Starting phenix.real_space_refine
on Tue Mar  3 12:10:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sj4_25153/03_2026/7sj4_25153.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sj4_25153/03_2026/7sj4_25153.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sj4_25153/03_2026/7sj4_25153.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sj4_25153/03_2026/7sj4_25153.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sj4_25153/03_2026/7sj4_25153.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sj4_25153/03_2026/7sj4_25153.cif"
  }
  resolution = 2.86
  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=  -0.000 sd=   0.108
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      23      5.16       5
     C    2485      2.51       5
     N     647      2.21       5
     O     754      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3909
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2502
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 2502
          Classifications: {'peptide': 304}
          Link IDs: {'PTRANS': 9, 'TRANS': 294}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1383
          Classifications: {'peptide': 177}
          Link IDs: {'PTRANS': 11, 'TRANS': 165}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}
  Time building chain proxies: 1.03, per 1000 atoms: 0.26
  Number of scatterers: 3909
  At special positions: 0
  Unit cell: (71.28, 82.08, 85.32, 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      23     16.00
     O     754      8.00
     N     647      7.00
     C    2485      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: 0.31
  Conformation dependent library (CDL) restraints added in 165.8 milliseconds
  

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  910

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 2 sheets defined
      58.4% alpha, 16.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1282 through 1325
      removed outlier: 3.685A  pdb=" N   ALA A1306 " --> pdb=" O   GLN A1302 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU A1319 " --> pdb=" O   MET A1315 " (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   TRP A1320 " --> pdb=" O   ASP A1316 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLU A1321 " --> pdb=" O   THR A1317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1330 through 1334
      removed outlier: 3.830A  pdb=" N   VAL A1334 " --> pdb=" O   PRO A1331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1336 through 1342
    Processing helix  chain 'A' and resid 1343 through 1354
      removed outlier: 3.547A  pdb=" N   ASN A1353 " --> pdb=" O   GLU A1349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1354 through 1362
      removed outlier: 3.687A  pdb=" N   TYR A1362 " --> pdb=" O   GLU A1358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1365 through 1367
      No H-bonds generated for 'chain 'A' and resid 1365 through 1367'
    Processing helix  chain 'A' and resid 1368 through 1376
      removed outlier: 4.122A  pdb=" N   CYS A1372 " --> pdb=" O   ASP A1368 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   PHE A1373 " --> pdb=" O   VAL A1369 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TRP A1376 " --> pdb=" O   CYS A1372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1379
      No H-bonds generated for 'chain 'A' and resid 1377 through 1379'
    Processing helix  chain 'A' and resid 1380 through 1398
      removed outlier: 3.883A  pdb=" N   VAL A1384 " --> pdb=" O   PHE A1380 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS A1388 " --> pdb=" O   VAL A1384 " (cutoff:3.500A)
      Proline residue:  A1391  - end of helix
      removed outlier: 3.596A  pdb=" N   GLN A1395 " --> pdb=" O   PRO A1391 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU A1396 " --> pdb=" O   ASP A1392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1403 through 1413
    Processing helix  chain 'A' and resid 1417 through 1423
    Processing helix  chain 'A' and resid 1423 through 1430
      removed outlier: 3.754A  pdb=" N   THR A1430 " --> pdb=" O   VAL A1426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1431 through 1441
    Processing helix  chain 'A' and resid 1446 through 1471
      removed outlier: 3.522A  pdb=" N   ILE A1450 " --> pdb=" O   GLY A1446 " (cutoff:3.500A)
      Proline residue:  A1461  - end of helix
    Processing helix  chain 'A' and resid 1480 through 1484
    Processing helix  chain 'A' and resid 1575 through 1594
    Processing helix  chain 'B' and resid 12 through 14
      No H-bonds generated for 'chain 'B' and resid 12 through 14'
    Processing helix  chain 'B' and resid 15 through 26
      removed outlier: 3.572A  pdb=" N   TYR B  23 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 72
      removed outlier: 3.568A  pdb=" N   SER B  71 " --> pdb=" O   ARG B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 96
      removed outlier: 3.626A  pdb=" N   PHE B  90 " --> pdb=" O   SER B  86 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ARG B  94 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 96 through 105
      removed outlier: 3.533A  pdb=" N   GLU B 100 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 120
    Processing helix  chain 'B' and resid 124 through 132
      removed outlier: 3.710A  pdb=" N   LYS B 132 " --> pdb=" O   LYS B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 149
    Processing helix  chain 'B' and resid 164 through 177
