Starting phenix.real_space_refine
on Thu Mar 13 13:55:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xdd_33144/03_2025/7xdd_33144.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xdd_33144/03_2025/7xdd_33144.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xdd_33144/03_2025/7xdd_33144.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xdd_33144/03_2025/7xdd_33144.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xdd_33144/03_2025/7xdd_33144.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xdd_33144/03_2025/7xdd_33144.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      38      5.16       5
     C    5754      2.51       5
     N    1541      2.21       5
     O    1688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9021
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4062
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 19, 'TRANS': 492}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4959
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 611, 4959
          Classifications: {'peptide': 611}
          Link IDs: {'PTRANS': 22, 'TRANS': 588}
          Chain breaks: 1
  Time building chain proxies: 5.45, per 1000 atoms: 0.60
  Number of scatterers: 9021
  At special positions: 0
  Unit cell: (94.444, 132.222, 101.19, 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      38     16.00
     O    1688      8.00
     N    1541      7.00
     C    5754      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 5 sheets defined
      65.5% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 19
      removed outlier: 3.693A  pdb=" N   THR A  19 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 36
      removed outlier: 4.272A  pdb=" N   THR A  23 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 97
    Processing helix  chain 'A' and resid 97 through 104
      removed outlier: 3.923A  pdb=" N   LEU A 104 " --> pdb=" O   GLU A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 133
    Processing helix  chain 'A' and resid 155 through 164
    Processing helix  chain 'A' and resid 166 through 168
      No H-bonds generated for 'chain 'A' and resid 166 through 168'
    Processing helix  chain 'A' and resid 207 through 222
    Processing helix  chain 'A' and resid 226 through 230
    Processing helix  chain 'A' and resid 231 through 240
    Processing helix  chain 'A' and resid 241 through 245
      removed outlier: 3.761A  pdb=" N   LEU A 244 " --> pdb=" O   HIS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 270
    Processing helix  chain 'A' and resid 276 through 326
      Proline residue:  A 296  - end of helix
      Proline residue:  A 312  - end of helix
    Processing helix  chain 'A' and resid 332 through 339
    Processing helix  chain 'A' and resid 342 through 369
    Processing helix  chain 'A' and resid 378 through 403
      Proline residue:  A 394  - end of helix
    Processing helix  chain 'A' and resid 418 through 430
      removed outlier: 3.777A  pdb=" N   GLU A 422 " --> pdb=" O   PRO A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 468
    Processing helix  chain 'A' and resid 471 through 495
      Proline residue:  A 484  - end of helix
    Processing helix  chain 'A' and resid 499 through 503
    Processing helix  chain 'A' and resid 507 through 520
    Processing helix  chain 'B' and resid 2 through 8
    Processing helix  chain 'B' and resid 10 through 24
    Processing helix  chain 'B' and resid 48 through 53
    Processing helix  chain 'B' and resid 87 through 98
    Processing helix  chain 'B' and resid 102 through 113
    Processing helix  chain 'B' and resid 123 through 140
    Processing helix  chain 'B' and resid 163 through 173
    Processing helix  chain 'B' and resid 188 through 193
      removed outlier: 4.531A  pdb=" N   MET B 193 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 201
      removed outlier: 3.644A  pdb=" N   VAL B 200 " --> pdb=" O   ARG B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 212
    Processing helix  chain 'B' and resid 222 through 248
      removed outlier: 3.551A  pdb=" N   THR B 248 " --> pdb=" O   VAL B 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 260
      removed outlier: 4.160A  pdb=" N   SER B 260 " --> pdb=" O   GLU B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 297
    Processing helix  chain 'B' and resid 302 through 316
      Proline residue:  B 310  - end of helix
      removed outlier: 3.766A  pdb=" N   ILE B 314 " --> pdb=" O   PRO B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 327
    Processing helix  chain 'B' and resid 328 through 330
      No H-bonds generated for 'chain 'B' and resid 328 through 330'
    Processing helix  chain 'B' and resid 341 through 348
    Processing helix  chain 'B' and resid 351 through 381
