_start: 0.8459 (m-80) cc_final: 0.8023 (m-80)
REVERT: A  209 MET cc_start: 0.2340 (mmt) cc_final: 0.1242 (mmm)
REVERT: A  315 MET cc_start: 0.7094 (tpp) cc_final: 0.6832 (mmm)
REVERT: B  405 TYR cc_start: 0.8224 (t80) cc_final: 0.7954 (t80)
REVERT: B  529 ASP cc_start: 0.7312 (t0) cc_final: 0.7075 (t0)
REVERT: B  555 ILE cc_start: 0.8255 (pp) cc_final: 0.7554 (mt)
  outliers start: 20
  outliers final: 19
  residues processed: 102
  average time/residue: 0.0795
  time to fit residues: 11.4558
Evaluate side-chains
  103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
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  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  192 LEU
Chi-restraints excluded: chain B residue  235 GLN
Chi-restraints excluded: chain B residue  237 HIS
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  612 LEU
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 78 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0050
   chunk 12 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 67 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0170
   overall best weight:    0.7634

-------------------------------------------------------------------------------
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 = 0.4196 r_free = 0.4196 target = 0.200968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.158062 restraints weight = 8698.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.156885 restraints weight = 11669.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.156967 restraints weight = 12985.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.156545 restraints weight = 8663.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.157137 restraints weight = 8310.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7455  Z= 0.122
  Angle     :  0.615   9.712  10143  Z= 0.300
  Chirality :  0.040   0.369   1164
  Planarity :  0.004   0.061   1273
  Dihedral  :  4.178  45.213   1000
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.56 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.29), residues: 930
  helix:  1.91 (0.25), residues: 485
  sheet: -1.12 (0.55), residues: 71
  loop : -1.50 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 363 
 TYR   0.012   0.001   TYR A 163 
 PHE   0.012   0.001   PHE A 432 
 TRP   0.009   0.001   TRP A 398 
 HIS   0.002   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7454)
  covalent geometry    : angle       0.61506 (10141)
  SS BOND              : bond        0.00053 (    1)
  SS BOND              : angle       1.43317 (    2)
  hydrogen bonds       : bond        0.04657 (  380)
  hydrogen bonds       : angle       4.07894 ( 1089)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1229.11 seconds
wall clock time: 22 minutes 0.88 seconds (1320.88 seconds total)