      removed outlier: 4.089A  pdb=" N   PHE B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASP B 170 " --> pdb=" O   LYS B 166 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL B 176 " --> pdb=" O   ALA B 172 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1473 through 1474
      removed outlier: 3.571A  pdb=" N   LYS A1530 " --> pdb=" O   VAL A1522 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   PHE A1518 " --> pdb=" O   LYS A1534 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LYS A1536 " --> pdb=" O   LEU A1516 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   LEU A1516 " --> pdb=" O   LYS A1536 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   SER A1515 " --> pdb=" O   PHE A1512 " (cutoff:3.500A)
      removed outlier: 5.232A  pdb=" N   GLU A1521 " --> pdb=" O   GLU A1506 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   GLU A1506 " --> pdb=" O   GLU A1521 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   PHE A1492 " --> pdb=" O   ARG A1507 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A1488 " --> pdb=" O   LEU A1511 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLN A1493 " --> pdb=" O   LYS A1572 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL A1570 " --> pdb=" O   TRP A1495 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 40 through 46
      removed outlier: 3.721A  pdb=" N   VAL B  46 " --> pdb=" O   LYS B  49 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   GLN B   2 " --> pdb=" O   PRO B  50 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   PHE B  78 " --> pdb=" O   ILE B 111 " (cutoff:3.500A)
      removed outlier: 7.300A  pdb=" N   VAL B 113 " --> pdb=" O   PHE B  78 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   ILE B  80 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   THR B 115 " --> pdb=" O   ILE B  80 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   PHE B  82 " --> pdb=" O   THR B 115 " (cutoff:3.500A)
      removed outlier: 7.436A  pdb=" N   ILE B 110 " --> pdb=" O   LYS B 153 " (cutoff:3.500A)
      removed outlier: 8.580A  pdb=" N   LEU B 155 " --> pdb=" O   ILE B 110 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   LEU B 112 " --> pdb=" O   LEU B 155 " (cutoff:3.500A)

    202 hydrogen bonds defined for protein.
    573 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: 0.77

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1254
        1.34 -     1.46: 812
        1.46 -     1.58: 1863
        1.58 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 3964
  Sorted by residual:
  bond pdb=" C   GLY A1504 "
       pdb=" O   GLY A1504 "
    ideal  model  delta    sigma   weight residual
    1.243  1.235  0.008 9.30e-03 1.16e+04 7.62e-01
  bond pdb=" C   ARG B  68 "
       pdb=" N   PRO B  69 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.016 2.34e-02 1.83e+03 4.44e-01
  bond pdb=" C   TYR B  72 "
       pdb=" N   PRO B  73 "
    ideal  model  delta    sigma   weight residual
    1.332  1.340 -0.008 1.30e-02 5.92e+03 3.87e-01
  bond pdb=" CA  ASP A1551 "
       pdb=" C   ASP A1551 "
    ideal  model  delta    sigma   weight residual
    1.517  1.523 -0.006 1.07e-02 8.73e+03 3.30e-01
  bond pdb=" CA  ILE A1301 "
       pdb=" C   ILE A1301 "
    ideal  model  delta    sigma   weight residual
    1.524  1.531 -0.007 1.30e-02 5.92e+03 2.98e-01
  ... (remaining 3959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 5189
        1.00 -     2.00: 131
        2.00 -     3.00: 20
        3.00 -     4.00: 2
        4.00 -     5.00: 8
  Bond angle restraints: 5350
  Sorted by residual:
  angle pdb=" N   TYR B  72 "
        pdb=" CA  TYR B  72 "
        pdb=" C   TYR B  72 "
      ideal   model   delta    sigma   weight residual
     109.81  114.15   -4.34 2.21e+00 2.05e-01 3.85e+00
  angle pdb=" N   GLY A1504 "
        pdb=" CA  GLY A1504 "
        pdb=" C   GLY A1504 "
      ideal   model   delta    sigma   weight residual
     110.97  113.51   -2.54 1.56e+00 4.11e-01 2.65e+00
  angle pdb=" CA  TYR B  72 "
        pdb=" C   TYR B  72 "
        pdb=" N   PRO B  73 "
      ideal   model   delta    sigma   weight residual
     118.44  120.56   -2.12 1.59e+00 3.96e-01 1.78e+00
  angle pdb=" N   ILE A1354 "
        pdb=" CA  ILE A1354 "
        pdb=" C   ILE A1354 "
      ideal   model   delta    sigma   weight residual
     109.34  111.93   -2.59 2.08e+00 2.31e-01 1.56e+00
  angle pdb=" C   VAL A1460 "
        pdb=" N   PRO A1461 "
        pdb=" CD  PRO A1461 "
      ideal   model   delta    sigma   weight residual
     125.00  130.00   -5.00 4.10e+00 5.95e-02 1.49e+00
  ... (remaining 5345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.43: 2180
       11.43 -    22.86: 169
       22.86 -    34.29: 43
       34.29 -    45.72: 15
       45.72 -    57.15: 5
  Dihedral angle restraints: 2412
    sinusoidal: 1006
      harmonic: 1406
  Sorted by residual:
  dihedral pdb=" CA  MET A1457 "
           pdb=" C   MET A1457 "
           pdb=" N   LEU A1458 "
           pdb=" CA  LEU A1458 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.34   15.66     0      5.00e+00 4.00e-02 9.81e+00
  dihedral pdb=" N   LYS B 166 "
           pdb=" CA  LYS B 166 "
           pdb=" CB  LYS B 166 "
           pdb=" CG  LYS B 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.15   57.15     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" CA  ARG A1505 "
           pdb=" CB  ARG A1505 "
           pdb=" CG  ARG A1505 "