    Processing helix  chain 'B' and resid 381 through 394
      removed outlier: 3.847A  pdb=" N   LYS B 387 " --> pdb=" O   ARG B 383 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU B 388 " --> pdb=" O   PHE B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 402
      removed outlier: 3.617A  pdb=" N   LYS B 398 " --> pdb=" O   GLU B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 412
    Processing helix  chain 'B' and resid 415 through 441
    Processing helix  chain 'B' and resid 445 through 450
      removed outlier: 4.140A  pdb=" N   GLU B 449 " --> pdb=" O   ASP B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 476
      Proline residue:  B 467  - end of helix
    Processing helix  chain 'B' and resid 477 through 481
    Processing helix  chain 'B' and resid 484 through 489
    Processing helix  chain 'B' and resid 491 through 507
      removed outlier: 3.606A  pdb=" N   ILE B 495 " --> pdb=" O   PRO B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 510
      No H-bonds generated for 'chain 'B' and resid 508 through 510'
    Processing helix  chain 'B' and resid 512 through 525
      removed outlier: 3.613A  pdb=" N   ASN B 525 " --> pdb=" O   VAL B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 537
    Processing helix  chain 'B' and resid 544 through 546
      No H-bonds generated for 'chain 'B' and resid 544 through 546'
    Processing helix  chain 'B' and resid 547 through 556
    Processing helix  chain 'B' and resid 559 through 562
    Processing helix  chain 'B' and resid 563 through 580
      removed outlier: 4.147A  pdb=" N   GLY B 575 " --> pdb=" O   GLU B 571 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   GLU B 576 " --> pdb=" O   GLY B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 589
      removed outlier: 3.968A  pdb=" N   ILE B 588 " --> pdb=" O   ASP B 584 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   PHE B 589 " --> pdb=" O   ASP B 585 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 584 through 589'
    Processing helix  chain 'B' and resid 593 through 600
    Processing helix  chain 'B' and resid 603 through 610
    Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 43
      removed outlier: 6.245A  pdb=" N   THR A  47 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   THR A 115 " --> pdb=" O   THR A  47 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL A  49 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   HIS A 117 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ILE A  51 " --> pdb=" O   HIS A 117 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY A 116 " --> pdb=" O   ILE A 145 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 64
    Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 154
      removed outlier: 4.506A  pdb=" N   GLY A 153 " --> pdb=" O   TRP A 189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 35
      removed outlier: 4.447A  pdb=" N   HIS B 122 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 65

    535 hydrogen bonds defined for protein.
    1554 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: 2.69

  Time building geometry restraints manager: 2.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2582
        1.33 -     1.45: 1541
        1.45 -     1.57: 5044
        1.57 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 9225
  Sorted by residual:
  bond pdb=" N   VAL A  85 "
       pdb=" CA  VAL A  85 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.11e-02 8.12e+03 1.15e+01
  bond pdb=" N   ILE B 379 "
       pdb=" CA  ILE B 379 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.033 1.06e-02 8.90e+03 9.72e+00
  bond pdb=" N   VAL B 412 "
       pdb=" CA  VAL B 412 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.43e+00
  bond pdb=" C   ARG B 490 "
       pdb=" N   PRO B 491 "
    ideal  model  delta    sigma   weight residual
    1.332  1.370 -0.038 1.30e-02 5.92e+03 8.63e+00
  bond pdb=" N   LYS B  58 "
       pdb=" CA  LYS B  58 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.033 1.12e-02 7.97e+03 8.56e+00
  ... (remaining 9220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 11954
        1.65 -     3.30: 439
        3.30 -     4.96: 60
        4.96 -     6.61: 13
        6.61 -     8.26: 2
  Bond angle restraints: 12468
  Sorted by residual:
  angle pdb=" C   SER B 123 "
        pdb=" CA  SER B 123 "
        pdb=" CB  SER B 123 "
      ideal   model   delta    sigma   weight residual
     116.54  110.79    5.75 1.15e+00 7.56e-01 2.50e+01
  angle pdb=" N   GLU B 416 "
        pdb=" CA  GLU B 416 "
        pdb=" C   GLU B 416 "
      ideal   model   delta    sigma   weight residual
     111.71  106.98    4.73 1.15e+00 7.56e-01 1.69e+01
  angle pdb=" N   PRO A  81 "
        pdb=" CA  PRO A  81 "
        pdb=" C   PRO A  81 "
      ideal   model   delta    sigma   weight residual
     112.47  104.47    8.00 2.06e+00 2.36e-01 1.51e+01
  angle pdb=" N   GLN A 230 "
        pdb=" CA  GLN A 230 "
        pdb=" C   GLN A 230 "
      ideal   model   delta    sigma   weight residual
     113.16  108.58    4.58 1.24e+00 6.50e-01 1.36e+01
  angle pdb=" CA  ARG B 490 "
        pdb=" C   ARG B 490 "
        pdb=" N   PRO B 491 "
      ideal   model   delta    sigma   weight residual
     118.85  122.26   -3.41 9.50e-01 1.11e+00 1.29e+01
  ... (remaining 12463 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 4993
       17.91 -    35.83: 426
       35.83 -    53.74: 82
       53.74 -    71.65: 21
       71.65 -    89.57: 9
  Dihedral angle restraints: 5531
    sinusoidal: 2255
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" CA  ARG A 339 "
           pdb=" C   ARG A 339 "
           pdb=" N   TYR A 340 "
           pdb=" CA  TYR A 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.31  -19.69     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  SER B 184 "
           pdb=" C   SER B 184 "
           pdb=" N   ARG B 185 "
           pdb=" CA  ARG B 185 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.37  -18.63     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  GLU B 392 "
           pdb=" C   GLU B 392 "
           pdb=" N   ASP B 393 "
           pdb=" CA  ASP B 393 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.93  -18.07     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 5528 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 942
       0.044 -    0.088: 317
       0.088 -    0.132: 80
       0.132 -    0.176: 9
       0.176 -    0.220: 8
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" CB  ILE B 188 "
            pdb=" CA  ILE B 188 "
            pdb=" CG1 ILE B 188 "
            pdb=" CG2 ILE B 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  SER B 413 "
            pdb=" N   SER B 413 "
            pdb=" C   SER B 413 "
            pdb=" CB  SER B 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  GLU A  80 "
            pdb=" N   GLU A  80 "
            pdb=" C   GLU A  80 "
            pdb=" CB  GLU A  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 1353 not shown)

  Planarity restraints: 1602
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 483 "    0.046 5.00e-02 4.00e+02   6.82e-02 7.44e+00
        pdb=" N   PRO A 484 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 484 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 484 "    0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 187 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.09e+00
        pdb=" C   ASP B 187 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ASP B 187 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ILE B 188 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 130 "    0.009 2.00e-02 2.50e+03   1.86e-02 3.45e+00
        pdb=" C   ILE B 130 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ILE B 130 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU B 131 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1599 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1007
        2.74 -     3.28: 9273
        3.28 -     3.82: 15467
        3.82 -     4.36: 18622
        4.36 -     4.90: 31330
  Nonbonded interactions: 75699
  Sorted by model distance:
  nonbonded pdb=" O   SER B  19 "
            pdb=" NE2 GLN B  23 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" OD1 ASP B 408 "
            pdb=" OG1 THR B 594 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   SER B 608 "
            pdb=" NH2 ARG B 613 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OE1 GLU A 513 "
            pdb=" NZ  LYS A 517 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" NZ  LYS B  32 "
            pdb=" OE2 GLU B  34 "
     model   vdw
     2.248 3.120
  ... (remaining 75694 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 individual isotropic
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:             2.130
  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:             0.000
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.160
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:17.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
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      :  0.005   0.080   9225  Z= 0.355
  Angle     :  0.717   8.262  12468  Z= 0.460
  Chirality :  0.048   0.220   1356
  Planarity :  0.004   0.068   1602
  Dihedral  : 14.359  89.568   3413
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  1.12 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.25), residues: 1115