           pdb=" CD  ARG A1505 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  115.55  -55.55     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 2409 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 340
       0.026 -    0.053: 147
       0.053 -    0.079: 65
       0.079 -    0.105: 29
       0.105 -    0.132: 12
  Chirality restraints: 593
  Sorted by residual:
  chirality pdb=" CA  ILE A1329 "
            pdb=" N   ILE A1329 "
            pdb=" C   ILE A1329 "
            pdb=" CB  ILE A1329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  LYS A1424 "
            pdb=" N   LYS A1424 "
            pdb=" C   LYS A1424 "
            pdb=" CB  LYS A1424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.30e-01
  chirality pdb=" CA  ILE B 111 "
            pdb=" N   ILE B 111 "
            pdb=" C   ILE B 111 "
            pdb=" CB  ILE B 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.09e-01
  ... (remaining 590 not shown)

  Planarity restraints: 681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1329 "    0.021 5.00e-02 4.00e+02   3.15e-02 1.59e+00
        pdb=" N   PRO A1330 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A1330 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A1330 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 135 "   -0.019 5.00e-02 4.00e+02   2.83e-02 1.28e+00
        pdb=" N   PRO B 136 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO B 136 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 136 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  68 "   -0.016 5.00e-02 4.00e+02   2.40e-02 9.23e-01
        pdb=" N   PRO B  69 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO B  69 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B  69 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 678 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 959
        2.80 -     3.33: 3554
        3.33 -     3.85: 6215
        3.85 -     4.38: 7413
        4.38 -     4.90: 12867
  Nonbonded interactions: 31008
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A1351 "
            pdb=" OH  TYR A1383 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" OD1 ASN B  39 "
            pdb=" O   HOH B 201 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O   GLY B  10 "
            pdb=" O   HOH B 202 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   ASP B  57 "
            pdb=" O   HOH B 203 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   THR B  35 "
            pdb=" O   HOH B 204 "
     model   vdw
     2.308 3.040
  ... (remaining 31003 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:             0.640
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.210
  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:6.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7019
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      :  0.002   0.018   3964  Z= 0.098
  Angle     :  0.432   5.003   5350  Z= 0.234
  Chirality :  0.041   0.132    593
  Planarity :  0.003   0.032    681
  Dihedral  :  9.562  57.150   1502
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  2.09 %
    Favored  : 96.98 %
  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 are not related in a simple way.
  whole:  0.95 (0.40), residues: 473
  helix:  1.15 (0.35), residues: 239
  sheet:  0.12 (0.52), residues: 89
  loop :  0.34 (0.55), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  68 
 TYR   0.011   0.001   TYR A1404 
 PHE   0.011   0.001   PHE A1518 
 TRP   0.009   0.001   TRP B  97 
 HIS   0.002   0.000   HIS A1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 3964)
  covalent geometry    : angle       0.43210 ( 5350)
  hydrogen bonds       : bond        0.19163 (  202)
  hydrogen bonds       : angle       7.33557 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A 1352 ASN cc_start: 0.8470 (t0) cc_final: 0.7964 (t0)
REVERT: A 1389 ASN cc_start: 0.7254 (t0) cc_final: 0.7044 (t0)
REVERT: A 1479 ASN cc_start: 0.7846 (m-40) cc_final: 0.7319 (p0)
REVERT: A 1505 ARG cc_start: 0.7473 (mpp80) cc_final: 0.7030 (mtp180)
REVERT: A 1588 GLU cc_start: 0.8096 (tp30) cc_final: 0.7846 (tp30)
REVERT: B  107 ASN cc_start: 0.7676 (m-40) cc_final: 0.7399 (m-40)
REVERT: B  120 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.5397 (ttt-90)
REVERT: B  128 LYS cc_start: 0.8000 (mttt) cc_final: 0.7675 (mptt)
REVERT: B  156 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8262 (mt-10)
  outliers start: 4
  outliers final: 1
  residues processed: 102
  average time/residue: 0.6427
  time to fit residues: 67.3008
Evaluate side-chains
  75 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain B residue  120 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A1353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.192736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.157088 restraints weight = 4094.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 2.29
r_work: 0.3821 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3685 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.1894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3964  Z= 0.149
  Angle     :  0.539   5.077   5350  Z= 0.291
  Chirality :  0.044   0.159    593
  Planarity :  0.004   0.040    681
  Dihedral  :  4.995  55.766    522
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 10.67 %
    Favored  : 87.01 %
  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 are not related in a simple way.