  helix:  1.00 (0.20), residues: 663
  sheet: -0.81 (0.50), residues: 93
  loop : -0.87 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  26 
 HIS   0.006   0.001   HIS A  41 
 PHE   0.014   0.002   PHE B 311 
 TYR   0.029   0.002   TYR A 333 
 ARG   0.008   0.001   ARG B 143 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7932 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8214 (m-10) cc_final: 0.7776 (m-10)
REVERT: A  386 GLN cc_start: 0.8159 (tt0) cc_final: 0.7870 (pt0)
REVERT: B  412 VAL cc_start: 0.8817 (t) cc_final: 0.8469 (m)
REVERT: B  570 LEU cc_start: 0.8704 (tp) cc_final: 0.8374 (tp)
REVERT: B  580 ASP cc_start: 0.7464 (m-30) cc_final: 0.7254 (m-30)
  outliers start: 20
  outliers final: 2
  residues processed: 169
  average time/residue: 1.7273
  time to fit residues: 307.9567
Evaluate side-chains
  102 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   28 GLU
Chi-restraints excluded: chain B residue   59 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 65 optimal weight:    0.1980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 403 ASN
** B 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.126939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.094893 restraints weight = 13130.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.43
r_work: 0.3089 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9225  Z= 0.192
  Angle     :  0.564   8.512  12468  Z= 0.293
  Chirality :  0.040   0.156   1356
  Planarity :  0.004   0.043   1602
  Dihedral  :  5.873 135.093   1225
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  :  8.44 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.26), residues: 1115
  helix:  1.51 (0.21), residues: 684
  sheet: -0.44 (0.49), residues: 93
  loop : -0.58 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  26 
 HIS   0.005   0.001   HIS A 411 
 PHE   0.016   0.001   PHE A 451 
 TYR   0.017   0.002   TYR A 334 
 ARG   0.007   0.001   ARG A 165 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 1.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ARG cc_start: 0.8563 (ttm170) cc_final: 0.8345 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8354 (m-10) cc_final: 0.8016 (m-10)
REVERT: A  383 TYR cc_start: 0.8211 (m-10) cc_final: 0.7900 (m-10)
REVERT: A  386 GLN cc_start: 0.8362 (tt0) cc_final: 0.8091 (pt0)
REVERT: A  387 PHE cc_start: 0.8140 (m-10) cc_final: 0.7893 (m-10)
REVERT: A  502 VAL cc_start: 0.8629 (t) cc_final: 0.8381 (m)
REVERT: B   71 PHE cc_start: 0.9032 (m-80) cc_final: 0.8711 (m-80)
REVERT: B  570 LEU cc_start: 0.8738 (tp) cc_final: 0.8398 (tp)
REVERT: B  580 ASP cc_start: 0.8164 (m-30) cc_final: 0.7841 (m-30)
  outliers start: 24
  outliers final: 8
  residues processed: 134
  average time/residue: 1.4373
  time to fit residues: 204.1485
Evaluate side-chains
  104 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  448 ASP
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue  414 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 86 optimal weight:    0.9990
   chunk 17 optimal weight:    0.3980
   chunk 94 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 403 ASN
B 539 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.127346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.095078 restraints weight = 13341.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 2.41
r_work: 0.3088 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9225  Z= 0.173
  Angle     :  0.516   6.780  12468  Z= 0.270
  Chirality :  0.040   0.132   1356
  Planarity :  0.004   0.040   1602
  Dihedral  :  4.100  30.172   1221
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 10.89 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1115
  helix:  1.70 (0.21), residues: 684
  sheet: -0.36 (0.48), residues: 94
  loop : -0.37 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  26 
 HIS   0.009   0.001   HIS A 411 
 PHE   0.021   0.001   PHE A 451 
 TYR   0.014   0.001   TYR A 333 
 ARG   0.004   0.000   ARG B  29 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ARG cc_start: 0.8551 (ttm170) cc_final: 0.8292 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8354 (m-10) cc_final: 0.7961 (m-10)
REVERT: A  383 TYR cc_start: 0.8204 (m-10) cc_final: 0.7751 (m-80)
REVERT: A  387 PHE cc_start: 0.8142 (m-10) cc_final: 0.7886 (m-10)
REVERT: A  411 HIS cc_start: 0.8055 (m90) cc_final: 0.7847 (m-70)
REVERT: A  502 VAL cc_start: 0.8574 (t) cc_final: 0.8370 (m)
REVERT: B   23 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7987 (mp10)
REVERT: B   71 PHE cc_start: 0.9033 (m-80) cc_final: 0.8782 (m-80)
REVERT: B  394 GLU cc_start: 0.8439 (mp0) cc_final: 0.8051 (mp0)
REVERT: B  570 LEU cc_start: 0.8736 (tp) cc_final: 0.8438 (tp)
REVERT: B  580 ASP cc_start: 0.8134 (m-30) cc_final: 0.7818 (m-30)
  outliers start: 29
  outliers final: 12
  residues processed: 125
  average time/residue: 1.4033
  time to fit residues: 186.4204
Evaluate side-chains
  114 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  242 MET
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   23 GLN
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  555 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 101 optimal weight:    0.0000
   chunk 40 optimal weight:    0.0670
   chunk 82 optimal weight:    0.6980
   chunk 43 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0370
   chunk 96 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0980
   chunk 79 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    0.1800

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

Flipped N/Q/H residues before XYZ refinement:
A 386 GLN
A 403 ASN
B 503 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.129392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.097505 restraints weight = 13150.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.24
r_work: 0.3129 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9225  Z= 0.134
  Angle     :  0.494   6.678  12468  Z= 0.256
  Chirality :  0.038   0.129   1356
  Planarity :  0.004   0.041   1602
  Dihedral  :  3.885  22.924   1221
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 12.31 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.26), residues: 1115
  helix:  1.89 (0.21), residues: 686
  sheet: -0.27 (0.48), residues: 94
  loop : -0.23 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  26 
 HIS   0.005   0.001   HIS A 411 
 PHE   0.012   0.001   PHE B  43 
 TYR   0.013   0.001   TYR A 334 
 ARG   0.005   0.000   ARG B 315 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8260 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8282 (m-10) cc_final: 0.7960 (m-10)
REVERT: A  411 HIS cc_start: 0.8012 (m90) cc_final: 0.7777 (m-70)
REVERT: A  502 VAL cc_start: 0.8544 (t) cc_final: 0.8335 (m)
REVERT: B   33 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8084 (tm-30)
REVERT: B   51 ASP cc_start: 0.8027 (m-30) cc_final: 0.7775 (m-30)
REVERT: B  252 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7468 (mp0)
REVERT: B  304 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7453 (tm-30)
REVERT: B  394 GLU cc_start: 0.8420 (mp0) cc_final: 0.8185 (mp0)
REVERT: B  488 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8143 (mtp180)
REVERT: B  570 LEU cc_start: 0.8682 (tp) cc_final: 0.8397 (tp)
REVERT: B  580 ASP cc_start: 0.8077 (m-30) cc_final: 0.7747 (m-30)
  outliers start: 25
  outliers final: 9
  residues processed: 128
  average time/residue: 1.3912
  time to fit residues: 189.8192
Evaluate side-chains
  112 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  414 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0870
   chunk 45 optimal weight:    8.9990
   chunk 70 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0010
   chunk 46 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.5164

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

Flipped N/Q/H residues before XYZ refinement:
A 403 ASN
** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.128919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.097217 restraints weight = 13157.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 2.33
r_work: 0.3124 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9225  Z= 0.149
  Angle     :  0.499   8.415  12468  Z= 0.256
  Chirality :  0.039   0.128   1356
  Planarity :  0.004   0.041   1602
  Dihedral  :  3.813  21.086   1221
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 13.43 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.26), residues: 1115
  helix:  1.97 (0.20), residues: 686
  sheet: -0.27 (0.48), residues: 94
  loop : -0.18 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  26 
 HIS   0.004   0.001   HIS A 411 
 PHE   0.019   0.001   PHE A 451 
 TYR   0.013   0.001   TYR A 334 
 ARG   0.007   0.000   ARG B 383 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 109
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8267 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8258 (m-10) cc_final: 0.7985 (m-10)
REVERT: A  383 TYR cc_start: 0.8026 (m-10) cc_final: 0.7765 (m-10)
REVERT: A  411 HIS cc_start: 0.8048 (m90) cc_final: 0.7767 (m-70)
REVERT: A  502 VAL cc_start: 0.8538 (t) cc_final: 0.8322 (m)
REVERT: B   33 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8120 (tm-30)
REVERT: B  252 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7480 (mp0)
REVERT: B  304 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7446 (tm-30)
REVERT: B  394 GLU cc_start: 0.8435 (mp0) cc_final: 0.8235 (mp0)