  whole:  1.23 (0.39), residues: 473
  helix:  1.55 (0.34), residues: 234
  sheet:  0.13 (0.52), residues: 89
  loop :  0.25 (0.53), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  68 
 TYR   0.011   0.002   TYR A1432 
 PHE   0.012   0.002   PHE B  90 
 TRP   0.008   0.001   TRP B  97 
 HIS   0.002   0.001   HIS A1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 3964)
  covalent geometry    : angle       0.53944 ( 5350)
  hydrogen bonds       : bond        0.05315 (  202)
  hydrogen bonds       : angle       5.68271 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A 1349 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7099 (mp0)
REVERT: A 1352 ASN cc_start: 0.8399 (t0) cc_final: 0.7917 (t0)
REVERT: A 1357 LYS cc_start: 0.7536 (mttt) cc_final: 0.7186 (mtpm)
REVERT: A 1398 LEU cc_start: 0.7683 (mt) cc_final: 0.7399 (mm)
REVERT: A 1410 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7281 (tm-30)
REVERT: A 1479 ASN cc_start: 0.8015 (m-40) cc_final: 0.7133 (p0)
REVERT: A 1490 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6958 (tp30)
REVERT: A 1505 ARG cc_start: 0.6981 (mpp80) cc_final: 0.6590 (mtt180)
REVERT: A 1507 ARG cc_start: 0.6864 (mmt-90) cc_final: 0.6483 (mmt90)
REVERT: B  107 ASN cc_start: 0.7665 (m-40) cc_final: 0.7414 (m-40)
REVERT: B  120 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.5346 (ttt-90)
REVERT: B  128 LYS cc_start: 0.7895 (mttt) cc_final: 0.7310 (mppt)
  outliers start: 10
  outliers final: 3
  residues processed: 82
  average time/residue: 0.6070
  time to fit residues: 51.2178
Evaluate side-chains
  73 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1410 GLN
Chi-restraints excluded: chain A residue 1468 MET
Chi-restraints excluded: chain A residue 1490 GLU
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue  120 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 10 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A1353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.193294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.159043 restraints weight = 4084.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 2.26
r_work: 0.3838 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3702 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7057
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3964  Z= 0.161
  Angle     :  0.555   6.994   5350  Z= 0.292
  Chirality :  0.044   0.174    593
  Planarity :  0.004   0.044    681
  Dihedral  :  5.066  54.291    522
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 10.21 %
    Favored  : 86.08 %
  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 are not related in a simple way.
  whole:  1.13 (0.39), residues: 473
  helix:  1.59 (0.34), residues: 234
  sheet:  0.14 (0.52), residues: 91
  loop : -0.06 (0.52), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1309 
 TYR   0.011   0.002   TYR A1404 
 PHE   0.012   0.002   PHE B  90 
 TRP   0.009   0.002   TRP B  97 
 HIS   0.003   0.001   HIS A1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3964)
  covalent geometry    : angle       0.55481 ( 5350)
  hydrogen bonds       : bond        0.05112 (  202)
  hydrogen bonds       : angle       5.42850 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A 1322 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6506 (ttt)
REVERT: A 1352 ASN cc_start: 0.8326 (t0) cc_final: 0.7860 (t0)
REVERT: A 1410 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7367 (tm-30)
REVERT: A 1479 ASN cc_start: 0.7984 (m-40) cc_final: 0.7193 (p0)
REVERT: B  107 ASN cc_start: 0.7781 (m-40) cc_final: 0.7522 (m-40)
REVERT: B  120 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.5514 (ttt-90)
REVERT: B  128 LYS cc_start: 0.8002 (mttt) cc_final: 0.7455 (mppt)
  outliers start: 16
  outliers final: 4
  residues processed: 71
  average time/residue: 0.5870
  time to fit residues: 43.0106
Evaluate side-chains
  67 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1410 GLN
Chi-restraints excluded: chain A residue 1468 MET
Chi-restraints excluded: chain A residue 1488 LEU
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue  120 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    1.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.190709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.155184 restraints weight = 4036.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 2.30
r_work: 0.3797 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3663 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3964  Z= 0.160
  Angle     :  0.555   6.093   5350  Z= 0.291
  Chirality :  0.045   0.170    593
  Planarity :  0.004   0.045    681
  Dihedral  :  5.139  52.103    522
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 12.76 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.38), residues: 473
  helix:  1.59 (0.34), residues: 235
  sheet:  0.07 (0.52), residues: 91
  loop : -0.16 (0.51), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1528 
 TYR   0.013   0.002   TYR B  32 
 PHE   0.011   0.002   PHE A1518 
 TRP   0.009   0.002   TRP B  97 
 HIS   0.003   0.001   HIS A1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 3964)
  covalent geometry    : angle       0.55495 ( 5350)
  hydrogen bonds       : bond        0.04986 (  202)
  hydrogen bonds       : angle       5.32265 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A 1322 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6463 (ttt)
REVERT: A 1349 GLU cc_start: 0.7916 (tm-30) cc_final: 0.6875 (mp0)
REVERT: A 1352 ASN cc_start: 0.8280 (t0) cc_final: 0.7823 (t0)
REVERT: A 1357 LYS cc_start: 0.7536 (mttt) cc_final: 0.7117 (mtpt)
REVERT: A 1374 VAL cc_start: 0.7941 (t) cc_final: 0.7707 (t)
REVERT: A 1410 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7292 (tm-30)
REVERT: A 1479 ASN cc_start: 0.8017 (m-40) cc_final: 0.7126 (p0)
REVERT: A 1490 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6841 (tp30)
REVERT: B  102 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7421 (tpp-160)
REVERT: B  107 ASN cc_start: 0.7738 (m-40) cc_final: 0.7482 (m-40)
REVERT: B  120 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.5618 (ttt-90)
REVERT: B  128 LYS cc_start: 0.7921 (mttt) cc_final: 0.7338 (mppt)
  outliers start: 16
  outliers final: 6
  residues processed: 70
  average time/residue: 0.5972
  time to fit residues: 43.1192
Evaluate side-chains
  69 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1410 GLN
Chi-restraints excluded: chain A residue 1468 MET
Chi-restraints excluded: chain A residue 1488 LEU
Chi-restraints excluded: chain A residue 1490 GLU
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue  102 ARG
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  152 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0370
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.8860

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

Flipped N/Q/H residues before XYZ refinement:
A1353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.191485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.156148 restraints weight = 4069.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 2.29
r_work: 0.3769 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3634 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
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   0.033   3964  Z= 0.142
  Angle     :  0.541   7.124   5350  Z= 0.282
  Chirality :  0.043   0.137    593
  Planarity :  0.004   0.047    681
  Dihedral  :  5.122  50.952    522
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 13.92 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.21 (0.39), residues: 473
  helix:  1.74 (0.34), residues: 235
  sheet:  0.11 (0.53), residues: 91
  loop : -0.15 (0.51), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1528 
 TYR   0.012   0.002   TYR A1533 
 PHE   0.010   0.001   PHE A1518 
 TRP   0.011   0.002   TRP B  56 
 HIS   0.002   0.001   HIS A1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3964)
  covalent geometry    : angle       0.54140 ( 5350)
  hydrogen bonds       : bond        0.04680 (  202)
  hydrogen bonds       : angle       5.23640 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.117 
Fit side-chains
REVERT: A 1322 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6473 (ttt)
REVERT: A 1349 GLU cc_start: 0.7778 (tm-30) cc_final: 0.6789 (mp0)
REVERT: A 1352 ASN cc_start: 0.8236 (t0) cc_final: 0.7785 (t0)
REVERT: A 1374 VAL cc_start: 0.7899 (t) cc_final: 0.7668 (t)
REVERT: A 1410 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7275 (tm-30)
REVERT: A 1479 ASN cc_start: 0.8033 (m-40) cc_final: 0.7118 (p0)
REVERT: A 1490 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7028 (tp30)
REVERT: A 1558 TRP cc_start: 0.7275 (p-90) cc_final: 0.7000 (p-90)
REVERT: B  107 ASN cc_start: 0.7705 (m-40) cc_final: 0.7419 (m-40)
REVERT: B  120 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.5641 (ttt-90)
REVERT: B  128 LYS cc_start: 0.7896 (mttt) cc_final: 0.7306 (mppt)
REVERT: B  133 LYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6647 (mptp)
  outliers start: 14
  outliers final: 5
  residues processed: 67
  average time/residue: 0.5650
  time to fit residues: 39.1031
Evaluate side-chains
  68 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1410 GLN
Chi-restraints excluded: chain A residue 1468 MET
Chi-restraints excluded: chain A residue 1488 LEU
Chi-restraints excluded: chain A residue 1490 GLU
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  133 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0970
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A1353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.192737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.157378 restraints weight = 4096.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 2.32
r_work: 0.3820 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3685 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3964  Z= 0.128
  Angle     :  0.532   6.886   5350  Z= 0.275
  Chirality :  0.042   0.134    593
  Planarity :  0.004   0.048    681
  Dihedral  :  5.046  49.832    522
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.15 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.39), residues: 473
  helix:  1.85 (0.34), residues: 235
  sheet:  0.19 (0.53), residues: 91
  loop : -0.13 (0.51), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1528 
 TYR   0.023   0.002   TYR B  32 
 PHE   0.010   0.001   PHE A1518 
 TRP   0.013   0.002   TRP B  56 
 HIS   0.002   0.000   HIS A1585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3964)
  covalent geometry    : angle       0.53169 ( 5350)
  hydrogen bonds       : bond        0.04364 (  202)