REVERT: B  488 ARG cc_start: 0.8372 (mtp85) cc_final: 0.8154 (mtp180)
REVERT: B  535 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7539 (tp30)
REVERT: B  570 LEU cc_start: 0.8703 (tp) cc_final: 0.8416 (tp)
REVERT: B  573 MET cc_start: 0.8320 (mmm) cc_final: 0.7876 (mpp)
REVERT: B  580 ASP cc_start: 0.8057 (m-30) cc_final: 0.7747 (m-30)
REVERT: B  587 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7698 (tt0)
  outliers start: 28
  outliers final: 15
  residues processed: 125
  average time/residue: 1.2925
  time to fit residues: 172.2257
Evaluate side-chains
  115 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain B residue   14 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  414 ASN
Chi-restraints excluded: chain B residue  587 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 66 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 104 optimal weight:   10.0000
   chunk 4 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 403 ASN
** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.127806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.096460 restraints weight = 13077.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.17
r_work: 0.3117 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9225  Z= 0.175
  Angle     :  0.507   8.065  12468  Z= 0.262
  Chirality :  0.039   0.130   1356
  Planarity :  0.004   0.041   1602
  Dihedral  :  3.830  20.878   1221
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.34 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.26), residues: 1115
  helix:  1.99 (0.20), residues: 686
  sheet: -0.27 (0.47), residues: 94
  loop : -0.18 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  26 
 HIS   0.004   0.001   HIS A 411 
 PHE   0.011   0.001   PHE B 166 
 TYR   0.016   0.001   TYR A 333 
 ARG   0.007   0.000   ARG B 383 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 1.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8337 (mp) cc_final: 0.8050 (mm)
REVERT: A  163 ARG cc_start: 0.8541 (ttm170) cc_final: 0.8272 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8254 (m-10) cc_final: 0.7982 (m-10)
REVERT: A  383 TYR cc_start: 0.8030 (m-10) cc_final: 0.7743 (m-10)
REVERT: A  411 HIS cc_start: 0.8031 (m90) cc_final: 0.7531 (m-70)
REVERT: A  502 VAL cc_start: 0.8543 (t) cc_final: 0.8317 (m)
REVERT: B   33 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8110 (tm-30)
REVERT: B  252 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7503 (mp0)
REVERT: B  304 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7460 (tm-30)
REVERT: B  394 GLU cc_start: 0.8420 (mp0) cc_final: 0.8209 (mp0)
REVERT: B  535 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7530 (tp30)
REVERT: B  570 LEU cc_start: 0.8730 (tp) cc_final: 0.8450 (tp)
REVERT: B  573 MET cc_start: 0.8314 (mmm) cc_final: 0.7895 (mpp)
REVERT: B  580 ASP cc_start: 0.8036 (m-30) cc_final: 0.7746 (m-30)
  outliers start: 25
  outliers final: 15
  residues processed: 116
  average time/residue: 1.3076
  time to fit residues: 162.1919
Evaluate side-chains
  115 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  414 ASN
Chi-restraints excluded: chain B residue  439 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 111 optimal weight:    0.1980
   chunk 38 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 94 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 37 optimal weight:    0.1980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 403 ASN
** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.128661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.096797 restraints weight = 13254.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.22
r_work: 0.3136 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9225  Z= 0.151
  Angle     :  0.507   8.860  12468  Z= 0.258
  Chirality :  0.039   0.129   1356
  Planarity :  0.004   0.042   1602
  Dihedral  :  3.771  20.457   1221
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.45 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.26), residues: 1115
  helix:  2.04 (0.20), residues: 686
  sheet: -0.20 (0.48), residues: 94
  loop : -0.09 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  26 
 HIS   0.004   0.001   HIS A 411 
 PHE   0.019   0.001   PHE A 451 
 TYR   0.013   0.001   TYR A 334 
 ARG   0.006   0.000   ARG B 383 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8298 (mp) cc_final: 0.8031 (mm)
REVERT: A  163 ARG cc_start: 0.8540 (ttm170) cc_final: 0.8266 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8247 (m-10) cc_final: 0.7991 (m-10)
REVERT: A  383 TYR cc_start: 0.8055 (m-10) cc_final: 0.7773 (m-10)
REVERT: A  401 TYR cc_start: 0.8416 (m-80) cc_final: 0.7856 (m-10)
REVERT: A  411 HIS cc_start: 0.7874 (m90) cc_final: 0.7484 (m-70)
REVERT: A  502 VAL cc_start: 0.8499 (t) cc_final: 0.8279 (m)
REVERT: B  252 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7526 (mp0)
REVERT: B  304 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7435 (tm-30)
REVERT: B  394 GLU cc_start: 0.8415 (mp0) cc_final: 0.8095 (mp0)
REVERT: B  535 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7519 (tp30)
REVERT: B  570 LEU cc_start: 0.8723 (tp) cc_final: 0.8455 (tp)
REVERT: B  573 MET cc_start: 0.8306 (mmm) cc_final: 0.7875 (mpp)
REVERT: B  580 ASP cc_start: 0.8039 (m-30) cc_final: 0.7738 (m-30)
  outliers start: 30
  outliers final: 15
  residues processed: 124
  average time/residue: 1.2550
  time to fit residues: 166.2290
Evaluate side-chains
  114 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  414 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 101 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 106 optimal weight:    8.9990
   chunk 93 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 229 HIS
A 403 ASN
** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 506 ASN
B 503 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.125478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.093402 restraints weight = 13167.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.22
r_work: 0.3065 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080   9225  Z= 0.303
  Angle     :  0.598  10.609  12468  Z= 0.308
  Chirality :  0.043   0.194   1356
  Planarity :  0.004   0.041   1602
  Dihedral  :  4.104  21.646   1221
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 15.16 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.26), residues: 1115
  helix:  1.84 (0.20), residues: 688
  sheet: -0.19 (0.48), residues: 93
  loop : -0.13 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  26 
 HIS   0.005   0.001   HIS A 229 
 PHE   0.014   0.002   PHE B 166 
 TYR   0.018   0.002   TYR A 334 
 ARG   0.007   0.000   ARG B 383 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8362 (mp) cc_final: 0.8105 (mm)
REVERT: A  163 ARG cc_start: 0.8536 (ttm170) cc_final: 0.8303 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8270 (m-10) cc_final: 0.8008 (m-10)
REVERT: A  383 TYR cc_start: 0.8123 (m-10) cc_final: 0.7841 (m-10)
REVERT: A  401 TYR cc_start: 0.8452 (m-80) cc_final: 0.8061 (m-80)
REVERT: A  411 HIS cc_start: 0.7980 (m90) cc_final: 0.7534 (m-70)
REVERT: A  502 VAL cc_start: 0.8569 (t) cc_final: 0.8366 (m)
REVERT: B   33 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8085 (tm-30)
REVERT: B  252 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7531 (mp0)
REVERT: B  304 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7486 (tm-30)
REVERT: B  394 GLU cc_start: 0.8409 (mp0) cc_final: 0.8160 (mp0)
REVERT: B  570 LEU cc_start: 0.8807 (tp) cc_final: 0.8539 (tp)
REVERT: B  580 ASP cc_start: 0.8092 (m-30) cc_final: 0.7711 (m-30)
  outliers start: 29
  outliers final: 19
  residues processed: 114
  average time/residue: 1.2768
  time to fit residues: 155.4282
Evaluate side-chains
  116 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  414 ASN
Chi-restraints excluded: chain B residue  482 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0980
   chunk 46 optimal weight:    9.9990
   chunk 75 optimal weight:    0.0370
   chunk 82 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    0.8262

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 506 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.127058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.094575 restraints weight = 13248.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 2.41
r_work: 0.3077 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9225  Z= 0.182
  Angle     :  0.560  11.686  12468  Z= 0.283
  Chirality :  0.040   0.164   1356
  Planarity :  0.004   0.042   1602
  Dihedral  :  3.983  21.081   1221
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 15.87 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.26), residues: 1115
  helix:  1.93 (0.20), residues: 688
  sheet: -0.23 (0.47), residues: 94
  loop : -0.05 (0.36), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  26 
 HIS   0.004   0.001   HIS A 411 
 PHE   0.022   0.001   PHE A 451 
 TYR   0.019   0.001   TYR A 334 
 ARG   0.007   0.000   ARG B 315 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8374 (mp) cc_final: 0.8122 (mm)
REVERT: A  163 ARG cc_start: 0.8532 (ttm170) cc_final: 0.8308 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8251 (m-10) cc_final: 0.7967 (m-10)
REVERT: A  376 HIS cc_start: 0.8333 (p-80) cc_final: 0.8102 (p-80)
REVERT: A  383 TYR cc_start: 0.8136 (m-10) cc_final: 0.7872 (m-10)
REVERT: A  401 TYR cc_start: 0.8414 (m-80) cc_final: 0.8019 (m-80)
REVERT: A  411 HIS cc_start: 0.7952 (m90) cc_final: 0.7505 (m-70)