  hydrogen bonds       : angle       5.10540 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A 1322 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6514 (ttt)
REVERT: A 1349 GLU cc_start: 0.7752 (tm-30) cc_final: 0.6859 (mp0)
REVERT: A 1352 ASN cc_start: 0.8189 (t0) cc_final: 0.7775 (t0)
REVERT: A 1361 LYS cc_start: 0.6738 (tmtm) cc_final: 0.6304 (ttpp)
REVERT: A 1374 VAL cc_start: 0.7908 (t) cc_final: 0.7682 (t)
REVERT: A 1395 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7557 (tm-30)
REVERT: A 1410 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7269 (tm-30)
REVERT: A 1479 ASN cc_start: 0.8064 (m-40) cc_final: 0.7086 (p0)
REVERT: A 1490 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7040 (tp30)
REVERT: A 1558 TRP cc_start: 0.7250 (p-90) cc_final: 0.6938 (p-90)
REVERT: B  102 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7471 (tpp-160)
REVERT: B  107 ASN cc_start: 0.7673 (m-40) cc_final: 0.7399 (m-40)
REVERT: B  120 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.5507 (ttt-90)
REVERT: B  128 LYS cc_start: 0.7921 (mttt) cc_final: 0.7296 (mppt)
REVERT: B  156 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8129 (mm-30)
  outliers start: 13
  outliers final: 4
  residues processed: 70
  average time/residue: 0.5467
  time to fit residues: 39.5518
Evaluate side-chains
  70 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1410 GLN
Chi-restraints excluded: chain A residue 1468 MET
Chi-restraints excluded: chain A residue 1490 GLU
Chi-restraints excluded: chain A residue 1542 LEU
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue  102 ARG
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  152 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.192548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.157239 restraints weight = 4154.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3930 rms_B_bonded: 2.33
r_work: 0.3809 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3674 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3964  Z= 0.129
  Angle     :  0.536   8.733   5350  Z= 0.276
  Chirality :  0.042   0.134    593
  Planarity :  0.004   0.050    681
  Dihedral  :  4.957  48.937    521
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 14.15 %
    Favored  : 82.13 %
  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 are not related in a simple way.
  whole:  1.31 (0.39), residues: 473
  helix:  1.81 (0.34), residues: 235
  sheet:  0.18 (0.53), residues: 91
  loop : -0.12 (0.51), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1309 
 TYR   0.012   0.001   TYR A1533 
 PHE   0.010   0.001   PHE A1518 
 TRP   0.016   0.002   TRP B  56 
 HIS   0.002   0.001   HIS A1351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 3964)
  covalent geometry    : angle       0.53622 ( 5350)
  hydrogen bonds       : bond        0.04348 (  202)
  hydrogen bonds       : angle       5.10915 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A 1322 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6565 (ttt)
REVERT: A 1352 ASN cc_start: 0.8202 (t0) cc_final: 0.7780 (t0)
REVERT: A 1361 LYS cc_start: 0.6762 (tmtm) cc_final: 0.6361 (ttpp)
REVERT: A 1374 VAL cc_start: 0.7914 (t) cc_final: 0.7689 (t)
REVERT: A 1395 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7627 (tm-30)
REVERT: A 1410 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7281 (tm-30)
REVERT: A 1479 ASN cc_start: 0.8052 (m-40) cc_final: 0.7085 (p0)
REVERT: A 1490 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7063 (tp30)
REVERT: B  102 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7525 (tpp-160)
REVERT: B  107 ASN cc_start: 0.7696 (m-40) cc_final: 0.7399 (m-40)
REVERT: B  120 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.5561 (ttt-90)
REVERT: B  128 LYS cc_start: 0.7995 (mttt) cc_final: 0.7367 (mppt)
REVERT: B  133 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6636 (mptp)
REVERT: B  156 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8130 (mm-30)
  outliers start: 16
  outliers final: 7
  residues processed: 73
  average time/residue: 0.5296
  time to fit residues: 39.9544
Evaluate side-chains
  79 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1410 GLN
Chi-restraints excluded: chain A residue 1468 MET
Chi-restraints excluded: chain A residue 1490 GLU
Chi-restraints excluded: chain A residue 1542 LEU
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   63 ASP
Chi-restraints excluded: chain B residue  102 ARG
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  152 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0070
   chunk 30 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A1353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.193408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.158245 restraints weight = 4110.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 2.32
r_work: 0.3833 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3699 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3964  Z= 0.122
  Angle     :  0.552   9.969   5350  Z= 0.283
  Chirality :  0.042   0.132    593
  Planarity :  0.004   0.051    681
  Dihedral  :  4.912  48.847    521
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.55 %
    Favored  : 80.97 %
  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 are not related in a simple way.
  whole:  1.39 (0.39), residues: 473
  helix:  1.91 (0.34), residues: 235
  sheet:  0.16 (0.54), residues: 91
  loop : -0.10 (0.51), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1309 
 TYR   0.024   0.002   TYR B  32 
 PHE   0.009   0.001   PHE A1518 
 TRP   0.020   0.002   TRP B  56 
 HIS   0.002   0.000   HIS A1351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3964)
  covalent geometry    : angle       0.55162 ( 5350)
  hydrogen bonds       : bond        0.04174 (  202)
  hydrogen bonds       : angle       5.04958 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A 1322 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6474 (ttt)
REVERT: A 1349 GLU cc_start: 0.7752 (tm-30) cc_final: 0.6754 (mp0)
REVERT: A 1352 ASN cc_start: 0.8135 (t0) cc_final: 0.7707 (t0)
REVERT: A 1374 VAL cc_start: 0.7916 (t) cc_final: 0.7693 (t)
REVERT: A 1395 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7475 (tm-30)
REVERT: A 1399 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6694 (tt0)
REVERT: A 1410 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7317 (tm-30)
REVERT: A 1479 ASN cc_start: 0.8061 (m-40) cc_final: 0.7093 (p0)
REVERT: A 1490 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6947 (tp30)
REVERT: A 1558 TRP cc_start: 0.7279 (p-90) cc_final: 0.6959 (p-90)
REVERT: B  102 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7521 (tpp-160)
REVERT: B  107 ASN cc_start: 0.7687 (m-40) cc_final: 0.7392 (m-40)
REVERT: B  120 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.5528 (ttt-90)
REVERT: B  128 LYS cc_start: 0.7993 (mttt) cc_final: 0.7399 (mppt)
REVERT: B  133 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6648 (mptp)
REVERT: B  156 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8171 (mm-30)
  outliers start: 15
  outliers final: 7
  residues processed: 71
  average time/residue: 0.5648
  time to fit residues: 41.3934
Evaluate side-chains
  77 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1410 GLN
Chi-restraints excluded: chain A residue 1468 MET
Chi-restraints excluded: chain A residue 1490 GLU
Chi-restraints excluded: chain A residue 1542 LEU
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  102 ARG
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  152 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 27 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 31 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.192962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.157825 restraints weight = 4081.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.31
r_work: 0.3812 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3676 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3964  Z= 0.131
  Angle     :  0.565  10.712   5350  Z= 0.289
  Chirality :  0.042   0.134    593
  Planarity :  0.004   0.053    681
  Dihedral  :  4.919  47.816    521
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 15.31 %
    Favored  : 80.97 %
  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 are not related in a simple way.
  whole:  1.28 (0.39), residues: 473
  helix:  1.83 (0.34), residues: 235
  sheet:  0.11 (0.54), residues: 91
  loop : -0.16 (0.51), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1309 
 TYR   0.012   0.001   TYR A1533 
 PHE   0.009   0.001   PHE A1518 
 TRP   0.028   0.002   TRP B  56 
 HIS   0.002   0.001   HIS A1351 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3964)
  covalent geometry    : angle       0.56535 ( 5350)
  hydrogen bonds       : bond        0.04278 (  202)
  hydrogen bonds       : angle       5.10590 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A 1322 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6478 (ttt)
REVERT: A 1349 GLU cc_start: 0.7816 (tm-30) cc_final: 0.6797 (mp0)
REVERT: A 1352 ASN cc_start: 0.8143 (t0) cc_final: 0.7730 (t0)
REVERT: A 1374 VAL cc_start: 0.7923 (t) cc_final: 0.7701 (t)
REVERT: A 1395 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7447 (tm-30)
REVERT: A 1399 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6731 (tt0)
REVERT: A 1410 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7325 (tm-30)
REVERT: A 1479 ASN cc_start: 0.8038 (m-40) cc_final: 0.7079 (p0)
REVERT: A 1490 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7061 (tp30)
REVERT: B  102 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7498 (tpp-160)
REVERT: B  107 ASN cc_start: 0.7719 (m-40) cc_final: 0.7418 (m-40)
REVERT: B  120 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.5496 (ttt-90)
REVERT: B  128 LYS cc_start: 0.7975 (mttt) cc_final: 0.7389 (mppt)
REVERT: B  133 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6626 (mptp)
REVERT: B  156 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8139 (mm-30)
  outliers start: 16
  outliers final: 8
  residues processed: 71
  average time/residue: 0.5559
  time to fit residues: 40.7452
Evaluate side-chains
  79 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 65
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1410 GLN
Chi-restraints excluded: chain A residue 1468 MET
Chi-restraints excluded: chain A residue 1490 GLU
Chi-restraints excluded: chain A residue 1542 LEU
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   63 ASP
Chi-restraints excluded: chain B residue  102 ARG
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  152 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A1353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.192374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.157427 restraints weight = 4080.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.27
r_work: 0.3811 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3678 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3964  Z= 0.145
  Angle     :  0.591  11.820   5350  Z= 0.302
  Chirality :  0.043   0.134    593
  Planarity :  0.004   0.054    681
  Dihedral  :  4.942  47.277    521
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 15.31 %
    Favored  : 81.21 %
  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 are not related in a simple way.