REVERT: A  502 VAL cc_start: 0.8545 (t) cc_final: 0.8331 (m)
REVERT: B  252 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7552 (mp0)
REVERT: B  304 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7500 (tm-30)
REVERT: B  394 GLU cc_start: 0.8424 (mp0) cc_final: 0.8146 (mp0)
REVERT: B  535 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7528 (tp30)
REVERT: B  570 LEU cc_start: 0.8763 (tp) cc_final: 0.8508 (tp)
REVERT: B  573 MET cc_start: 0.8334 (mmm) cc_final: 0.7874 (mpp)
REVERT: B  580 ASP cc_start: 0.8112 (m-30) cc_final: 0.7730 (m-30)
  outliers start: 24
  outliers final: 17
  residues processed: 112
  average time/residue: 1.2486
  time to fit residues: 149.7146
Evaluate side-chains
  116 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 110 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 77 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.125512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.093693 restraints weight = 13244.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.36
r_work: 0.3071 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9225  Z= 0.234
  Angle     :  0.586  12.193  12468  Z= 0.299
  Chirality :  0.041   0.167   1356
  Planarity :  0.004   0.041   1602
  Dihedral  :  4.043  21.311   1221
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.07 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.26), residues: 1115
  helix:  1.90 (0.20), residues: 688
  sheet: -0.24 (0.48), residues: 94
  loop : -0.07 (0.35), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  26 
 HIS   0.004   0.001   HIS A 411 
 PHE   0.012   0.001   PHE B 166 
 TYR   0.020   0.001   TYR A 334 
 ARG   0.009   0.000   ARG B 315 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.8395 (mp) cc_final: 0.8148 (mm)
REVERT: A  163 ARG cc_start: 0.8554 (ttm170) cc_final: 0.8324 (ttm-80)
REVERT: A  346 PHE cc_start: 0.8297 (m-10) cc_final: 0.8035 (m-10)
REVERT: A  376 HIS cc_start: 0.8333 (p-80) cc_final: 0.8110 (p-80)
REVERT: A  383 TYR cc_start: 0.8140 (m-10) cc_final: 0.7884 (m-10)
REVERT: A  401 TYR cc_start: 0.8452 (m-80) cc_final: 0.8064 (m-80)
REVERT: A  411 HIS cc_start: 0.8008 (m90) cc_final: 0.7569 (m-70)
REVERT: A  502 VAL cc_start: 0.8560 (t) cc_final: 0.8348 (m)
REVERT: B  252 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7594 (mp0)
REVERT: B  303 GLU cc_start: 0.8201 (tp30) cc_final: 0.7509 (tm-30)
REVERT: B  304 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7500 (tm-30)
REVERT: B  394 GLU cc_start: 0.8448 (mp0) cc_final: 0.8167 (mp0)
REVERT: B  535 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7552 (tp30)
REVERT: B  570 LEU cc_start: 0.8793 (tp) cc_final: 0.8533 (tp)
REVERT: B  573 MET cc_start: 0.8357 (mmm) cc_final: 0.7914 (mpp)
REVERT: B  580 ASP cc_start: 0.8127 (m-30) cc_final: 0.7752 (m-30)
  outliers start: 24
  outliers final: 18
  residues processed: 113
  average time/residue: 1.3870
  time to fit residues: 166.8146
Evaluate side-chains
  119 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 THR
Chi-restraints excluded: chain A residue   23 THR
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  139 SER
Chi-restraints excluded: chain A residue  250 LEU
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  277 THR
Chi-restraints excluded: chain A residue  482 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   70 GLN
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  124 SER
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  304 GLN
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 70 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 78 optimal weight:    0.5980
   chunk 47 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 106 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  23 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.127263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.094871 restraints weight = 13168.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 2.44
r_work: 0.3094 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9225  Z= 0.176
  Angle     :  0.566  12.278  12468  Z= 0.286
  Chirality :  0.040   0.166   1356
  Planarity :  0.004   0.041   1602
  Dihedral  :  3.952  20.754   1221
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.17 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.26), residues: 1115
  helix:  1.98 (0.20), residues: 688
  sheet: -0.21 (0.47), residues: 94
  loop : -0.02 (0.36), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  26 
 HIS   0.004   0.001   HIS A 411 
 PHE   0.024   0.001   PHE A 451 
 TYR   0.019   0.001   TYR A 334 
 ARG   0.011   0.000   ARG B 315 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7600.67 seconds
wall clock time: 132 minutes 27.74 seconds (7947.74 seconds total)