  whole:  1.26 (0.39), residues: 473
  helix:  1.86 (0.34), residues: 233
  sheet:  0.11 (0.54), residues: 91
  loop : -0.23 (0.51), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1309 
 TYR   0.025   0.002   TYR B  32 
 PHE   0.009   0.001   PHE A1518 
 TRP   0.034   0.003   TRP B  56 
 HIS   0.002   0.001   HIS A1508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3964)
  covalent geometry    : angle       0.59112 ( 5350)
  hydrogen bonds       : bond        0.04392 (  202)
  hydrogen bonds       : angle       5.15256 (  573)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A 1322 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6534 (ttt)
REVERT: A 1349 GLU cc_start: 0.7822 (tm-30) cc_final: 0.6734 (mp0)
REVERT: A 1352 ASN cc_start: 0.8152 (t0) cc_final: 0.7745 (t0)
REVERT: A 1374 VAL cc_start: 0.7926 (t) cc_final: 0.7702 (t)
REVERT: A 1395 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7425 (tm-30)
REVERT: A 1399 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6664 (tt0)
REVERT: A 1410 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7319 (tm-30)
REVERT: A 1479 ASN cc_start: 0.8032 (m-40) cc_final: 0.7083 (p0)
REVERT: A 1490 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7052 (tp30)
REVERT: B  102 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7464 (tpp-160)
REVERT: B  107 ASN cc_start: 0.7720 (m-40) cc_final: 0.7417 (m-40)
REVERT: B  120 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.5608 (ttt-90)
REVERT: B  128 LYS cc_start: 0.8010 (mttt) cc_final: 0.7410 (mppt)
REVERT: B  133 LYS cc_start: 0.7001 (OUTLIER) cc_final: 0.6643 (mptp)
  outliers start: 15
  outliers final: 8
  residues processed: 66
  average time/residue: 0.5785
  time to fit residues: 39.3265
Evaluate side-chains
  78 residues out of total 431 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain A residue 1410 GLN
Chi-restraints excluded: chain A residue 1468 MET
Chi-restraints excluded: chain A residue 1481 GLU
Chi-restraints excluded: chain A residue 1490 GLU
Chi-restraints excluded: chain A residue 1542 LEU
Chi-restraints excluded: chain A residue 1544 VAL
Chi-restraints excluded: chain B residue   19 LEU
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue  102 ARG
Chi-restraints excluded: chain B residue  117 LEU
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  133 LYS
Chi-restraints excluded: chain B residue  152 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0570
   chunk 42 optimal weight:    0.4980
   chunk 46 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 35 optimal weight:    0.8980
   chunk 38 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A1353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.194881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.159922 restraints weight = 4049.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.30
r_work: 0.3844 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3707 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6922
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3964  Z= 0.120
  Angle     :  0.566  12.074   5350  Z= 0.291
  Chirality :  0.041   0.131    593
  Planarity :  0.004   0.052    681
  Dihedral  :  4.813  46.695    521
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.78 %
    Favored  : 81.21 %
  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 are not related in a simple way.
  whole:  1.40 (0.39), residues: 473
  helix:  1.98 (0.34), residues: 234
  sheet:  0.15 (0.55), residues: 91
  loop : -0.18 (0.51), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1309 
 TYR   0.012   0.001   TYR A1533 
 PHE   0.009   0.001   PHE A1518 
 TRP   0.038   0.002   TRP B  56 
 HIS   0.002   0.000   HIS A1585 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3964)
  covalent geometry    : angle       0.56648 ( 5350)
  hydrogen bonds       : bond        0.03985 (  202)
  hydrogen bonds       : angle       5.05479 (  573)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1663.14 seconds
wall clock time: 29 minutes 4.25 seconds (1744.25 seconds total)